ProteoWizard
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cv.hpp File Reference
#include <string>
#include <vector>
#include <map>
#include "pwiz/utility/misc/Export.hpp"

Go to the source code of this file.

Classes

struct  pwiz::cv::CV
 Information about an ontology or CV source and a short 'lookup' tag to refer to. More...
struct  pwiz::cv::CVTermInfo
 structure for holding CV term info More...

Namespaces

namespace  pwiz
 AMTContainer.hpp.
namespace  pwiz::cv

Macros

#define _PSI_MS_OBO_
#define _UNIMOD_OBO_
#define _UNIT_OBO_

Functions

PWIZ_API_DECL const CV & pwiz::cv::cv (const std::string &prefix)
 returns a CV object for the specified namespace (prefix); currently supported namespaces are: MS UO
PWIZ_API_DECL const CVTermInfo & pwiz::cv::cvTermInfo (CVID cvid)
 returns CV term info for the specified CVID
PWIZ_API_DECL const CVTermInfo & pwiz::cv::cvTermInfo (const char *id)
 returns CV term info for the specified id (accession number)
PWIZ_API_DECL const CVTermInfo & pwiz::cv::cvTermInfo (const std::string &id)
PWIZ_API_DECL bool pwiz::cv::cvIsA (CVID child, CVID parent)
 returns true iff child IsA parent in the CV
PWIZ_API_DECL const
std::vector< CVID > & 
pwiz::cv::cvids ()
 returns vector of all valid CVIDs

Variables

 CVID_Unknown = -1
 MS_Proteomics_Standards_Initiative_Mass_Spectrometry_Vocabularies = 0
 Proteomics Standards Initiative Mass Spectrometry Vocabularies: Proteomics Standards Initiative Mass Spectrometry Vocabularies.
 MS_sample_number = 1000001
 sample number: A reference number relevant to the sample under study.
 MS_sample_name = 1000002
 sample name: A reference string relevant to the sample under study.
 MS_sample_state = 1000003
 sample state: The chemical phase of a pure sample, or the state of a mixed sample.
 MS_sample_mass = 1000004
 sample mass: Total mass of sample used.
 MS_sample_volume = 1000005
 sample volume: Total volume of solution used.
 MS_sample_concentration = 1000006
 sample concentration: Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used.
 MS_inlet_type = 1000007
 inlet type: The nature of the sample inlet.
 MS_ionization_type = 1000008
 ionization type: The method by which gas phase ions are generated from the sample.
 MS_ionization_mode_OBSOLETE = 1000009
 ionization mode: Whether positive or negative ions are selected for analysis by the spectrometer.
 MS_analyzer_type = 1000010
 analyzer type: The common name of the particular analyzer stage being described. Synonym of mass analyzer, should be obsoleted.
 MS_mass_resolution = 1000011
 mass resolution: Smallest mass difference between two equal magnitude peaks so that the valley between them is a specified fraction of the peak height.
 MS_resolution_measurement_method = 1000012
 resolution measurement method: Which of the available standard measures is used to define whether two peaks are separate.
 MS_resolution_type = 1000013
 resolution type: Specify the nature of resolution for the mass analyzer. Resolution is usually either constant with respect to m/z or proportional to m/z.
 MS_accuracy = 1000014
 accuracy: Accuracy is the degree of conformity of a measured mass to its actual value.
 MS_scan_rate = 1000015
 scan rate: Rate in Th/sec for scanning analyzers.
 MS_scan_start_time = 1000016
 scan start time: The time that an analyzer started a scan, relative to the start of the MS run.
 MS_Scan_Function = 1000017
 Scan Function: Describes the type of mass analysis being performed. Two primary modes are: typical acquisition over a range of masses (Mass Scan), and Selected Ion Detection. The primary difference is that Selected Ion Detection produces a single value for the signal at the selected mass rather than producing a mass spectrum.
 MS_scan_direction = 1000018
 scan direction: Direction in terms of m/z of the scan for scanning analyzers (low to high, or high to low).
 MS_scan_law = 1000019
 scan law: Describes the function in control of the m/z scan (for scanning instruments). Commonly the scan function is linear, but in principle any function can be used.
 MS_scanning_method = 1000020
 scanning method: Describes the acquisition data type produced by a tandem mass spectrometry experiment.
 MS_reflectron_state = 1000021
 reflectron state: Status of the reflectron, turned on or off.
 MS_TOF_Total_Path_Length = 1000022
 TOF Total Path Length: The length of the field free drift space in a time of flight mass spectrometer.
 MS_isolation_width = 1000023
 isolation width: The total width (i.e. not half for plus-or-minus) of the gate applied around a selected precursor ion.
 MS_final_MS_exponent = 1000024
 final MS exponent: Final MS level achieved when performing PFF with the ion trap (e.g. MS E10).
 MS_magnetic_field_strength = 1000025
 magnetic field strength: A property of space that produces a force on a charged particle equal to qv x B where q is the particle charge and v its velocity.
 MS_B = MS_magnetic_field_strength
 B (magnetic field strength): A property of space that produces a force on a charged particle equal to qv x B where q is the particle charge and v its velocity.
 MS_detector_type = 1000026
 detector type: Type of detector used in the mass spectrometer.
 MS_detector_acquisition_mode = 1000027
 detector acquisition mode: Method by which detector signal is acquired by the data system.
 MS_detector_resolution = 1000028
 detector resolution: The resolving power of the detector to detect the smallest difference between two ions so that the valley between them is a specified fraction of the peak height.
 MS_sampling_frequency = 1000029
 sampling frequency: The rate of signal sampling (measurement) with respect to time.
 MS_vendor_OBSOLETE = 1000030
 vendor: Name of instrument vendor.
 MS_instrument_model = 1000031
 instrument model: Instrument model name not including the vendor's name.
 MS_customization = 1000032
 customization: Free text description of a single customization made to the instrument; for several modifications, use several entries.
 MS_deisotoping = 1000033
 deisotoping: The removal of isotope peaks to represent the fragment ion as one data point and is commonly done to reduce complexity. It is done in conjunction with the charge state deconvolution.
 MS_charge_deconvolution = 1000034
 charge deconvolution: The determination of the mass of an ion based on the mass spectral peaks that represent multiple-charge ions.
 MS_peak_picking = 1000035
 peak picking: Spectral peak processing conducted on the acquired data to convert profile data to centroided data.
 MS_scan_mode_OBSOLETE = 1000036
 scan mode: OBSOLETE.
 MS_polarity = 1000037
 polarity: Terms to describe the polarity setting of the instrument.
 MS_minute_OBSOLETE = 1000038
 minute: Acquisition time in minutes.
 MS_second_OBSOLETE = 1000039
 second: Acquisition time in seconds.
 MS_m_z = 1000040
 m/z: Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion in unified atomic mass units by its charge number (regardless of sign). The symbol is written in italicized lower case letters with no spaces. Note 1: The term mass-to-charge-ratio is deprecated. Mass-to-charge ratio has been used for the abscissa of a mass spectrum, although the quantity measured is not the quotient of the ion's mass to its electric charge. The three-character symbol m/z is recommended for the quantity that is the independent variable in a mass spectrum Note 2: The proposed unit thomson (Th) is deprecated.
 MS_mass_to_charge_ratio = MS_m_z
 mass-to-charge ratio (m/z): Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion in unified atomic mass units by its charge number (regardless of sign). The symbol is written in italicized lower case letters with no spaces. Note 1: The term mass-to-charge-ratio is deprecated. Mass-to-charge ratio has been used for the abscissa of a mass spectrum, although the quantity measured is not the quotient of the ion's mass to its electric charge. The three-character symbol m/z is recommended for the quantity that is the independent variable in a mass spectrum Note 2: The proposed unit thomson (Th) is deprecated.
 MS_Th = MS_m_z
 Th (m/z): Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion in unified atomic mass units by its charge number (regardless of sign). The symbol is written in italicized lower case letters with no spaces. Note 1: The term mass-to-charge-ratio is deprecated. Mass-to-charge ratio has been used for the abscissa of a mass spectrum, although the quantity measured is not the quotient of the ion's mass to its electric charge. The three-character symbol m/z is recommended for the quantity that is the independent variable in a mass spectrum Note 2: The proposed unit thomson (Th) is deprecated.
 MS_thomson = MS_m_z
 thomson (m/z): Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion in unified atomic mass units by its charge number (regardless of sign). The symbol is written in italicized lower case letters with no spaces. Note 1: The term mass-to-charge-ratio is deprecated. Mass-to-charge ratio has been used for the abscissa of a mass spectrum, although the quantity measured is not the quotient of the ion's mass to its electric charge. The three-character symbol m/z is recommended for the quantity that is the independent variable in a mass spectrum Note 2: The proposed unit thomson (Th) is deprecated.
 MS_charge_state = 1000041
 charge state: The charge state of the ion, single or multiple and positive or negatively charged.
 MS_z = MS_charge_state
 z (charge state): The charge state of the ion, single or multiple and positive or negatively charged.
 MS_peak_intensity = 1000042
 peak intensity: Intensity of ions as measured by the height or area of a peak in a mass spectrum.
 MS_intensity_unit = 1000043
 intensity unit: Intensity units are commonly arbitrary. Detected in counts per second (cps) when using counting detectors, but measured in volts when using analog detectors.
 MS_dissociation_method = 1000044
 dissociation method: Fragmentation method used for dissociation or fragmentation.
 MS_collision_energy = 1000045
 collision energy: Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion.
 MS_energy_unit_OBSOLETE = 1000046
 energy unit: Energy units are represented in either eV or Joules.
 MS_emulsion = 1000047
 emulsion: State if the sample is in emulsion form.
 MS_gas = 1000048
 gas: State if the sample is in gaseous form.
 MS_liquid = 1000049
 liquid: State if the sample is in liquid form.
 MS_solid = 1000050
 solid: State if the sample is in solid form.
 MS_solution = 1000051
 solution: State if the sample is in solution form.
 MS_suspension = 1000052
 suspension: State if the sample is in suspension form.
 MS_sample_batch = 1000053
 sample batch: Sample batch lot identifier.
 MS_chromatography = 1000054
 chromatography: Chromatographic conditions used to obtain the sample.
 MS_continuous_flow_fast_atom_bombardment = 1000055
 continuous flow fast atom bombardment: Fast atom bombardment ionization in which the analyte in solution is entrained in a flowing liquid matrix.
 MS_CF_FAB = MS_continuous_flow_fast_atom_bombardment
 CF-FAB (continuous flow fast atom bombardment): Fast atom bombardment ionization in which the analyte in solution is entrained in a flowing liquid matrix.
 MS_direct_inlet = 1000056
 direct inlet: The sample is directly inserted into the ion source, usually on the end of a heatable probe.
 MS_electrospray_inlet = 1000057
 electrospray inlet: Inlet used for introducing the liquid sample into an electrospray ionization source.
 MS_flow_injection_analysis = 1000058
 flow injection analysis: Sample is directly injected or infused into the ionization source.
 MS_inductively_coupled_plasma = 1000059
 inductively coupled plasma: A gas discharge ion source in which the energy to the plasma is supplied by electromagnetic induction.
 MS_infusion = 1000060
 infusion: The continuous flow of solution of a sample into the ionization source.
 MS_jet_separator = 1000061
 jet separator: A device that separates carrier gas from gaseous analyte molecules on the basis of diffusivity.
 MS_membrane_separator = 1000062
 membrane separator: A device to separate carrier molecules from analyte molecules on the basis of ease of diffusion across a semipermeable membrane.
 MS_moving_belt = 1000063
 moving belt: Continuous moving surface in the form of a belt which passes through an ionsource carrying analyte molecules.
 MS_moving_wire = 1000064
 moving wire: Continuous moving surface in the form of a wire which passes through an ionsource carrying analyte molecules.
 MS_open_split = 1000065
 open split: A division of flowing stream of liquid into two streams.
 MS_particle_beam = 1000066
 particle beam: Method for generating ions from a solution of an analyte.
 MS_reservoir = 1000067
 reservoir: A sample inlet method involving a reservoir.
 MS_septum = 1000068
 septum: A disc composed of a flexible material that seals the entrance to the reservoir. Can also be enterance to the vaccum chamber.
 MS_thermospray_inlet = 1000069
 thermospray inlet: A method for generating gas phase ions from a solution of an analyte by rapid heating of the sample.
 MS_atmospheric_pressure_chemical_ionization = 1000070
 atmospheric pressure chemical ionization: Chemical ionization that takes place at atmospheric pressure as opposed to the reduced pressure is normally used for chemical ionization.
 MS_APCI = MS_atmospheric_pressure_chemical_ionization
 APCI (atmospheric pressure chemical ionization): Chemical ionization that takes place at atmospheric pressure as opposed to the reduced pressure is normally used for chemical ionization.
 MS_chemical_ionization = 1000071
 chemical ionization: The formation of a new ion by the reaction of a neutral species with an ion. The process may involve transfer of an electron, a proton or other charged species between the reactants. When a positive ion results from chemical ionization the term may be used without qualification. When a negative ion results the term negative ion chemical ionization should be used. Note that this term is not synonymous with chemi-ionization.
 MS_CI = MS_chemical_ionization
 CI (chemical ionization): The formation of a new ion by the reaction of a neutral species with an ion. The process may involve transfer of an electron, a proton or other charged species between the reactants. When a positive ion results from chemical ionization the term may be used without qualification. When a negative ion results the term negative ion chemical ionization should be used. Note that this term is not synonymous with chemi-ionization.
 MS_Electronic_Ionization_OBSOLETE = 1000072
 Electronic Ionization: The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended.
 MS_EI_OBSOLETE = MS_Electronic_Ionization_OBSOLETE
 EI (Electronic Ionization): The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended.
 MS_electrospray_ionization = 1000073
 electrospray ionization: A process in which ionized species in the gas phase are produced from an analyte-containing solution via highly charged fine droplets, by means of spraying the solution from a narrow-bore needle tip at atmospheric pressure in the presence of a high electric field. When a pressurized gas is used to aid in the formation of a stable spray, the term pneumatically assisted electrospray ionization is used. The term ion spray is not recommended.
 MS_ESI = MS_electrospray_ionization
 ESI (electrospray ionization): A process in which ionized species in the gas phase are produced from an analyte-containing solution via highly charged fine droplets, by means of spraying the solution from a narrow-bore needle tip at atmospheric pressure in the presence of a high electric field. When a pressurized gas is used to aid in the formation of a stable spray, the term pneumatically assisted electrospray ionization is used. The term ion spray is not recommended.
 MS_fast_atom_bombardment_ionization = 1000074
 fast atom bombardment ionization: The ionization of any species by the interaction of a focused beam of neutral atoms having a translational energy of several thousand eV with a sample that is typically dissolved in a solvent matrix. See also secondary ionization.
 MS_FAB = MS_fast_atom_bombardment_ionization
 FAB (fast atom bombardment ionization): The ionization of any species by the interaction of a focused beam of neutral atoms having a translational energy of several thousand eV with a sample that is typically dissolved in a solvent matrix. See also secondary ionization.
 MS_matrix_assisted_laser_desorption_ionization = 1000075
 matrix-assisted laser desorption ionization: The formation of gas-phase ions from molecules that are present in a solid or solvent matrix that is irradiated with a pulsed laser. See also laser desorption/ionization.
 MS_MALDI = MS_matrix_assisted_laser_desorption_ionization
 MALDI (matrix-assisted laser desorption ionization): The formation of gas-phase ions from molecules that are present in a solid or solvent matrix that is irradiated with a pulsed laser. See also laser desorption/ionization.
 MS_negative_ion_mode_OBSOLETE = 1000076
 negative ion mode: OBSOLETE.
 MS_positive_ion_mode_OBSOLETE = 1000077
 positive ion mode: OBSOLETE.
 MS_axial_ejection_linear_ion_trap = 1000078
 axial ejection linear ion trap: A linear ion trap mass spectrometer where ions are ejected along the axis of the analyzer.
 MS_fourier_transform_ion_cyclotron_resonance_mass_spectrometer = 1000079
 fourier transform ion cyclotron resonance mass spectrometer: A mass spectrometer based on the principle of ion cyclotron resonance in which an ion in a magnetic field moves in a circular orbit at a frequency characteristic of its m/z value. Ions are coherently excited to a larger radius orbit using a pulse of radio frequency energy and their image charge is detected on receiver plates as a time domain signal. Fourier transformation of the time domain signal results in a frequency domain signal which is converted to a mass spectrum based in the inverse relationship between frequency and m/z.
 MS_FT_ICR = MS_fourier_transform_ion_cyclotron_resonance_mass_spectrometer
 FT_ICR (fourier transform ion cyclotron resonance mass spectrometer): A mass spectrometer based on the principle of ion cyclotron resonance in which an ion in a magnetic field moves in a circular orbit at a frequency characteristic of its m/z value. Ions are coherently excited to a larger radius orbit using a pulse of radio frequency energy and their image charge is detected on receiver plates as a time domain signal. Fourier transformation of the time domain signal results in a frequency domain signal which is converted to a mass spectrum based in the inverse relationship between frequency and m/z.
 MS_magnetic_sector = 1000080
 magnetic sector: A device that produces a magnetic field perpendicular to a charged particle beam that deflects the beam to an extent that is proportional to the particle momentum per unit charge. For a monoenergetic beam, the deflection is proportional to m/z.
 MS_quadrupole = 1000081
 quadrupole: A mass spectrometer that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis.
 MS_quadrupole_ion_trap = 1000082
 quadrupole ion trap: Quadrupole Ion Trap mass analyzer captures the ions in a three dimensional ion trap and then selectively ejects them by varying the RF and DC potentials.
 MS_Paul_Ion_trap = MS_quadrupole_ion_trap
 Paul Ion trap (quadrupole ion trap): Quadrupole Ion Trap mass analyzer captures the ions in a three dimensional ion trap and then selectively ejects them by varying the RF and DC potentials.
 MS_QIT = MS_quadrupole_ion_trap
 QIT (quadrupole ion trap): Quadrupole Ion Trap mass analyzer captures the ions in a three dimensional ion trap and then selectively ejects them by varying the RF and DC potentials.
 MS_Quistor = MS_quadrupole_ion_trap
 Quistor (quadrupole ion trap): Quadrupole Ion Trap mass analyzer captures the ions in a three dimensional ion trap and then selectively ejects them by varying the RF and DC potentials.
 MS_radial_ejection_linear_ion_trap = 1000083
 radial ejection linear ion trap: A linear ion trap mass spectrometer where ions are ejected along the radius of the analyzer.
 MS_time_of_flight = 1000084
 time-of-flight: Instrument that separates ions by m/z in a field-free region after acceleration to a fixed acceleration energy.
 MS_TOF = MS_time_of_flight
 TOF (time-of-flight): Instrument that separates ions by m/z in a field-free region after acceleration to a fixed acceleration energy.
 MS_baseline = 1000085
 baseline: An attribute of resolution when recording the detector response in absence of the analyte.
 MS_full_width_at_half_maximum = 1000086
 full width at half-maximum: A measure of resolution represented as width of the peak at half peak height.
 MS_FWHM = MS_full_width_at_half_maximum
 FWHM (full width at half-maximum): A measure of resolution represented as width of the peak at half peak height.
 MS_ten_percent_valley = 1000087
 ten percent valley: An attribute of resolution when the ratio between adjacent signals is 10% of the signal height.
 MS_constant = 1000088
 constant: When resolution is constant with respect to m/z.
 MS_proportional = 1000089
 proportional: When resolution is proportional with respect to m/z.
 MS_mass_scan = 1000090
 mass scan: A variation of instrument where a selected mass is scanned.
 MS_selected_ion_detection = 1000091
 selected ion detection: Please see Single Ion Monitoring.
 MS_decreasing_m_z_scan = 1000092
 decreasing m/z scan: High to low direction in terms of m/z of the scan for scanning analyzers.
 MS_increasing_m_z_scan = 1000093
 increasing m/z scan: Low to high direction in terms of m/z of the scan for scanning analyzers.
 MS_exponential = 1000094
 exponential: The mass scan is done in exponential mode.
 MS_linear = 1000095
 linear: The mass scan is done in linear mode.
 MS_quadratic = 1000096
 quadratic: The mass scan is done in quadratic mode.
 MS_constant_neutral_mass_loss = 1000097
 constant neutral mass loss: A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum.
 MS_multiple_ion_monitoring = 1000098
 multiple ion monitoring: Data acquired when monitoring the ion current of a few specific m/z values. Remap to MS:1000205 -Selected Ion Monitoring.
 MS_multiple_reaction_monitoring_OBSOLETE = 1000099
 multiple reaction monitoring: This term is not recommended. See Selected Reaction Monitoring.
 MS_MRM_OBSOLETE = MS_multiple_reaction_monitoring_OBSOLETE
 MRM (multiple reaction monitoring): This term is not recommended. See Selected Reaction Monitoring.
 MS_precursor_ion_scan = 1000100
 precursor ion scan: The specific scan function or process that will record a precursor ion spectrum.
 MS_product_ion_scan = 1000101
 product ion scan: The specific scan function or process that records product ion spectrum.
 MS_single_ion_monitoring_OBSOLETE = 1000102
 single ion monitoring: The operation of a mass spectrometer to monitor a single ion rather than scanning entire mass spectrum.
 MS_single_reaction_monitoring_OBSOLETE = 1000103
 single reaction monitoring: This term is not recommended. See Selected Reaction Monitoring.
 MS_None_____OBSOLETE = 1000104
 None ??: None.
 MS_reflectron_off = 1000105
 reflectron off: Reflectron is off.
 MS_reflectron_on = 1000106
 reflectron on: Reflectron is on.
 MS_channeltron = 1000107
 channeltron: A horn-shaped (or cone-shaped) continuous dynode particle multiplier. The ion strikes the inner surface of the device and induces the production of secondary electrons that in turn impinge on the inner surfaces to produce more secondary electrons. This avalanche effect produces an increase in signal in the final measured current pulse.
 MS_Channeltron_Detector = MS_channeltron
 Channeltron Detector (channeltron): A horn-shaped (or cone-shaped) continuous dynode particle multiplier. The ion strikes the inner surface of the device and induces the production of secondary electrons that in turn impinge on the inner surfaces to produce more secondary electrons. This avalanche effect produces an increase in signal in the final measured current pulse.
 MS_conversion_dynode_electron_multiplier = 1000108
 conversion dynode electron multiplier: A surface that is held at high potential so that ions striking the surface produce electrons that are subsequently detected.
 MS_conversion_dynode_photomultiplier = 1000109
 conversion dynode photomultiplier: A detector in which ions strike a conversion dynode to produce electrons that in turn generate photons through a phosphorescent screen that are detected by a photomultiplier.
 MS_daly_detector = 1000110
 daly detector: Detector consisting of a conversion dynode, scintillator and photomultiplier. The metal knob at high potential emits secondary electrons when ions impinge on the surface. The secondary electrons are accelerated onto the scintillator that produces light that is then detected by the photomultiplier detector.
 MS_Daly = MS_daly_detector
 Daly (daly detector): Detector consisting of a conversion dynode, scintillator and photomultiplier. The metal knob at high potential emits secondary electrons when ions impinge on the surface. The secondary electrons are accelerated onto the scintillator that produces light that is then detected by the photomultiplier detector.
 MS_electron_multiplier_tube = 1000111
 electron multiplier tube: A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons.
 MS_EMT = MS_electron_multiplier_tube
 EMT (electron multiplier tube): A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons.
 MS_faraday_cup = 1000112
 faraday cup: A conducting cup or chamber that intercepts a charged particle beam and is electrically connected to a current measuring device.
 MS_focal_plane_array = 1000113
 focal plane array: An array of detectors for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane.
 MS_microchannel_plate_detector = 1000114
 microchannel plate detector: A thin plate that contains a closely spaced array of channels that each act as a continuous dynode particle multiplier. A charged particle, fast neutral particle, or photon striking the plate causes a cascade of secondary electrons that ultimately exits the opposite side of the plate.
 MS_multichannel_plate = MS_microchannel_plate_detector
 multichannel plate (microchannel plate detector): A thin plate that contains a closely spaced array of channels that each act as a continuous dynode particle multiplier. A charged particle, fast neutral particle, or photon striking the plate causes a cascade of secondary electrons that ultimately exits the opposite side of the plate.
 MS_multi_collector = 1000115
 multi-collector: A detector system commonly used in inductively coupled plasma mass spectrometers.
 MS_photomultiplier = 1000116
 photomultiplier: A detector for conversion of the ion/electron signal into photon(s) which are then amplified and detected.
 MS_PMT = MS_photomultiplier
 PMT (photomultiplier): A detector for conversion of the ion/electron signal into photon(s) which are then amplified and detected.
 MS_analog_digital_converter = 1000117
 analog-digital converter: Analog-to-digital converter (abbreviated ADC, A/D or A to D) is an electronic integrated circuit (i/c) that converts continuous signals to discrete digital numbers.
 MS_ADC = MS_analog_digital_converter
 ADC (analog-digital converter): Analog-to-digital converter (abbreviated ADC, A/D or A to D) is an electronic integrated circuit (i/c) that converts continuous signals to discrete digital numbers.
 MS_pulse_counting = 1000118
 pulse counting: Definition to do.
 MS_time_digital_converter = 1000119
 time-digital converter: A device for converting a signal of sporadic pluses into a digital representation of their time indices.
 MS_TDC = MS_time_digital_converter
 TDC (time-digital converter): A device for converting a signal of sporadic pluses into a digital representation of their time indices.
 MS_transient_recorder = 1000120
 transient recorder: A detector acquisition mode used for detecting transient signals.
 MS_AB_SCIEX_instrument_model = 1000121
 AB SCIEX instrument model: The brand of instruments from the joint venture between Applied Biosystems and MDS Analytical Technologies (formerly MDS SCIEX). Previously branded as "Applied Biosystems|MDS SCIEX".
 MS_Bruker_Daltonics_instrument_model = 1000122
 Bruker Daltonics instrument model: Bruker Daltonics instrument model.
 MS_IonSpec_instrument_model = 1000123
 IonSpec instrument model: IonSpec corporation instrument model.
 MS_Shimadzu_instrument_model = 1000124
 Shimadzu instrument model: Shimadzu corporation instrument model.
 MS_Thermo_Finnigan_instrument_model = 1000125
 Thermo Finnigan instrument model: ThermoFinnigan from Thermo Electron Corporation instrument model.
 MS_Waters_instrument_model = 1000126
 Waters instrument model: Waters Corporation instrument model.
 MS_centroid_spectrum = 1000127
 centroid spectrum: Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset.
 MS_Discrete_Mass_Spectrum = MS_centroid_spectrum
 Discrete Mass Spectrum (centroid spectrum): Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset.
 MS_profile_spectrum = 1000128
 profile spectrum: A profile mass spectrum is created when data is recorded with ion current (counts per second) on one axis and mass/charge ratio on another axis.
 MS_continuous_mass_spectrum = MS_profile_spectrum
 continuous mass spectrum (profile spectrum): A profile mass spectrum is created when data is recorded with ion current (counts per second) on one axis and mass/charge ratio on another axis.
 MS_Continuum_Mass_Spectrum = MS_profile_spectrum
 Continuum Mass Spectrum (profile spectrum): A profile mass spectrum is created when data is recorded with ion current (counts per second) on one axis and mass/charge ratio on another axis.
 MS_negative_scan = 1000129
 negative scan: Polarity of the scan is negative.
 MS_positive_scan = 1000130
 positive scan: Polarity of the scan is positive.
 MS_number_of_counts = 1000131
 number of counts: The number of counted events observed in one or a group of elements of a detector.
 MS_percent_of_base_peak = 1000132
 percent of base peak: The magnitude of a peak or measurement element expressed in terms of the percentage of the magnitude of the base peak intensity.
 MS_collision_induced_dissociation = 1000133
 collision-induced dissociation: The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended.
 MS_CID = MS_collision_induced_dissociation
 CID (collision-induced dissociation): The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended.
 MS_CAD = MS_collision_induced_dissociation
 CAD (collision-induced dissociation): The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended.
 MS_collision_activated_dissociation = MS_collision_induced_dissociation
 collision activated dissociation (collision-induced dissociation): The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended.
 MS_plasma_desorption = 1000134
 plasma desorption: The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization.
 MS_PD = MS_plasma_desorption
 PD (plasma desorption): The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization.
 MS_post_source_decay = 1000135
 post-source decay: A technique specific to reflectron time-of-flight mass spectrometers where product ions of metastable transitions or collision-induced dissociations generated in the drift tube prior to entering the reflectron are m/z separated to yield product ion spectra.
 MS_PSD = MS_post_source_decay
 PSD (post-source decay): A technique specific to reflectron time-of-flight mass spectrometers where product ions of metastable transitions or collision-induced dissociations generated in the drift tube prior to entering the reflectron are m/z separated to yield product ion spectra.
 MS_surface_induced_dissociation = 1000136
 surface-induced dissociation: Fragmentation that results from the collision of an ion with a surface.
 MS_SID = MS_surface_induced_dissociation
 SID (surface-induced dissociation): Fragmentation that results from the collision of an ion with a surface.
 MS_electron_volt_OBSOLETE = 1000137
 electron volt: A non-SI unit of energy (eV) defined as the energy acquired by a particle containing one unit of charge through a potential difference of one volt. An electron-volt is equal to 1.602 176 53(14) x 10^-19 J.
 MS_eV_OBSOLETE = MS_electron_volt_OBSOLETE
 eV (electron volt): A non-SI unit of energy (eV) defined as the energy acquired by a particle containing one unit of charge through a potential difference of one volt. An electron-volt is equal to 1.602 176 53(14) x 10^-19 J.
 MS_percent_collision_energy = 1000138
 percent collision energy: Collision energy required to fragment an ion represented as a percent value.
 MS_4000_QTRAP = 1000139
 4000 QTRAP: Applied Biosystems/MDS SCIEX Q 4000 TRAP MS.
 MS_4700_Proteomics_Analyzer = 1000140
 4700 Proteomics Analyzer: Applied Biosystems/MDS SCIEX 4700 Proteomics Analyzer MS.
 MS_apex_IV = 1000141
 apex IV: Bruker Daltonics' apex IV: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR.
 MS_apex_Q = 1000142
 apex Q: Bruker Daltonics' apex Q: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR.
 MS_API_150EX = 1000143
 API 150EX: Applied Biosystems/MDS SCIEX API 150EX MS.
 MS_API_150EX_Prep = 1000144
 API 150EX Prep: Applied Biosystems/MDS SCIEX API 150EX Prep MS.
 MS_API_2000 = 1000145
 API 2000: Applied Biosystems/MDS SCIEX API 2000 MS.
 MS_API_3000 = 1000146
 API 3000: Applied Biosystems/MDS SCIEX API 3000 MS.
 MS_API_4000 = 1000147
 API 4000: Applied Biosystems/MDS SCIEX API 4000 MS.
 MS_autoflex_II = 1000148
 autoflex II: Bruker Daltonics' autoflex II: MALDI TOF.
 MS_autoflex_TOF_TOF = 1000149
 autoflex TOF/TOF: Bruker Daltonics' autoflex TOF/TOF MS: MALDI TOF.
 MS_Auto_Spec_Ultima_NT = 1000150
 Auto Spec Ultima NT: Waters AutoSpec Ultima NT MS.
 MS_BioTOF_II = 1000151
 BioTOF II: Bruker Daltonics' BioTOF II: ESI TOF.
 MS_BioTOF_Q = 1000152
 BioTOF-Q: Bruker Daltonics' BioTOF-Q: ESI Q-TOF.
 MS_DELTA_plusAdvantage = 1000153
 DELTA plusAdvantage: ThermoFinnigan DELTA plusAdvantage MS.
 MS_DELTAplusXP = 1000154
 DELTAplusXP: ThermoFinnigan DELTAplusXP MS.
 MS_ELEMENT2 = 1000155
 ELEMENT2: ThermoFinnigan ELEMENT2 MS.
 MS_esquire_4000 = 1000156
 esquire 4000: Bruker Daltonics' esquire 4000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI.
 MS_esquire_6000 = 1000157
 esquire 6000: Bruker Daltonics' esquire 6000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI.
 MS_explorer = 1000158
 explorer: IonSpec Explorer MS.
 MS_GCT = 1000159
 GCT: Waters GCT MS.
 MS_HCT = 1000160
 HCT: Bruker Daltonics' HCT: ESI Q-TOF, Nanospray, APCI, APPI.
 MS_HCTplus = 1000161
 HCTplus: Bruker Daltonics' HCTplus: ESI Q-TOF, Nanospray, APCI, APPI.
 MS_HiRes_ESI = 1000162
 HiRes ESI: IonSpec HiResESI MS.
 MS_HiRes_MALDI = 1000163
 HiRes MALDI: IonSpec HiResMALDI MS.
 MS_IsoPrime = 1000164
 IsoPrime: Waters IsoPrime MS.
 MS_IsoProbe = 1000165
 IsoProbe: Waters IsoProbe MS.
 MS_IsoProbe_T = 1000166
 IsoProbe T: Waters IsoProbe T MS.
 MS_LCQ_Advantage = 1000167
 LCQ Advantage: ThermoFinnigan LCQ Advantage MS.
 MS_LCQ_Classic = 1000168
 LCQ Classic: ThermoFinnigan LCQ Classic MS.
 MS_LCQ_Deca_XP_Plus = 1000169
 LCQ Deca XP Plus: ThermoFinnigan LCQ Deca XP Plus MS.
 MS_M_LDI_L = 1000170
 M L: Waters MALDI L MS.
 MS_M_LDI_LR = 1000171
 M LR: Waters MALDI LR MS.
 MS_MAT253 = 1000172
 MAT253: ThermoFinnigan MAT253 MS.
 MS_MAT900XP = 1000173
 MAT900XP: ThermoFinnigan MAT900XP MS.
 MS_MAT900XP_Trap = 1000174
 MAT900XP Trap: ThermoFinnigan MAT900XP Trap MS.
 MS_MAT95XP = 1000175
 MAT95XP: ThermoFinnigan MAT95XP MS.
 MS_MAT95XP_Trap = 1000176
 MAT95XP Trap: ThermoFinnigan MAT95XP Trap MS.
 MS_microflex = 1000177
 microflex: Bruker Daltonics' microflex: MALDI TOF.
 MS_microTOF_LC = 1000178
 microTOF LC: Bruker Daltonics' microTOF LC: ESI TOF, Nanospray, APCI, APPI.
 MS_neptune = 1000179
 neptune: ThermoFinnigan NEPTUNE MS.
 MS_NG_5400 = 1000180
 NG-5400: Waters NG-5400 MS.
 MS_OMEGA = 1000181
 OMEGA: IonSpec OMEGA MS.
 MS_OMEGA_2001 = 1000182
 OMEGA-2001: IonSpec OMEGA-2001 MS.
 MS_OmniFlex = 1000183
 OmniFlex: Bruker Daltonics' OmniFlex: MALDI TOF.
 MS_Platform_ICP = 1000184
 Platform ICP: Waters Platform ICP MS.
 MS_PolarisQ = 1000185
 PolarisQ: ThermoFinnigan PolarisQ MS.
 MS_proteomics_solution_1 = 1000186
 proteomics solution 1: Applied Biosystems/MDS SCIEX Proteomics Solution 1 MS.
 MS_Q_TRAP = 1000187
 Q TRAP: Applied Biosystems/MDS SCIEX Q TRAP MS.
 MS_Q_Tof_micro = 1000188
 Q-Tof micro: Waters Q-Tof micro MS.
 MS_Q_Tof_ultima = 1000189
 Q-Tof ultima: Waters Q-Tof Ultima MS.
 MS_QSTAR = 1000190
 QSTAR: Applied Biosystems/MDS SCIEX QSTAR MS.
 MS_quattro_micro = 1000191
 quattro micro: Waters Quattro micro MS.
 MS_Quattro_UItima = 1000192
 Quattro UItima: Waters Quattro Uitima MS.
 MS_Surveyor_MSQ = 1000193
 Surveyor MSQ: ThermoFinnigan Surveyor MSQ MS.
 MS_SymBiot_I = 1000194
 SymBiot I: Applied Biosystems/MDS SCIEX SymBiot I MS.
 MS_SymBiot_XVI = 1000195
 SymBiot XVI: Applied Biosystems/MDS SCIEX SymBiot XVI MS.
 MS_TEMPUS_TOF = 1000196
 TEMPUS TOF: ThermoFinnigan TEMPUS TOF MS.
 MS_TRACE_DSQ = 1000197
 TRACE DSQ: ThermoFinnigan TRACE DSQ MS.
 MS_TRITON = 1000198
 TRITON: ThermoFinnigan TRITON MS.
 MS_TSQ_Quantum = 1000199
 TSQ Quantum: ThermoFinnigan TSQ Quantum MS.
 MS_ultima = 1000200
 ultima: IonSpec Ultima MS.
 MS_ultraflex = 1000201
 ultraflex: Bruker Daltonics' ultraflex: MALDI TOF.
 MS_ultraflex_TOF_TOF = 1000202
 ultraflex TOF/TOF: Bruker Daltonics' ultraflex TOF/TOF: MALDI TOF.
 MS_Voyager_DE_PRO = 1000203
 Voyager-DE PRO: Applied Biosystems/MDS SCIEX Voyager-DE PRO MS.
 MS_Voyager_DE_STR = 1000204
 Voyager-DE STR: Applied Biosystems/MDS SCIEX Voyager-DE STR MS.
 MS_selected_ion_monitoring = 1000205
 selected ion monitoring: The operation of a mass spectrometer in which the intensities of several specific m/z values are recorded rather than the entire mass spectrum.
 MS_Multiple_Ion_Monitoring = MS_selected_ion_monitoring
 Multiple Ion Monitoring (selected ion monitoring): The operation of a mass spectrometer in which the intensities of several specific m/z values are recorded rather than the entire mass spectrum.
 MS_SIM = MS_selected_ion_monitoring
 SIM (selected ion monitoring): The operation of a mass spectrometer in which the intensities of several specific m/z values are recorded rather than the entire mass spectrum.
 MS_selected_reaction_monitoring = 1000206
 selected reaction monitoring: Data acquired from specific product ions corresponding to m/z selected precursor ions recorded via multiple stages of mass spectrometry. Selected reaction monitoring can be performed in time or in space.
 MS_SRM = MS_selected_reaction_monitoring
 SRM (selected reaction monitoring): Data acquired from specific product ions corresponding to m/z selected precursor ions recorded via multiple stages of mass spectrometry. Selected reaction monitoring can be performed in time or in space.
 MS_accurate_mass = 1000207
 accurate mass: An experimentally determined mass that is can be to determine a unique elemental formula. For ions less than 200 u, a measurement with 5 ppm accuracy is sufficient to determine the elemental composition.
 MS_average_mass = 1000208
 average mass: The mass of an ion or molecule calculated using the average mass of each element weighted for its natural isotopic abundance.
 MS_appearance_energy = 1000209
 appearance energy: The minimum energy that must be imparted to an atom or molecule to produce a specified ion. The term appearance potential is not recommended.
 MS_AE = MS_appearance_energy
 AE (appearance energy): The minimum energy that must be imparted to an atom or molecule to produce a specified ion. The term appearance potential is not recommended.
 MS_base_peak = 1000210
 base peak: The peak in a mass spectrum that has the greatest intensity. This term may be applied to the spectra of pure substances or mixtures.
 MS_BP = MS_base_peak
 BP (base peak): The peak in a mass spectrum that has the greatest intensity. This term may be applied to the spectra of pure substances or mixtures.
 MS_OBSOLETE_charge_number_OBSOLETE = 1000211
 OBSOLETE charge number: OBSOLETE. The total charge on an ion divided by the electron charge e. OBSOLETED 2009-10-27 since this was viewed as a duplication of 00041 charge state.
 MS_z_OBSOLETE = MS_OBSOLETE_charge_number_OBSOLETE
 z (OBSOLETE charge number): OBSOLETE. The total charge on an ion divided by the electron charge e. OBSOLETED 2009-10-27 since this was viewed as a duplication of 00041 charge state.
 MS_dalton_OBSOLETE = 1000212
 dalton: A non-SI unit of mass (symbol Da) that is equal to the unified atomic mass unit: 1.660 538 86(28) x 10^-27 kg.
 MS_Da_OBSOLETE = MS_dalton_OBSOLETE
 Da (dalton): A non-SI unit of mass (symbol Da) that is equal to the unified atomic mass unit: 1.660 538 86(28) x 10^-27 kg.
 MS_electron_affinity = 1000213
 electron affinity: The electron affinity of M is the minimum energy required for the process M- ? M + e where M- and M are in their ground rotational, vibrational and electronic states and the electron has zero kinetic energy.
 MS_EA = MS_electron_affinity
 EA (electron affinity): The electron affinity of M is the minimum energy required for the process M- ? M + e where M- and M are in their ground rotational, vibrational and electronic states and the electron has zero kinetic energy.
 MS_electron_energy_obsolete = 1000214
 electron energy obsolete: The potential difference through which electrons are accelerated before they are used to bring about electron ionization.
 MS_exact_mass = 1000215
 exact mass: The calculated mass of an ion or molecule containing a single isotope of each atom.
 MS_field_free_region = 1000216
 field-free region: A section of a mass spectrometer in which there are no electric or magnetic fields.
 MS_FFR = MS_field_free_region
 FFR (field-free region): A section of a mass spectrometer in which there are no electric or magnetic fields.
 MS_ionization_cross_section = 1000217
 ionization cross section: A measure of the probability that a given ionization process will occur when an atom or molecule interacts with a photon, electron, atom or molecule.
 MS_ionization_efficiency_OBSOLETE = 1000218
 ionization efficiency: The ratio of the number of ions formed to the number of electrons, molecules or photons used.
 MS_ionization_energy = 1000219
 ionization energy: The minimum energy required to remove an electron from an atom or molecule to produce a positive ion.
 MS_IE = MS_ionization_energy
 IE (ionization energy): The minimum energy required to remove an electron from an atom or molecule to produce a positive ion.
 MS_isotope_dilution_mass_spectrometry = 1000220
 isotope dilution mass spectrometry: A quantitative mass spectrometry technique in which an isotopically enriched compound is used as an internal standard.
 MS_IDMS = MS_isotope_dilution_mass_spectrometry
 IDMS (isotope dilution mass spectrometry): A quantitative mass spectrometry technique in which an isotopically enriched compound is used as an internal standard.
 MS_magnetic_deflection = 1000221
 magnetic deflection: The deflection of charged particles in a magnetic field due to a force equal to qv B where q is the particle charge, v its velocity and B the magnetic field. Magnetic deflection of an ion beam is used for m/z separation in a magnetic sector mass spectrometer.
 MS_mass_defect = 1000222
 mass defect: The difference between the monoisotipic and nominal mass of a molecule or atom.
 MS_mass_number = 1000223
 mass number: The sum of the protons and neutrons in an atom, molecule or ion.
 MS_molecular_mass = 1000224
 molecular mass: The mass of one mole of a molecular substance (6.022 1415(10) x 10^23 molecules).
 MS_monoisotopic_mass = 1000225
 monoisotopic mass: The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element.
 MS_molecular_beam_mass_spectrometry = 1000226
 molecular beam mass spectrometry: A mass spectrometry technique in which the sample is introduced into the mass spectrometer as a molecular beam.
 MS_MBMS = MS_molecular_beam_mass_spectrometry
 MBMS (molecular beam mass spectrometry): A mass spectrometry technique in which the sample is introduced into the mass spectrometer as a molecular beam.
 MS_multiphoton_ionization = 1000227
 multiphoton ionization: Photoionization of an atom or molecule in which in two or more photons are absorbed.
 MS_MPI = MS_multiphoton_ionization
 MPI (multiphoton ionization): Photoionization of an atom or molecule in which in two or more photons are absorbed.
 MS_nitrogen_rule = 1000228
 nitrogen rule: An organic molecule containing the elements C, H, O, S, P, or halogen has an odd nominal mass if it contains an odd number of nitrogen atoms.
 MS_nominal_mass = 1000229
 nominal mass: The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element rounded to the nearest integer value.
 MS_odd_electron_rule = 1000230
 odd-electron rule: Odd-electron ions may dissociate to form either odd or even-electron ions, whereas even-electron ions generally form even-electron fragment ions.
 MS_peak = 1000231
 peak: A localized region of relatively large ion signal in a mass spectrum. Although peaks are often associated with particular ions, the terms peak and ion should not be used interchangeably.
 MS_peak_intensity_OBSOLETE = 1000232
 peak intensity: The height or area of a peak in a mass spectrum.
 MS_proton_affinity = 1000233
 proton affinity: The proton affinity of a species M is defined as the negative of the enthalpy change for the reaction M + H+ ->[M+H]+, where all species are in their ground rotational, vibrational and electronic states.
 MS_PA = MS_proton_affinity
 PA (proton affinity): The proton affinity of a species M is defined as the negative of the enthalpy change for the reaction M + H+ ->[M+H]+, where all species are in their ground rotational, vibrational and electronic states.
 MS_mass_resolving_power_OBSOLETE = 1000234
 mass resolving power: In a mass spectrum, the observed mass divided by the difference between two masses that can be separated. The method by which delta m was obtained and the mass at which the measurement was made should be reported.
 MS_total_ion_current_chromatogram = 1000235
 total ion current chromatogram: Chromatogram obtained by plotting the total ion current detected in each of a series of mass spectra recorded as a function of retention time.
 MS_TIC_chromatogram = MS_total_ion_current_chromatogram
 TIC chromatogram (total ion current chromatogram): Chromatogram obtained by plotting the total ion current detected in each of a series of mass spectra recorded as a function of retention time.
 MS_transmission = 1000236
 transmission: The ratio of the number of ions leaving a region of a mass spectrometer to the number entering that region.
 MS_unified_atomic_mass_unit_OBSOLETE = 1000237
 unified atomic mass unit: A non-SI unit of mass (u) defined as one twelfth of ^12 C in its ground state and equal to 1.660 538 86(28) x 10^-27 kg.
 MS_u_OBSOLETE = MS_unified_atomic_mass_unit_OBSOLETE
 u (unified atomic mass unit): A non-SI unit of mass (u) defined as one twelfth of ^12 C in its ground state and equal to 1.660 538 86(28) x 10^-27 kg.
 MS_accelerator_mass_spectrometry = 1000238
 accelerator mass spectrometry: A mass spectrometry technique in which atoms extracted from a sample are ionized, accelerated to MeV energies and separated according to their momentum, charge and energy.
 MS_AMS = MS_accelerator_mass_spectrometry
 AMS (accelerator mass spectrometry): A mass spectrometry technique in which atoms extracted from a sample are ionized, accelerated to MeV energies and separated according to their momentum, charge and energy.
 MS_atmospheric_pressure_matrix_assisted_laser_desorption_ionization = 1000239
 atmospheric pressure matrix-assisted laser desorption ionization: Matrix-assisted laser desorption ionization in which the sample target is at atmospheric pressure and the ions formed by the pulsed laser are sampled through a small aperture into the mass spectrometer.
 MS_AP_MALDI = MS_atmospheric_pressure_matrix_assisted_laser_desorption_ionization
 AP MALDI (atmospheric pressure matrix-assisted laser desorption ionization): Matrix-assisted laser desorption ionization in which the sample target is at atmospheric pressure and the ions formed by the pulsed laser are sampled through a small aperture into the mass spectrometer.
 MS_atmospheric_pressure_ionization = 1000240
 atmospheric pressure ionization: Any ionization process in which ions are formed in the gas phase at atmospheric pressure.
 MS_API = MS_atmospheric_pressure_ionization
 API (atmospheric pressure ionization): Any ionization process in which ions are formed in the gas phase at atmospheric pressure.
 MS_Atmostpheric_Pressure_Photoionization_OBSOLETE = 1000241
 Atmostpheric Pressure Photoionization: Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization.
 MS_APPI_OBSOLETE = MS_Atmostpheric_Pressure_Photoionization_OBSOLETE
 APPI (Atmostpheric Pressure Photoionization): Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization.
 MS_blackbody_infrared_radiative_dissociation = 1000242
 blackbody infrared radiative dissociation: A special case of infrared multiphoton dissociation wherein excitation of the reactant ion is caused by absorption of infrared photons radiating from heated blackbody surroundings, which are usually the walls of a vacuum chamber. See also infrared multiphoton dissociation.
 MS_BIRD = MS_blackbody_infrared_radiative_dissociation
 BIRD (blackbody infrared radiative dissociation): A special case of infrared multiphoton dissociation wherein excitation of the reactant ion is caused by absorption of infrared photons radiating from heated blackbody surroundings, which are usually the walls of a vacuum chamber. See also infrared multiphoton dissociation.
 MS_charge_remote_fragmentation = 1000243
 charge-remote fragmentation: A fragmentation of an even-electron ion in which the cleaved bond is not adjacent to the apparent charge site.
 MS_CRF = MS_charge_remote_fragmentation
 CRF (charge-remote fragmentation): A fragmentation of an even-electron ion in which the cleaved bond is not adjacent to the apparent charge site.
 MS_consecutive_reaction_monitoring = 1000244
 consecutive reaction monitoring: MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored.
 MS_CRM = MS_consecutive_reaction_monitoring
 CRM (consecutive reaction monitoring): MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored.
 MS_charge_stripping = 1000245
 charge stripping: The reaction of a positive ion with an atom or molecule that results in the removal of one or more electrons from the ion.
 MS_CS = MS_charge_stripping
 CS (charge stripping): The reaction of a positive ion with an atom or molecule that results in the removal of one or more electrons from the ion.
 MS_delayed_extraction = 1000246
 delayed extraction: The application of the accelerating voltage pulse after a time delay in desorption ionization from a surface. The extraction delay can produce energy focusing in a time-of-flight mass spectrometer.
 MS_DE = MS_delayed_extraction
 DE (delayed extraction): The application of the accelerating voltage pulse after a time delay in desorption ionization from a surface. The extraction delay can produce energy focusing in a time-of-flight mass spectrometer.
 MS_desorption_ionization = 1000247
 desorption ionization: The formation of ions from a solid or liquid material after the rapid vaporization of that sample.
 MS_DI = MS_desorption_ionization
 DI (desorption ionization): The formation of ions from a solid or liquid material after the rapid vaporization of that sample.
 MS_direct_insertion_probe = 1000248
 direct insertion probe: A device for introducing a solid or liquid sample into a mass spectrometer ion source for desorption ionization.
 MS_DIP = MS_direct_insertion_probe
 DIP (direct insertion probe): A device for introducing a solid or liquid sample into a mass spectrometer ion source for desorption ionization.
 MS_direct_liquid_introduction = 1000249
 direct liquid introduction: The delivery of a liquid sample into a mass spectrometer for spray or desorption ionization.
 MS_DLI = MS_direct_liquid_introduction
 DLI (direct liquid introduction): The delivery of a liquid sample into a mass spectrometer for spray or desorption ionization.
 MS_electron_capture_dissociation = 1000250
 electron capture dissociation: A process in which a multiply protonated molecules interacts with a low energy electrons. Capture of the electron leads the liberation of energy and a reduction in charge state of the ion with the production of the (M + nH) (n-1)+ odd electron ion, which readily fragments.
 MS_ECD = MS_electron_capture_dissociation
 ECD (electron capture dissociation): A process in which a multiply protonated molecules interacts with a low energy electrons. Capture of the electron leads the liberation of energy and a reduction in charge state of the ion with the production of the (M + nH) (n-1)+ odd electron ion, which readily fragments.
 MS_even_electron_ion = 1000251
 even-electron ion: An ion containing no unpaired electrons in its ground electronic state, e.g. CH3+ in its ground state.
 MS_EE = MS_even_electron_ion
 EE (even-electron ion): An ion containing no unpaired electrons in its ground electronic state, e.g. CH3+ in its ground state.
 MS_electron_induced_excitation_in_organics = 1000252
 electron-induced excitation in organics: The reaction of an ion with an electron in which the translational energy of the collision is converted into internal energy of the ion.
 MS_EIEIO = MS_electron_induced_excitation_in_organics
 EIEIO (electron-induced excitation in organics): The reaction of an ion with an electron in which the translational energy of the collision is converted into internal energy of the ion.
 MS_electron_multiplier = 1000253
 electron multiplier: A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons. The secondary electrons are then accelerated to other electrodes or parts of a continuous electrode to produce further secondary electrons.
 MS_EM = MS_electron_multiplier
 EM (electron multiplier): A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons. The secondary electrons are then accelerated to other electrodes or parts of a continuous electrode to produce further secondary electrons.
 MS_electrostatic_energy_analyzer = 1000254
 electrostatic energy analyzer: A device consisting of conducting parallel plates, concentric cylinders or concentric spheres that separates charged particles according to their kinetic energy by means of an electric field that is constant in time.
 MS_ESA = MS_electrostatic_energy_analyzer
 ESA (electrostatic energy analyzer): A device consisting of conducting parallel plates, concentric cylinders or concentric spheres that separates charged particles according to their kinetic energy by means of an electric field that is constant in time.
 MS_flowing_afterglow = 1000255
 flowing afterglow: An ion source immersed in a flow of helium or other inert buffer gas that carries the ions through a meter-long reactor at pressures around 100 Pa.
 MS_FA = MS_flowing_afterglow
 FA (flowing afterglow): An ion source immersed in a flow of helium or other inert buffer gas that carries the ions through a meter-long reactor at pressures around 100 Pa.
 MS_high_field_asymmetric_waveform_ion_mobility_spectrometry = 1000256
 high-field asymmetric waveform ion mobility spectrometry: The separation of ions between two concentric cylindrical electrodes due to application of a high voltage asymmetric waveform whereby ions migrate towards one of the two electrodes depending on the ratio of the high- to low-field mobility of the ion.
 MS_FAIMS = MS_high_field_asymmetric_waveform_ion_mobility_spectrometry
 FAIMS (high-field asymmetric waveform ion mobility spectrometry): The separation of ions between two concentric cylindrical electrodes due to application of a high voltage asymmetric waveform whereby ions migrate towards one of the two electrodes depending on the ratio of the high- to low-field mobility of the ion.
 MS_field_desorption = 1000257
 field desorption: The formation of gas-phase ions from a material deposited on a solid surface in the presence of a high electric field. Because this process may encompass ionization by field ionization or other mechanisms, it is not recommended as a synonym for field desorption ionization.
 MS_FD = MS_field_desorption
 FD (field desorption): The formation of gas-phase ions from a material deposited on a solid surface in the presence of a high electric field. Because this process may encompass ionization by field ionization or other mechanisms, it is not recommended as a synonym for field desorption ionization.
 MS_field_ionization = 1000258
 field ionization: The removal of electrons from any species by interaction with a high electric field.
 MS_FI = MS_field_ionization
 FI (field ionization): The removal of electrons from any species by interaction with a high electric field.
 MS_glow_discharge_ionization = 1000259
 glow discharge ionization: The formation of ions in the gas phase and from solid samples at the cathode by application of a voltage to a low pressure gas.
 MS_GD_MS = MS_glow_discharge_ionization
 GD-MS (glow discharge ionization): The formation of ions in the gas phase and from solid samples at the cathode by application of a voltage to a low pressure gas.
 MS_ion_kinetic_energy_spectrometry = 1000260
 ion kinetic energy spectrometry: A method of analysis in which a beam of ions is separated according to the ratio of its translational energy to charge.
 MS_IKES = MS_ion_kinetic_energy_spectrometry
 IKES (ion kinetic energy spectrometry): A method of analysis in which a beam of ions is separated according to the ratio of its translational energy to charge.
 MS_ion_mobility_spectrometry = 1000261
 ion mobility spectrometry: The separation of ions according to their velocity through a buffer gas under the influence of an electric field.
 MS_IMS = MS_ion_mobility_spectrometry
 IMS (ion mobility spectrometry): The separation of ions according to their velocity through a buffer gas under the influence of an electric field.
 MS_infrared_multiphoton_dissociation = 1000262
 infrared multiphoton dissociation: Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple infrared photons.
 MS_IRMPD = MS_infrared_multiphoton_dissociation
 IRMPD (infrared multiphoton dissociation): Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple infrared photons.
 MS_isotope_ratio_mass_spectrometry = 1000263
 isotope ratio mass spectrometry: The measurement of the relative quantity of the different isotopes of an element in a material with a mass spectrometer.
 MS_IRMS = MS_isotope_ratio_mass_spectrometry
 IRMS (isotope ratio mass spectrometry): The measurement of the relative quantity of the different isotopes of an element in a material with a mass spectrometer.
 MS_ion_trap = 1000264
 ion trap: A device for spatially confining ions using electric and magnetic fields alone or in combination.
 MS_IT = MS_ion_trap
 IT (ion trap): A device for spatially confining ions using electric and magnetic fields alone or in combination.
 MS_kinetic_energy_release_distribution = 1000265
 kinetic energy release distribution: Distribution of values of translational kinetic energy release for an ensemble of metastable ions undergoing a specific dissociation reaction.
 MS_KERD = MS_kinetic_energy_release_distribution
 KERD (kinetic energy release distribution): Distribution of values of translational kinetic energy release for an ensemble of metastable ions undergoing a specific dissociation reaction.
 MS_Laser_Desorption_OBSOLETE = 1000266
 Laser Desorption: The formation of ions through the interaction of a laser with a material or with gas-phase ions or molecules.
 MS_Laser_Ionization_MERGE_OBSOLETE = MS_Laser_Desorption_OBSOLETE
 Laser Ionization MERGE (Laser Desorption): The formation of ions through the interaction of a laser with a material or with gas-phase ions or molecules.
 MS_LD_OBSOLETE = MS_Laser_Desorption_OBSOLETE
 LD (Laser Desorption): The formation of ions through the interaction of a laser with a material or with gas-phase ions or molecules.
 MS_mass_analyzed_ion_kinetic_energy_spectrometry = 1000267
 mass analyzed ion kinetic energy spectrometry: Spectra that are obtained from a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector in reverse geometry. The accelerating voltage, V, and the magnetic sector field, B, are set at fixed values to select the precursor ions, which are then allowed to dissociate or to react in a field free region between the two sectors. The kinetic energy product ions of m/z selected precursor ions is analyzed by scanning the electric sector field, E. The width of the product ion spectrum peaks is related to the kinetic energy release distribution (KERD) for the dissociation process.
 MS_MIKES = MS_mass_analyzed_ion_kinetic_energy_spectrometry
 MIKES (mass analyzed ion kinetic energy spectrometry): Spectra that are obtained from a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector in reverse geometry. The accelerating voltage, V, and the magnetic sector field, B, are set at fixed values to select the precursor ions, which are then allowed to dissociate or to react in a field free region between the two sectors. The kinetic energy product ions of m/z selected precursor ions is analyzed by scanning the electric sector field, E. The width of the product ion spectrum peaks is related to the kinetic energy release distribution (KERD) for the dissociation process.
 MS_mass_spectrometry = 1000268
 mass spectrometry: The branch of science that deals with all aspects of mass spectrometers and the results obtained with these instruments.
 MS_MS = MS_mass_spectrometry
 MS (mass spectrometry): The branch of science that deals with all aspects of mass spectrometers and the results obtained with these instruments.
 MS_mass_spectrometry_mass_spectrometry = 1000269
 mass spectrometry/mass spectrometry: The acquisition, study and spectra of the electrically charged products or precursors of a m/z selected ion or ions.
 MS_MS_MS = MS_mass_spectrometry_mass_spectrometry
 MS/MS (mass spectrometry/mass spectrometry): The acquisition, study and spectra of the electrically charged products or precursors of a m/z selected ion or ions.
 MS_multiple_stage_mass_spectrometry = 1000270
 multiple stage mass spectrometry: Multiple stages of precursor ion m/z selection followed by product ion detection for successive progeny ions.
 MS_MSn = MS_multiple_stage_mass_spectrometry
 MSn (multiple stage mass spectrometry): Multiple stages of precursor ion m/z selection followed by product ion detection for successive progeny ions.
 MS_Negative_Ion_chemical_ionization = 1000271
 Negative Ion chemical ionization: Chemical ionization that results in the formation of negative ions.
 MS_NICI = MS_Negative_Ion_chemical_ionization
 NICI (Negative Ion chemical ionization): Chemical ionization that results in the formation of negative ions.
 MS_neutralization_reionization_mass_spectrometry = 1000272
 neutralization reionization mass spectrometry: With this technique, m/z selected ions form neutrals by charge transfer to a collision gas or by dissociation. The neutrals are separated from the remaining ions and ionized in collisions with a second gas. This method is used to investigate reaction intermediates and other unstable species.
 MS_NRMS = MS_neutralization_reionization_mass_spectrometry
 NRMS (neutralization reionization mass spectrometry): With this technique, m/z selected ions form neutrals by charge transfer to a collision gas or by dissociation. The neutrals are separated from the remaining ions and ionized in collisions with a second gas. This method is used to investigate reaction intermediates and other unstable species.
 MS_photoionization = 1000273
 photoionization: The ionization of an atom or molecule by a photon, written M + h? ? M^+ + e. The term photon impact is not recommended.
 MS_PI = MS_photoionization
 PI (photoionization): The ionization of an atom or molecule by a photon, written M + h? ? M^+ + e. The term photon impact is not recommended.
 MS_pyrolysis_mass_spectrometry = 1000274
 pyrolysis mass spectrometry: A mass spectrometry technique in which the sample is heated to the point of decomposition and the gaseous decomposition products are introduced into the ion source.
 MS_PyMS = MS_pyrolysis_mass_spectrometry
 PyMS (pyrolysis mass spectrometry): A mass spectrometry technique in which the sample is heated to the point of decomposition and the gaseous decomposition products are introduced into the ion source.
 MS_collision_quadrupole = 1000275
 collision quadrupole: A transmission quadrupole to which an oscillating potential is applied so as to focus a beam of ions through a collision gas with no m/z separation.
 MS_q = MS_collision_quadrupole
 q (collision quadrupole): A transmission quadrupole to which an oscillating potential is applied so as to focus a beam of ions through a collision gas with no m/z separation.
 MS_resonance_enhanced_multiphoton_ionization = 1000276
 resonance enhanced multiphoton ionization: Multiphoton ionization in which the ionization cross section is significantly enhanced because the energy of the incident photons is resonant with an intermediate excited state of the neutral species.
 MS_REMPI = MS_resonance_enhanced_multiphoton_ionization
 REMPI (resonance enhanced multiphoton ionization): Multiphoton ionization in which the ionization cross section is significantly enhanced because the energy of the incident photons is resonant with an intermediate excited state of the neutral species.
 MS_residual_gas_analyzer = 1000277
 residual gas analyzer: A mass spectrometer used to measure the composition and pressure of gasses in an evacuated chamber.
 MS_RGA = MS_residual_gas_analyzer
 RGA (residual gas analyzer): A mass spectrometer used to measure the composition and pressure of gasses in an evacuated chamber.
 MS_surface_enhanced_laser_desorption_ionization = 1000278
 surface enhanced laser desorption ionization: The formation of ionized species in the gas phase from analytes deposited on a particular surface substrate which is irradiated with a laser beam of which wavelength is absorbed by the surface. See also desorption/ionization on silicon and laser desorption/ionization.
 MS_SELDI = MS_surface_enhanced_laser_desorption_ionization
 SELDI (surface enhanced laser desorption ionization): The formation of ionized species in the gas phase from analytes deposited on a particular surface substrate which is irradiated with a laser beam of which wavelength is absorbed by the surface. See also desorption/ionization on silicon and laser desorption/ionization.
 MS_surface_enhanced_neat_desorption = 1000279
 surface enhanced neat desorption: Matrix-assisted laser desorption ionization in which the matrix is covalently linked to the target surface.
 MS_SEND = MS_surface_enhanced_neat_desorption
 SEND (surface enhanced neat desorption): Matrix-assisted laser desorption ionization in which the matrix is covalently linked to the target surface.
 MS_suface_ionization_OBSOLETE = 1000280
 suface ionization: The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature.
 MS_SI_OBSOLETE = MS_suface_ionization_OBSOLETE
 SI (suface ionization): The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature.
 MS_selected_ion_flow_tube = 1000281
 selected ion flow tube: A device in which m/z selected ions are entrained in an inert carrier gas and undergo ion-molecule reactions.
 MS_SIFT = MS_selected_ion_flow_tube
 SIFT (selected ion flow tube): A device in which m/z selected ions are entrained in an inert carrier gas and undergo ion-molecule reactions.
 MS_sustained_off_resonance_irradiation = 1000282
 sustained off-resonance irradiation: A technique associated with Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry to carry out ion/neutral reactions such as low-energy collision-induced dissociation. A radio-frequency electric field of slightly off-resonance to the cyclotron frequency of the reactant ion cyclically accelerates and decelerates the reactant ion that is confined in the Penning ion trap. The ion's orbit does not exceed the dimensions of ion trap while the ion undergoes an ion/neutral species process that produces a high average translational energy for an extended time.
 MS_SORI = MS_sustained_off_resonance_irradiation
 SORI (sustained off-resonance irradiation): A technique associated with Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry to carry out ion/neutral reactions such as low-energy collision-induced dissociation. A radio-frequency electric field of slightly off-resonance to the cyclotron frequency of the reactant ion cyclically accelerates and decelerates the reactant ion that is confined in the Penning ion trap. The ion's orbit does not exceed the dimensions of ion trap while the ion undergoes an ion/neutral species process that produces a high average translational energy for an extended time.
 MS_Spark_Source_Mass_Spectrometry_OBSOLETE = 1000283
 Spark Source Mass Spectrometry: Mass spectrometry using spark ionization.
 MS_SSMS_OBSOLETE = MS_Spark_Source_Mass_Spectrometry_OBSOLETE
 SSMS (Spark Source Mass Spectrometry): Mass spectrometry using spark ionization.
 MS_stored_waveform_inverse_fourier_transform = 1000284
 stored waveform inverse fourier transform: A technique to create excitation waveforms for ions in FT-ICR mass spectrometer or Paul ion trap. An excitation waveform in the time-domain is generated by taking the inverse Fourier transform of an appropriate frequency-domain programmed excitation spectrum, in which the resonance frequencies of ions to be excited are included. This technique may be used for selection of precursor ions in MS/MS experiments.
 MS_SWIFT = MS_stored_waveform_inverse_fourier_transform
 SWIFT (stored waveform inverse fourier transform): A technique to create excitation waveforms for ions in FT-ICR mass spectrometer or Paul ion trap. An excitation waveform in the time-domain is generated by taking the inverse Fourier transform of an appropriate frequency-domain programmed excitation spectrum, in which the resonance frequencies of ions to be excited are included. This technique may be used for selection of precursor ions in MS/MS experiments.
 MS_total_ion_current = 1000285
 total ion current: The sum of all the separate ion currents carried by the ions of different m/z contributing to a complete mass spectrum or in a specified m/z range of a mass spectrum.
 MS_TIC = MS_total_ion_current
 TIC (total ion current): The sum of all the separate ion currents carried by the ions of different m/z contributing to a complete mass spectrum or in a specified m/z range of a mass spectrum.
 MS_time_lag_focusing = 1000286
 time lag focusing: Energy focusing in a time-of-flight mass spectrometer that is accomplished by introducing a time delay between the formation of the ions and the application of the accelerating voltage pulse.
 MS_TLF = MS_time_lag_focusing
 TLF (time lag focusing): Energy focusing in a time-of-flight mass spectrometer that is accomplished by introducing a time delay between the formation of the ions and the application of the accelerating voltage pulse.
 MS_time_of_flight_mass_spectrometer = 1000287
 time-of-flight mass spectrometer: An instrument that separates ions by m/z in a field-free region after acceleration to a fixed kinetic energy.
 MS_TOF_MS = MS_time_of_flight_mass_spectrometer
 TOF-MS (time-of-flight mass spectrometer): An instrument that separates ions by m/z in a field-free region after acceleration to a fixed kinetic energy.
 MS_cyclotron = 1000288
 cyclotron: A device that uses an oscillating electric field and magnetic field to accelerate charged particles.
 MS_double_focusing_mass_spectrometer = 1000289
 double-focusing mass spectrometer: A mass spectrometer that uses a magnetic sector for m/z focusing and an electric sector for energy focusing of an ion beam.
 MS_hybrid_mass_spectrometer = 1000290
 hybrid mass spectrometer: A mass spectrometer that combines m/z analyzers of different types to perform tandem mass spectrometry.
 MS_linear_ion_trap = 1000291
 linear ion trap: A two dimensional Paul ion trap in which ions are confined in the axial dimension by means of an electric field at the ends of the trap.
 MS_mass_spectrograph_obsolete = 1000292
 mass spectrograph obsolete: An instrument that separates a beam of ions according to their mass-to-charge ratio in which the ions are directed onto a focal plane detector such as a photographic plate.
 MS_mass_spectrometer = 1000293
 mass spectrometer: An instrument that measures the mass-to-charge ratio and relative abundances of ions.
 MS_mass_spectrum = 1000294
 mass spectrum: A plot of the relative abundance of a beam or other collection of ions as a function of the mass-to-charge ratio (m/z).
 MS_mattauch_herzog_geometry = 1000295
 mattauch-herzog geometry: An arrangement for a double-focusing mass spectrometer in which a deflection of ?/(4 ?(2)) radians in a radial electric field is followed by a magnetic deflection of ?/2 radians.
 MS_nier_johnson_geometry = 1000296
 nier-johnson geometry: An arrangement for a double-focusing mass spectrometer in which a deflection of ?/2 radians in a radial electric field analyzer is followed by a magnetic deflection of ?/3 radians.
 MS_paul_ion_trap_OBSOLETE = 1000297
 paul ion trap: A device that permits the trapping of ions by means of an alternating current voltage. The ejection of ions with a m/z less than a prescribed value and retention of those with higher mass depends on the application of radio frequency voltages between a ring electrode and two end-cap electrodes to confine the ions in a circular path. The choice of these voltages determines the m/z below which ions are ejected.
 MS_prolate_traochoidal_mass_spectrometer = 1000298
 prolate traochoidal mass spectrometer: A mass spectrometer in which the ions of different m/z are separated by means of crossed electric and magnetic fields in such a way that the selected ions follow a prolate trochoidal path.
 MS_quistor = 1000299
 quistor: An abbreviation of quadrupole ion storage trap. This term is synonymous with Paul Ion Trap. If so then add a synonym to paul and obsolete this term.
 MS_reflectron = 1000300
 reflectron: A time-of-flight mass spectrometer that uses a static electric field to reverse the direction of travel of the ions entering it. A reflectron improves mass resolution by assuring that ions of the same m/z but different kinetic energy arrive at the detector at the same time.
 MS_sector_mass_spectrometer = 1000301
 sector mass spectrometer: A mass spectrometer consisting of one or more magnetic sectors for m/z selection in a beam of ions. Such instruments may also have one or more electric sectors for energy selection.
 MS_tandem_mass_spectrometer = 1000302
 tandem mass spectrometer: A mass spectrometer designed for mass spectrometry/mass spectrometry.
 MS_transmission_quadrupole_mass_spectrometer = 1000303
 transmission quadrupole mass spectrometer: A mass spectrometer that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis.
 MS_accelerating_voltage = 1000304
 accelerating voltage: The electrical potential used to impart kinetic energy to ions in a mass spectrometer.
 MS_cyclotron_motion = 1000305
 cyclotron motion: The circular motion of a charged particle moving at velocity v in a magnetic field B that results from the force qvB.
 MS_dynamic_mass_spectrometry = 1000306
 dynamic mass spectrometry: A mass spectrometer in which m/z separation using one or more electric fields that vary with time.
 MS_einzel_lens = 1000307
 einzel lens: Three element charged particle lens in which the first and third elements are held at the same voltage. Such a lens produces focusing without changing the translational energy of the particle.
 MS_electric_field_strength = 1000308
 electric field strength: The magnitude of the force per unit charge at a given point in space.
 MS_first_stability_region = 1000309
 first stability region: The region of a Mathieu stability diagram closest to the origin. Ions within this region can traverse the full length of a transmission quadrupole.
 MS_fringing_field = 1000310
 fringing field: The electric or magnetic field that extends from the edge of a sector, lens or other ion optics element.
 MS_kinetic_energy_analyzer = 1000311
 kinetic energy analyzer: A device for measuring the kinetic energy of charged particles using a retarding field, time-of-flight, or the extent of deflection in an electric or magnetic field.
 MS_mass_limit = 1000312
 mass limit: The m/z value above which ions cannot be detected in a mass spectrometer.
 MS_scan_m_z_range_ = 1000313
 scan m/z range?: The limit of m/z over which a mass spectrometer can detect ions.
 MS_mass_selective_axial_ejection = 1000314
 mass selective axial ejection: The use of mass selective instability to eject ions of selected m/z values from an ion trap.
 MS_mass_selective_instability = 1000315
 mass selective instability: A method for selective ejection of ions according to their m/z value in an ion trap.
 MS_mathieu_stability_diagram = 1000316
 mathieu stability diagram: A graphical representation expressed in terms of reduced coordinates that describes charged particle motion in a quadrupole mass filter or quadrupole ion trap mass spectrometer.
 MS_orthogonal_extraction = 1000317
 orthogonal extraction: The pulsed acceleration of ions perpendicular to their direction of travel into a time-of-flight mass spectrometer. Ions may be extracted from a directional ion source, drift tube or m/z separation stage.
 MS_resonance_ion_ejection = 1000318
 resonance ion ejection: A mode of ion ejection in a quadrupole ion trap that relies on a auxiliary radio frequency voltage that is applied to the end-cap electrodes. The voltage is tuned to the secular frequency of a particular ion to eject it.
 MS_space_charge_effect = 1000319
 space charge effect: The mutual repulsion of particles of like charge that limits the current in a charged-particle beam and causes beams or packets of charged particles to expand radially over time.
 MS_static_field = 1000320
 static field: An electric or magnetic field that does not change in time.
 MS_2E_Mass_Spectrum = 1000321
 2E Mass Spectrum: A mass spectrum obtained by setting the electric sector field E to twice the value required to transmit the main ion-beam thereby allowing ions with a kinetic energy-to-charge ratio twice that of the main ion-beam to be transmitted. Product ions resulting from partial charge transfer reactions such as m^2+ + N ? m^+ + N^+ that occur in a collision cell (containing a gas, N) located in a field-free region preceding a magnetic and electric sector combination are detected. When the magnetic sector field B is scanned, a mass spectrum of singly charged product ions of doubly charged precursor ions is obtained.
 MS_charge_inversion_mass_spectrum = 1000322
 charge inversion mass spectrum: The measurement of the relative abundance of ions that result from a charge inversion reaction as a function of m/z.
 MS_constant_neutral_loss_scan = 1000323
 constant neutral loss scan: Spectrum of all precursor ions that undergo a selected m/z decrement.
 MS_constant_neutral_gain_scan = 1000324
 constant neutral gain scan: Spectrum of all precursor ions that undergo a selected m/z increment.
 MS_Constant_Neutral_Mass_Gain_Scan = MS_constant_neutral_gain_scan
 Constant Neutral Mass Gain Scan (constant neutral gain scan): Spectrum of all precursor ions that undergo a selected m/z increment.
 MS_constant_neutral_gain_spectrum = 1000325
 constant neutral gain spectrum: A spectrum formed of all product ions that have been produced by gain of a pre-selected neutral mass following the reaction with and addition of the gas in a collision cell.
 MS_constant_neutral_mass_gain_spectrum = MS_constant_neutral_gain_spectrum
 constant neutral mass gain spectrum (constant neutral gain spectrum): A spectrum formed of all product ions that have been produced by gain of a pre-selected neutral mass following the reaction with and addition of the gas in a collision cell.
 MS_constant_neutral_loss_spectrum = 1000326
 constant neutral loss spectrum: A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum.
 MS_constant_neutral_mass_loss_spectrum = MS_constant_neutral_loss_spectrum
 constant neutral mass loss spectrum (constant neutral loss spectrum): A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum.
 MS_consecutive_reaction_monitoring_OBSOLETE = 1000327
 consecutive reaction monitoring: A type of MS/MS experiments with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored.
 MS_e_2_mass_spectrum = 1000328
 e/2 mass spectrum: A mass spectrum obtained using a sector mass spectrometer in which the electric sector field E is set to half the value required to transmit the main ion-beam. This spectrum records the signal from doubly charged product ions of charge-stripping reactions.
 MS_linked_scan = 1000329
 linked scan: A scan in an instrument with two or more m/z analysers or in a sector mass spectrometer that incorporates at least one magnetic sector and one electric sector. Two or more of the analyzers are scanned simultaneously so as to preserve a predetermined relationship between scan parameters to produce a product ion, precursor ion or constant neutral loss spectrum.
 MS_linked_scan_at_constant_b_e = 1000330
 linked scan at constant b/e: A linked scan at constant B/E may be performed on a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector. The magnetic field B and the electric field E are scanned simultaneously while the accelerating voltage V is held constant, so as to maintain the ratio of the two fields constant. This linked scan may record a product ion spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors.
 MS_Linked_Scan_at_Constant_E2_V = 1000331
 Linked Scan at Constant E2/V: A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector. The electric sector field, E, and the accelerating voltage, V, are scanned simultaneously, so as to maintain the ratio E2/V at a constant value. This linked scan recordss a product ion spectrum of dissociation or other reactions occurring in a field free region (FFR) preceding the two sectors.
 MS_Linked_Scan_at_Constant_B2_E = 1000332
 Linked Scan at Constant B2/E: A linked scan performed on a sector mass spectrometer that incorporates at least one electric sector plus one magnetic sector in either order. The accelerating voltage is fixed and the magnetic field, B, and the electric field, E, are scanned simultaneously so as to maintain the ratio B2/E at a constant value. This linked scan records a precursor ion spectrum of dissociation or other reactions occurring in the field free region preceding the two sectors. The term B2/E linked scan is not recommended.
 MS_Linked_Scan_at_Constant_B_1__E_E0___1_2___E = 1000333
 Linked Scan at Constant B[1-(E/E0)]^1/2 / E: A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector placed in either order. The accelerating voltage is fixed while scanning the magnetic field, B, and electric field, E, simultaneously, so as to maintain the quantity B[1-(E/E0)]1/2/E at a constant value. This linked scan records a constant neutral mass loss (or gain) spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors. E0 is the electric field required to transmit the singly charged analog of the desired neutral fragment. The term B[1-(E/E0)]1/2/E linked scan.
 MS_MS_MS_in_Time = 1000334
 MS/MS in Time: A tandem mass spectrometry method in which product ion spectra are recorded in a single m/z analyzer (such as a Paul Ion Trap or FTMS) in discreet steps over time. Ions in a specific m/z range are selected, dissociated, and the product ions analyzed sequentially in time.
 MS_MS_MS_in_Space = 1000335
 MS/MS in Space: A tandem mass spectrometry method in which product ion spectra are recorded in m/z analyzers separated in space. Specific m/z separation functions are designed such that in one section of the instrument ions are selected, dissociated in an intermediate region, and the product ions are then transmitted to another analyser for m/z separation and data acquisition.
 MS_neutral_loss = 1000336
 neutral loss: The loss of an uncharged species during a rearrangement process.
 MS_nth_generation_product_ion = 1000337
 nth generation product ion: Serial product ions from dissociation of selected precursor ions where n refers to the number of stages of dissociation. The term granddaughter ion is deprecated.
 MS_nth_generation_product_ion_scan = 1000338
 nth generation product ion scan: The specific scan functions or processes that record the appropriate generation of product ion or ions of any m/z selected precursor ions.
 MS_nth_generation_product_ion_spectrum_OBSOLETE = 1000339
 nth generation product ion spectrum: The mass spectrum recorded from any mass spectrometer in which the appropriate scan function can be set to record the appropriate generation product ion or ions of m/z selected precursor ions.
 MS_precursor_ion = 1000340
 precursor ion: An ion that reacts to form particular product ions. The reaction can be unimolecular dissociation, ion/molecule reaction, isomerization, or change in charge state. The term parent ion is not recommended.
 MS_precursor_ion_spectrum = 1000341
 precursor ion spectrum: Spectrum generated by scanning precursor m/z while monitoring a fixed product m/z.
 MS_product_ion = 1000342
 product ion: An ion formed as the product of a reaction involving a particular precursor ion. The reaction can be unimolecular dissociation to form fragment ions, an ion/molecule reaction, or simply involve a change in the number of charges. The term fragment ion is deprecated. The term daughter ion is deprecated.
 MS_product_ion_spectrum_OBSOLETE = 1000343
 product ion spectrum: A mass spectrum recorded from any spectrometer in which the appropriate m/z separation scan function is set to record the product ion or ions of selected precursor ions.
 MS_progeny_ion = 1000344
 progeny ion: A charged product of a series of consecutive reactions that includes product ions, 1st generation product ions, 2nd generation product ions, etc. Given the sequential fragmentation scheme: M1+ -> M2+ -> M3+ -> M4+ -> M5+. M4+ is the precursor ion of M5+, a 1st generation product ion of M3+, a 2nd generation product ion of M2+ and a 3rd generation product ion of M1+.
 MS_Progeny_Fragment_Ion = MS_progeny_ion
 Progeny Fragment Ion (progeny ion): A charged product of a series of consecutive reactions that includes product ions, 1st generation product ions, 2nd generation product ions, etc. Given the sequential fragmentation scheme: M1+ -> M2+ -> M3+ -> M4+ -> M5+. M4+ is the precursor ion of M5+, a 1st generation product ion of M3+, a 2nd generation product ion of M2+ and a 3rd generation product ion of M1+.
 MS_array_detector = 1000345
 array detector: Detector comprising several ion collection elements, arranged in a line or grid where each element is an individual detector.
 MS_conversion_dynode = 1000346
 conversion dynode: A surface that is held at high potential such that ions striking the surface produce electrons that are subsequently detected.
 MS_dynode = 1000347
 dynode: One of a series of electrodes in a photomultiplier tube. Such an arrangement is able to amplify the current emitted by the photocathode.
 MS_focal_plane_collector = 1000348
 focal plane collector: A detector for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane.
 MS_ion_to_photon_detector = 1000349
 ion-to-photon detector: A detector in which ions strike a conversion dynode to produce electrons that in turn strike a phosphor and the resulting photons are detected by a photomultiplier.
 MS_point_collector = 1000350
 point collector: A detector in which the ion beam is focused onto a point and the individual ions arrive sequentially.
 MS_postacceleration_detector = 1000351
 postacceleration detector: A detector in which the charged particles are accelerated to a high velocity and impinge on a conversion dynode, emitting secondary electrons. The electrons are accelerated onto a phosphor screen, which emits photons that are in turn detected using a photomultiplier or other photon detector.
 MS_secondary_electron = 1000352
 secondary electron: Electrons that are ejected from a sample surface as a result of bombardment by a primary beam of atoms, ions or photons. WAS IN DETECTOR TYPE. Where should it go?
 MS_adduct_ion = 1000353
 adduct ion: Ion formed by the interaction of an ion with one or more atoms or molecules to form an ion containing all the constituent atoms of the precursor ion as well as the additional atoms from the associated atoms or molecules.
 MS_aromatic_ion = 1000354
 aromatic ion: A planar cyclic ion that obeys the Hckel (4n + 2) rule where n is a positive integer representing the number of conjugated Pi electrons. Charge delocalization leads to greater stability compared to a hypothetical localized structure.
 MS_analog_ion = 1000355
 analog ion: Ions that have similar chemical valence, for example the acetyl cation CH3-CO+ and the thioacetyl cation CH3-CS+.
 MS_anti_aromatic_ion = 1000356
 anti-aromatic ion: A planar cyclic ion with 4n ? electrons and is therefore not aromatic.
 MS_cationized_molecule = 1000357
 cationized molecule: An ion formed by the association of a cation with a neutral molecule, M, for example [M+ Na]+ and [M + K]+. The terms quasi-molecular ion and pseudo-molecular ion should not be used.
 MS_cluster_ion = 1000358
 cluster ion: An ion formed by a multi-component atomic or molecular assembly of one or more ions with atoms or molecules, such as [(H20)nH]+, [(NaCl)nNa]+ and [(H3PO3)nHPO3]-.
 MS_Conventional_ion = 1000359
 Conventional ion: A radical cation or anion in which the charge site and the unpaired electron spin are both formally located in the same atom or group of atoms, as opposed to the spatially separate electronic configuration of distonic ions. The radical cation of methanol, CH3OH+, in which the charge and spin sites are formally located at the O atom is an example of a conventional ion, whereas .CH2-OH2+ is a distonic ion.
 MS_diagnostic_ion = 1000360
 diagnostic ion: A product ion whose formation reveals structural or compositional information of its precursor. For instance, the phenyl cation in an electron ionization mass spectrum is a diagnostic ion for benzene and derivatives.
 MS_dimeric_ion = 1000361
 dimeric ion: An ion formed by ionization of a dimer or by the association of an ion with its neutral counterpart such as [M2]+ or [M-H-M]+.
 MS_distonic_ion = 1000362
 distonic ion: A radical cation or anion in which the charge site and the unpaired electron spin cannot be both formally located in the same atom or group of atoms as it can be with a conventional ion. For example, CH2-OH2+ is a distonic ion whereas the radical cation of methanol, CH3OH+ is a conventional ion.
 MS_enium_ion = 1000363
 enium ion: A positively charged lower-valency ion of the nonmetallic elements. The methenium ion is CH3+. Other examples are the oxenium, sulfenium, nitrenium, phosphenium, and halenium ions.
 MS_fragment_ion_OBSOLETE = 1000364
 fragment ion: A product ion that results from the dissociation of a precursor ion.
 MS_ion_ = 1000365
 ion?: An atomic or molecular species having a net positive or negative electric charge.
 MS_Isotopologue_ion = 1000366
 Isotopologue ion: An ion that differs only in the isotopic composition of one or more of its constituent atoms. For example CH4+ and CH3D+ or 10BF3 and 11BF3. The term isotopologue is a contraction of isotopic homologue.
 MS_Isotopomeric_ion = 1000367
 Isotopomeric ion: Isomeric ion having the same numbers of each isotopic atom but differing in their positions. Isotopomeric ions can be either configurational isomers in which two atomic isotopes exchange positions or isotopic stereoisomers. The term isotopomer is a shortening of isotopic isomer.
 MS_metastable_ion = 1000368
 metastable ion: An ion that is formed with internal energy higher than the threshold for dissociation but with a lifetime great enough to allow it to exit the ion source and enter the mass spectrometer where it dissociates before detection.
 MS_molecular_ion = 1000369
 molecular ion: An ion formed by the removal of one or more electrons to form a positive ion or the addition off one or more electrons to form a negative ion.
 MS_negative_ion = 1000370
 negative ion: An atomic or molecular species having a net negative electric charge.
 MS_non_classical_ion = 1000371
 non-classical ion: Hyper-coordinated carbonium ion such as the penta-coordinated norbornyl cation. Note: Tri-coordinated carbenium ions are termed classical ions.
 MS_onium_ion = 1000372
 onium ion: A positively charged hypervalent ion of the nonmetallic elements. Examples are the methonium ion CH5+, the hydrogenonium ion H3+ and the hydronium ion H3O+. Other examples are the carbonium, oxonium, sulfonium, nitronium, diazonium, phosphonium, and halonium ions. Onium ions are not limited to monopositive ions; multiply-charged onium ions exist such as the gitonic (proximal) oxonium dication H4O2+ and the distonic oxonium dication H2O+-CH2-CH2-OH2+.
 MS_principal_ion = 1000373
 principal ion: Most abundant ion of an isotope cluster, such as the 11B79Br2 81Br+ ion of m/z 250 of the cluster of isotopologue molecular ions of BBr3. The term principal ion has also been used to describe ions that have been artificially isotopically enriched in one or more positions such as CH3 13CH3+ or CH2D2 +, but those are best defined as isotopologue ions.
 MS_positive_ion = 1000374
 positive ion: An atomic or molecular species having a net positive electric charge.
 MS_protonated_molecule = 1000375
 protonated molecule: An ion formed by interaction of a neutral molecule with a proton and represented by the symbol [M + H]+, where M is the neutral molecule. The term 'protonated molecular ion,' 'quasi-molecular ion' and 'pseudo-molecular ion' are not recommended.
 MS_radical_ion = 1000376
 radical ion: An ion, either a cation or anion, containing unpaired electrons in its ground state. The unpaired electron is denoted by a superscript dot alongside the superscript symbol for charge, such as for the molecular ion of a molecule M, that is, M+. Radical ions with more than one charge and/or more than one unpaired electron are denoted such as M(2+)(2). Unless the positions of the unpaired electron and charge can be associated with specific atoms, superscript charge designation should be placed before the superscript dot designation.
 MS_reference_ion = 1000377
 reference ion: A stable ion whose structure is known with certainty. These ions are usually formed by direct ionization of a neutral molecule of known structure and are used to verify by comparison the structure of an unknown ion.
 MS_stable_ion = 1000378
 stable ion: An ion with internal energy sufficiently low that it does not rearrange or dissociate prior to detection in a mass spectrometer.
 MS_unstable_ion = 1000379
 unstable ion: An ion with sufficient enerrgy to dissociate within the ion source.
 MS_adiabatic_ionization = 1000380
 adiabatic ionization: A process whereby an electron is removed from an atom, ion, or molecule to produce an ion in its lowest energy state.
 MS_associative_ionization = 1000381
 associative ionization: An ionization process in which two excited atoms or molecules react to form a single positive ion and an electron.
 MS_atmospheric_pressure_photoionization = 1000382
 atmospheric pressure photoionization: Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization.
 MS_autodetachment = 1000383
 autodetachment: The formation of a neutral when a negative ion in a disrtete state with an energy greater than the detachment threshold loses an electron spontaneously without further interaction with an energy source.
 MS_autoionization = 1000384
 autoionization: The formation of an ion when an atom or molecule in a discrete state with an energy greater than the ionization threshold loses an electron spontaneously without further interaction with an energy source.
 MS_charge_exchange_ionization = 1000385
 charge exchange ionization: The interaction of an ion with an atom or molecule in which the charge on the ion is transferred to the neutral without the dissociation of either. Synonymous with charge transfer ionization.
 MS_chemi_ionization = 1000386
 chemi-ionization: The reaction of a neutral molecule with an internally excited molecule to form an ion. Note that this term is not synonymous with chemical ionization.
 MS_desorption_ionization_on_silicon = 1000387
 desorption/ionization on silicon: The formation of ions by laser desorption ionization of a sample deposited on a porous silicon surface.
 MS_dissociative_ionization = 1000388
 dissociative ionization: The reaction of a gas-phase molecule that results in its decomposition to form products, one of which is an ion.
 MS_electron_ionization = 1000389
 electron ionization: The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended.
 MS_ion_desolvation = 1000390
 ion desolvation: The removal of solvent molecules clustered around a gas-phase ion by means of heating and/or collisions with gas molecules.
 MS_ion_pair_formation = 1000391
 ion-pair formation: The reaction of a molecule to form both a positive ion and negative ion fragment among the products.
 MS_ionization_efficiency = 1000392
 ionization efficiency: The ratio of the number of ions formed to the number of electrons, molecules or photons used.
 MS_laser_desorption_ionization = 1000393
 laser desorption ionization: The formation of gas-phase ions by the interaction of a pulsed laser with a solid or liquid material.
 MS_liquid_secondary_ionization = 1000395
 liquid secondary ionization: The ionization of any species by the interaction of a focused beam of ions with a sample that is dissolved in a solvent matrix. See also fast atom bombardment and secondary ionization.
 MS_membrane_inlet = 1000396
 membrane inlet: A semi-permeable membrane separator that permits the passage of gas sample directly to the mass spectrometer ion source.
 MS_microelectrospray = 1000397
 microelectrospray: Electrospray ionization at a solvent flow rate of 300-800 nL/min where the flow is a result of a mechanical pump. See nanaoelectrospray.
 MS_nanoelectrospray = 1000398
 nanoelectrospray: Electrospray ionization at a flow rate less than ~25 nL/min. Nanoelectrospray is synonymous with nanospray. The flow is dependent on the potenial on the tip of the electrospray needle and/or a gas presure to push the sample through the needle. See also electrospray ionization and microelectrospray.
 MS_nanospray = MS_nanoelectrospray
 nanospray (nanoelectrospray): Electrospray ionization at a flow rate less than ~25 nL/min. Nanoelectrospray is synonymous with nanospray. The flow is dependent on the potenial on the tip of the electrospray needle and/or a gas presure to push the sample through the needle. See also electrospray ionization and microelectrospray.
 MS_penning_ionization = 1000399
 penning ionization: Ionization that occurs through the interaction of two or more neutral gaseous species, at least one of which is internally excited.
 MS_plasma_desorption_ionization = 1000400
 plasma desorption ionization: The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization.
 MS_pre_ionization_state = 1000401
 pre-ionization state: An electronic state capable of undergoing auto-Ionization.
 MS_secondary_ionization = 1000402
 secondary ionization: The process in which ions are ejected from a sample surface as a result of bombardment by a primary beam of atoms or ions.
 MS_soft_ionization = 1000403
 soft ionization: The formation of gas-phase ions without extensive fragmentation.
 MS_spark_ionization = 1000404
 spark ionization: The formation of ions from a solid material by an intermittent electrical discharge.
 MS_surface_assisted_laser_desorption_ionization = 1000405
 surface-assisted laser desorption ionization: The formation of gas-phase ions from molecules that are deposited on a particular surface substrate that is irradiated with a pulsed laser. See also matrix-assisted laser desorption ionization.
 MS_surface_ionization = 1000406
 surface ionization: The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature.
 MS_thermal_ionization = 1000407
 thermal ionization: The ionization of a neutral species through contact with a high temperature surface.
 MS_vertical_ionization = 1000408
 vertical ionization: A process in which an electron is removed from or added to a molecule without a change in the positions of the atoms. The resulting ion is typically in an excited vibrational state.
 MS_association_reaction = 1000409
 association reaction: The reaction of an ion with a neutral species in which the reactants combine to form a single ion.
 MS_alpha_cleavage = 1000410
 alpha-cleavage: A homolytic cleavage where the bond fission occurs between at the atom adjacent to the atom at the apparent charge site and an atom removed from the aparent charge site by two bonds.
 MS_beta_cleavage = 1000411
 beta-cleavage: A homolytic cleavage where the bond fission occurs between at an atom removed from the apparent charge site atom by two bonds and an atom adjacent to that atom and removed from the aparent charge site by three bonds.
 MS_buffer_gas = 1000412
 buffer gas: An inert gas used for collisional deactivation of internally excited ions.
 MS_charge_induced_fragmentation = 1000413
 charge-induced fragmentation: Fragmentation of an odd electron ion in which the cleaved bond is adjacent to the apparent charge site. Synonymous with charge mediated fragmentation.
 MS_charge_inversion_reaction = 1000414
 charge inversion reaction: Reaction of an ion with a neutral species in which the charge on the product ion is reversed in sign with respect to the reactant ion.
 MS_charge_permutation_reaction = 1000415
 charge permutation reaction: The reaction of an ion with a neutral species with a resulting change in the magnitude or sign of the charge on the reactant ion.
 MS_charge_stripping_reaction = 1000416
 charge stripping reaction: Reaction of a positive ion with a neutral species in which the positive charge on the product ion is greater than that on the reactant ion.
 MS_charge_transfer_reaction = 1000417
 charge transfer reaction: The reaction of an ion with a neutral species in which some or all of the charge of the reactant ion is transferred to the neutral species.
 MS_collisional_excitation = 1000418
 collisional excitation: The reaction of an ion with a neutral species in which the translational energy of the collision is converted into internal energy of the ion.
 MS_collision_gas = 1000419
 collision gas: An inert gas used for collisional excitation. The term target gas is not recommended.
 MS_heterolytic_cleavage = 1000420
 heterolytic cleavage: Fragmentation of a molecule or ion in which both electrons forming the single bond that is broken remain on one of the atoms that were originally bonded. This term is synonymous with heterolysis.
 MS_high_energy_collision = 1000421
 high energy collision: Collision-induced dissociation process wherein the projectile ion has laboratory-frame translational energy higher than 1 keV.
 MS_high_energy_collision_induced_dissociation = 1000422
 high-energy collision-induced dissociation: A collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately 1000 eV.
 MS_HCD = MS_high_energy_collision_induced_dissociation
 HCD (high-energy collision-induced dissociation): A collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately 1000 eV.
 MS_homolytic_cleavage = 1000423
 homolytic cleavage: Fragmentation of an odd electron ion that results from one of a pair of electrons that form a bond between two atoms moving to form a pair with the odd electron on the atom at the apparent charge site. Fragmentation results in the formation of an even electron ion and a radical. This reaction involves the movement of a single electron and is symbolized by a single-barbed arrow. Synonymous with Homolysis.
 MS_hydrogen_deuterium_exchange = 1000424
 hydrogen/deuterium exchange: Exchange of hydrogen atoms with deuterium atoms in a molecule or pre-formed ion in solution prior to introduction into a mass spectrometer, or by reaction of an ion with a deuterated collision gas inside a mass spectrometer.
 MS_ion_energy_loss_spectrum = 1000425
 ion energy loss spectrum: A plot of the relative abundance of a beam or other collection of ions as a function their loss of translational energy in reactions with neutral species.
 MS_ionizing_collision = 1000426
 ionizing collision: The reaction of an ion with a neutral species in which one or more electrons are removed from either the ion or neutral.
 MS_ion_molecule_reaction = 1000427
 ion/molecule reaction: The reaction of an ion with a neutral molecule. The term ion-molecule reaction is not recommended because the hyphen suggests a single species that is that is both an ion and a molecule.
 MS_ion_neutral_complex = 1000428
 ion/neutral complex: A particular type of transition state that lies between precursor and product ions on the reaction coordinate of some ion reactions.
 MS_ion_neutral_species_reaction = 1000429
 ion/neutral species reaction: A process wherein a charged species interacts with a neutral reactant to produce either chemically different species or changes in the internal energy of one or both of the reactants.
 MS_ion_neutral_species_exchange_reaction = 1000430
 ion/neutral species exchange reaction: In this reaction an association reaction is accompanied by the subsequent or simultaneous liberation of a different neutral species as a product.
 MS_kinetic_method = 1000431
 kinetic method: An approach to determination of ion thermodynamic quantities by a bracketing procedure in which the relative probabilities of competing ion fragmentations are measured via the relative abundances of the reaction products. The extended kinetic method takes the associated entropy changes into account.
 MS_low_energy_collisions = 1000432
 low energy collisions: A collision between an ion and neutral species with translational energy approximately 1000 eV or lower.
 MS_low_energy_collision_induced_dissociation = 1000433
 low-energy collision-induced dissociation: A collision-induced dissociation process wherein the precursor ion has the translational energy lower than approximately 1000 eV. This process typically requires multiple collisions and the collisional excitation is cumulative.
 MS_McLafferty_Rearrangement = 1000434
 McLafferty Rearrangement: A dissociation reaction triggered by transfer of a hydrogen atom via a 6-member transition state to the formal radical/charge site from a carbon atom four atoms removed from the charge/radical site (the gamma-carbon); subsequent rearrangement of electron density leads to expulsion of an olefin molecule. This term was originally applied to ketone ions where the charge/radical site is the carbonyl oxygen, but it is now more widely applied.
 MS_photodissociation = 1000435
 photodissociation: A process wherein the reactant ion is dissociated as a result of absorption of one or more photons.
 MS_multiphoton_dissociation = MS_photodissociation
 multiphoton dissociation (photodissociation): A process wherein the reactant ion is dissociated as a result of absorption of one or more photons.
 MS_MPD = MS_photodissociation
 MPD (photodissociation): A process wherein the reactant ion is dissociated as a result of absorption of one or more photons.
 MS_partial_charge_transfer_reaction = 1000436
 partial charge transfer reaction: Reaction of an ion with a neutral species in which some but not all of the ion charge is transferred to the neutral.
 MS_ion_reaction = 1000437
 ion reaction: Chemical transformation involving an ion.
 MS_superelastic_collision = 1000438
 superelastic collision: Collision in which the translational energy of the fast-moving collision partner is increased at the expense of internal energy of one or both collision partners.
 MS_surface_induced_reaction = 1000439
 surface-induced reaction: A process wherein a reactant ion interacts with a surface to produce either chemically different species or a change in the internal energy of the reactant ion.
 MS_unimolecular_dissociation = 1000440
 unimolecular dissociation: Fragmentation reaction in which the molecularity is treated as one, irrespective of whether the dissociative state is that of a metastable ion produced in the ion source or results from collisional excitation of a stable ion.
 MS_scan = 1000441
 scan: Function or process of the mass spectrometer where it records a spectrum.
 MS_spectrum = 1000442
 spectrum: A mass spectrum is an intensity vs m/z (mass-to-charge ratio) plot representing a chemical analysis.
 MS_mass_analyzer_type = 1000443
 mass analyzer type: Mass analyzer separates the ions according to their mass-to-charge ratio.
 MS_m_z_Separation_Method = 1000444
 m/z Separation Method: m/z Separation Method.
 MS_sequential_m_z_separation_method = 1000445
 sequential m/z separation method: Sequential m/z separation method.
 MS_fast_ion_bombardment = 1000446
 fast ion bombardment: The ionization of any species by the interaction of a focused beam of ions having a translational energy of several thousand eV with a solid sample.
 MS_FIB = MS_fast_ion_bombardment
 FIB (fast ion bombardment): The ionization of any species by the interaction of a focused beam of ions having a translational energy of several thousand eV with a solid sample.
 MS_LTQ = 1000447
 LTQ: Finnigan LTQ MS.
 MS_LTQ_FT = 1000448
 LTQ FT: Finnigan LTQ FT MS.
 MS_LTQ_Orbitrap = 1000449
 LTQ Orbitrap: Finnigan LTQ Orbitrap MS.
 MS_LXQ = 1000450
 LXQ: Finnigan LXQ MS.
 MS_mass_analyzer = 1000451
 mass analyzer: Terms used to describe the Analyzer.
 MS_analyzer = MS_mass_analyzer
 analyzer (mass analyzer): Terms used to describe the Analyzer.
 MS_data_transformation = 1000452
 data transformation: Terms used to describe types of data processing.
 MS_data_processing = MS_data_transformation
 data processing (data transformation): Terms used to describe types of data processing.
 MS_detector = 1000453
 detector: The device that detects ions.
 MS_instrument_additional_description = 1000454
 instrument additional description: Additional terms to describe the instrument as outlined in the mass spec doc, Appendix 1, section 1.5.
 MS_ion_selection_attribute = 1000455
 ion selection attribute: Ion selection properties that are associated with a value.
 MS_precursor_activation = 1000456
 precursor activation: Terms to describe the precursor activation.
 MS_activation = MS_precursor_activation
 activation (precursor activation): Terms to describe the precursor activation.
 MS_sample = 1000457
 sample: Terms to describe the sample.
 MS_source = 1000458
 source: Terms to describe the source.
 MS_spectrum_instrument_description = 1000459
 spectrum instrument description: Terms used to describe the spectrum.
 MS_unit = 1000460
 unit: Terms to describe units.
 MS_additional_description = 1000461
 additional description: Terms to describe Additional.
 MS_ion_optics = 1000462
 ion optics: Device used in the construction of a mass spectrometer to focus, contain or otherwise manipulate ions.
 MS_instrument = 1000463
 instrument: Description of the instrument or the mass spectrometer.
 MS_instrument_configuration = MS_instrument
 instrument configuration (instrument): Description of the instrument or the mass spectrometer.
 MS_mass_unit_OBSOLETE = 1000464
 mass unit: A unit of measurement for mass.
 MS_scan_polarity = 1000465
 scan polarity: An acquisition mode to which specifies weather polarity is negative, positive or alternating.
 MS_alternating_OBSOLETE = 1000466
 alternating: Alternating.
 MS_1200_series_LC_MSD_SL = 1000467
 1200 series LC/MSD SL: The 1200 Series LC/MSD SL ion trap belongs to the Agilent LC/MSD ion trap family. It provides fast polarity switching and multisignal data acquisition capabilities in a single run while also providing 5 stages of automated data dependent MS/MS and 11 stages of manual MS/MS.
 MS_6110_Quadrupole_LC_MS = 1000468
 6110 Quadrupole LC/MS: The 6110 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with an entry level single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6110 Quadrupole mass spectrometer has m/z range of 10-1500 and 2500 u/s scan speed. It proves useful for wide range of SIM quantitative applications.
 MS_6120_Quadrupole_LC_MS = 1000469
 6120 Quadrupole LC/MS: The 6120 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. 6120 quadrupole mass spectrometer has m/z range of 10-1500, 2500 u/s scan speed and utilizes multiple signal acquisition.
 MS_6130_Quadrupole_LC_MS = 1000470
 6130 Quadrupole LC/MS: The 6130 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 series of Agilent mass spectrometers. The 6130 quadrupole mass spectrometer has m/z range of 2-3000, 2500 u/s scan speed in standard mode and 5250 u/s speed in fast-scan mode. It also uses multiple signal acquisition.
 MS_6140_Quadrupole_LC_MS = 1000471
 6140 Quadrupole LC/MS: The 6140 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6140 Quadrupole mass spectrometer has m/z range of 10-1350, 2500 u/s scan speed in standard mode and 10000 u/s speed in fast-scan mode. It also uses multiple signal acquisition.
 MS_6210_Time_of_Flight_LC_MS = 1000472
 6210 Time-of-Flight LC/MS: The 6210 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources.
 MS_6310_Ion_Trap_LC_MS = 1000473
 6310 Ion Trap LC/MS: The 6310 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.35 resolution and mass range of 200-4000 with resolution of 3-4. The scan speed varies from 1650-27000 for the respective mass ranges.
 MS_6320_Ion_Trap_LC_MS = 1000474
 6320 Ion Trap LC/MS: The 6320 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges.
 MS_6330_Ion_Trap_LC_MS = 1000475
 6330 Ion Trap LC/MS: The 6330 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges.
 MS_6340_Ion_Trap_LC_MS = 1000476
 6340 Ion Trap LC/MS: The 6340 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges.
 MS_6410_Triple_Quadrupole_LC_MS = 1000477
 6410 Triple Quadrupole LC/MS: The 6410 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. Mass range of the mass spectrometer is 15-1650 m/z, resolution is at three settings of 0.7 u (unit), 1.2 u (wide) and 2.5 u (widest). The mass accuracy for 6410 mass spectrometer is 0.1 across the mass range. The collision cell is a hexapole with linear acceleration.
 MS_6410_Triple_Quad_LC_MS = MS_6410_Triple_Quadrupole_LC_MS
 6410 Triple Quad LC/MS (6410 Triple Quadrupole LC/MS): The 6410 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. Mass range of the mass spectrometer is 15-1650 m/z, resolution is at three settings of 0.7 u (unit), 1.2 u (wide) and 2.5 u (widest). The mass accuracy for 6410 mass spectrometer is 0.1 across the mass range. The collision cell is a hexapole with linear acceleration.
 MS_1200_series_LC_MSD_VL = 1000478
 1200 series LC/MSD VL: The LC/MSD VL ion trap is part of the family of Agilent ion trap mass spectrometers. It has ESI, APCI and APPI ion sources and is a useful ion trap when the amount of sample is not the limiting factor.
 MS_purgatory = 1000479
 purgatory: Terms that will likely become obsolete unless there are wails of dissent.
 MS_mass_analyzer_attribute = 1000480
 mass analyzer attribute: Analyzer properties that are associated with a value.
 MS_detector_attribute = 1000481
 detector attribute: Detector attribute recognized as a value.
 MS_source_attribute = 1000482
 source attribute: Property of a source device that need a value.
 MS_Thermo_Fisher_Scientific_instrument_model = 1000483
 Thermo Fisher Scientific instrument model: Thermo Fisher Scientific instrument model. The company has gone through several names including Thermo Finnigan, Thermo Scientific.
 MS_orbitrap = 1000484
 orbitrap: An ion trapping device that consists of an outer barrel-like electrode and a coaxial inner spindle-like electrode that form an electrostatic field with quadro-logarithmic potential distribution. The frequency of harmonic oscillations of the orbitally trapped ions along the axis of the electrostatic field is independent of the ion velocity and is inversely proportional to the square root of m/z so that the trap can be used as a mass analyzer.
 MS_nanospray_inlet = 1000485
 nanospray inlet: Nanospray Inlet.
 MS_source_potential = 1000486
 source potential: Potential difference at the MS source in volts.
 MS_ion_optics_attribute = 1000487
 ion optics attribute: Ion optics involves components that help focus ion streams in mass spectrometry.
 MS_Hitachi_instrument_model = 1000488
 Hitachi instrument model: Hitachi instrument model.
 MS_Varian_instrument_model = 1000489
 Varian instrument model: Varian instrument model.
 MS_Agilent_instrument_model = 1000490
 Agilent instrument model: Agilent instrument model.
 MS_Dionex_instrument_model = 1000491
 Dionex instrument model: Dionex instrument model.
 MS_Thermo_Electron_instrument_model = 1000492
 Thermo Electron instrument model: Thermo Electron Corporation instrument model.
 MS_Finnigan_MAT_instrument_model = 1000493
 Finnigan MAT instrument model: Finnigan MAT instrument model.
 MS_Thermo_Scientific_instrument_model = 1000494
 Thermo Scientific instrument model: Thermo Scientific instrument model.
 MS_Applied_Biosystems_instrument_model = 1000495
 Applied Biosystems instrument model: Applied Biosystems instrument model.
 MS_ABI = MS_Applied_Biosystems_instrument_model
 ABI (Applied Biosystems instrument model): Applied Biosystems instrument model.
 MS_instrument_attribute = 1000496
 instrument attribute: Instrument properties that are associated with a value.
 MS_zoom_scan = 1000497
 zoom scan: Special scan mode, where data with improved resoltuion is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate.
 MS_enhanced_resolution_scan = MS_zoom_scan
 enhanced resolution scan (zoom scan): Special scan mode, where data with improved resoltuion is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate.
 MS_full_scan = 1000498
 full scan: Feature of the ion trap mass spectrometer where MS data is acquired over a mass range.
 MS_spectrum_attribute = 1000499
 spectrum attribute: Spectrum properties that are associated with a value.
 MS_scan_window_upper_limit = 1000500
 scan window upper limit: The lower m/z bound of a mass spectrometer scan window.
 MS_scan_window_lower_limit = 1000501
 scan window lower limit: The upper m/z bound of a mass spectrometer scan window.
 MS_dwell_time = 1000502
 dwell time: The time spent gathering data across a peak.
 MS_scan_attribute = 1000503
 scan attribute: Scan properties that are associated with a value.
 MS_base_peak_m_z = 1000504
 base peak m/z: M/z value of the signal of highest intensity in the mass spectrum.
 MS_base_peak_intensity = 1000505
 base peak intensity: The intensity of the greatest peak in the mass spectrum.
 MS_ion_role = 1000506
 ion role: Ion Role.
 MS_ion_attribute = 1000507
 ion attribute: Ion properties that are associated with a value.
 MS_ion_chemical_type = 1000508
 ion chemical type: Ion Type.
 MS_activation_energy = 1000509
 activation energy: Activation Energy.
 MS_precursor_activation_attribute = 1000510
 precursor activation attribute: Precursor Activation Attribute.
 MS_ms_level = 1000511
 ms level: Stages of ms achieved in a multi stage mass spectrometry experiment.
 MS_filter_string = 1000512
 filter string: A string unique to Thermo instrument describing instrument settings for the scan.
 MS_binary_data_array = 1000513
 binary data array: A data array of values.
 MS_m_z_array = 1000514
 m/z array: A data array of m/z values.
 MS_intensity_array = 1000515
 intensity array: A data array of intensity values.
 MS_charge_array = 1000516
 charge array: A data array of charge values.
 MS_signal_to_noise_array = 1000517
 signal to noise array: A data array of signal-to-noise values.
 MS_binary_data_type = 1000518
 binary data type: Encoding type of binary data specifying the binary representation and precision, e.g. 64-bit float.
 MS_32_bit_integer = 1000519
 32-bit integer: Signed 32-bit little-endian integer.
 MS_16_bit_float_OBSOLETE = 1000520
 16-bit float: Signed 16-bit float.
 MS_32_bit_float = 1000521
 32-bit float: 32-bit precision little-endian floating point conforming to IEEE-754.
 MS_64_bit_integer = 1000522
 64-bit integer: Signed 64-bit little-endian integer.
 MS_64_bit_float = 1000523
 64-bit float: 64-bit precision little-endian floating point conforming to IEEE-754.
 MS_data_file_content = 1000524
 data file content: Describes the data content on the file.
 MS_spectrum_representation = 1000525
 spectrum representation: Way in which the spectrum is represented, either with regularly spaced data points or with a list of centroided peaks.
 MS_Waters_raw_file = 1000526
 Waters raw file: Waters data file found in a Waters RAW directory, generated from an MS acquisition.
 MS_highest_observed_m_z = 1000527
 highest observed m/z: Highest m/z value observed in the m/z array.
 MS_lowest_observed_m_z = 1000528
 lowest observed m/z: Lowest m/z value observed in the m/z array.
 MS_instrument_serial_number = 1000529
 instrument serial number: Serial Number of the instrument.
 MS_file_format_conversion = 1000530
 file format conversion: Conversion of one file format to another.
 MS_software = 1000531
 software: Software related to the recording or transformation of spectra.
 MS_Xcalibur = 1000532
 Xcalibur: Thermo Finnigan software for data acquisition and analysis.
 MS_Bioworks = 1000533
 Bioworks: Thermo Finnigan software for data analysis of peptides and proteins.
 MS_MassLynx = 1000534
 MassLynx: Micromass software for data acquisition and analysis.
 MS_FlexAnalysis = 1000535
 FlexAnalysis: Bruker software for data analysis.
 MS_Data_Explorer = 1000536
 Data Explorer: Applied Biosystems software for data acquisition and analysis.
 MS_4700_Explorer = 1000537
 4700 Explorer: Applied Biosystems software for data acquisition and analysis.
 MS_massWolf = 1000538
 massWolf: A software for converting Waters raw directory format to mzXML or mzML. massWolf was originally developed at the Institute for Systems Biology.
 MS_wolf = MS_massWolf
 wolf (massWolf): A software for converting Waters raw directory format to mzXML or mzML. massWolf was originally developed at the Institute for Systems Biology.
 MS_Voyager_Biospectrometry_Workstation_System = 1000539
 Voyager Biospectrometry Workstation System: Applied Biosystems MALDI-TOF data acquisition and analysis system.
 MS_FlexControl = 1000540
 FlexControl: Bruker software for data acquisition.
 MS_ReAdW = 1000541
 ReAdW: A software program for converting Thermo Finnigan RAW file format to mzXML or mzML. ReAdW was originally developed at the Institute for Systems Biology. Its whimsical interleaved spelling and capitalization is pronounced "readraw".
 MS_MzStar = 1000542
 MzStar: A software program for converting Applied Biosystems wiff file format to mzXML format. MzStar was originally developed at the Institute for Systems Biology. It is now obsoleted by the MzWiff program.
 MS_data_processing_action = 1000543
 data processing action: Data processing attribute used to describe the type of data processing performed on the data file.
 MS_Conversion_to_mzML = 1000544
 Conversion to mzML: Conversion of a file format to Proteomics Standards Initiative mzData file format.
 MS_Conversion_to_mzXML = 1000545
 Conversion to mzXML: Conversion of a file format to Institute of Systems Biology mzXML file format.
 MS_Conversion_to_mzData = 1000546
 Conversion to mzData: Conversion of a file format to Proteomics Standards Initiative mzData file format.
 MS_object_attribute = 1000547
 object attribute: Object Attribute.
 MS_sample_attribute = 1000548
 sample attribute: Sample properties that are associated with a value.
 MS_selection_window_attribute = 1000549
 selection window attribute: Selection window properties that are associated with a value.
 MS_time_unit_OBSOLETE = 1000550
 time unit: Time Unit.
 MS_Analyst = 1000551
 Analyst: AB SCIEX or Applied Biosystems|MDS SCIEX software for data acquisition.
 MS_maldi_spot_identifier = 1000552
 maldi spot identifier: Maldi Spot Identifier.
 MS_Trapper = 1000553
 Trapper: A software program for converting Agilent MassHunter format to mzXML or mzML. Trapper was originally developed at the Institute for Systems Biology.
 MS_LCQ_Deca = 1000554
 LCQ Deca: ThermoFinnigan LCQ Deca.
 MS_LTQ_Orbitrap_Discovery = 1000555
 LTQ Orbitrap Discovery: LTQ Orbitrap Discovery.
 MS_LTQ_Orbitrap_XL = 1000556
 LTQ Orbitrap XL: LTQ Orbitrap XL.
 MS_LTQ_FT_Ultra = 1000557
 LTQ FT Ultra: LTQ FT Ultra.
 MS_GC_Quantum = 1000558
 GC Quantum: GC Quantum.
 MS_spectrum_type = 1000559
 spectrum type: Spectrum type.
 MS_mass_spectrometer_file_format = 1000560
 mass spectrometer file format: The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format.
 MS_data_file_checksum_type = 1000561
 data file checksum type: Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data.
 MS_ABI_WIFF_file = 1000562
 ABI WIFF file: Applied Biosystems WIFF file format.
 MS_Thermo_RAW_file = 1000563
 Thermo RAW file: Thermo Scientific RAW file format.
 MS_PSI_mzData_file = 1000564
 PSI mzData file: Proteomics Standards Inititative mzData file format.
 MS_Micromass_PKL_file = 1000565
 Micromass PKL file: Micromass PKL file format.
 MS_ISB_mzXML_file = 1000566
 ISB mzXML file: Institute of Systems Biology mzXML file format.
 MS_Bruker_Agilent_YEP_file = 1000567
 Bruker/Agilent YEP file: Bruker/Agilent YEP file format.
 MS_MD5 = 1000568
 MD5: MD5 (Message-Digest algorithm 5) is a cryptographic hash function with a 128-bit hash value used to check the integrity of files.
 MS_SHA_1 = 1000569
 SHA-1: SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity.
 MS_spectra_combination = 1000570
 spectra combination: Method used to combine the mass spectra.
 MS_sum_of_spectra = 1000571
 sum of spectra: Spectra Sum.
 MS_binary_data_compression_type = 1000572
 binary data compression type: Compression Type.
 MS_median_of_spectra = 1000573
 median of spectra: Spectra is combined by calculating the median of the spectra.
 MS_zlib_compression = 1000574
 zlib compression: Zlib.
 MS_mean_of_spectra = 1000575
 mean of spectra: Spectra is combined by calculating the mean of the spectra.
 MS_no_compression = 1000576
 no compression: No Compression.
 MS_raw_data_file = 1000577
 raw data file: Describes the type of file and its content.
 MS_source_file = MS_raw_data_file
 source file (raw data file): Describes the type of file and its content.
 MS_LCQ_Fleet = 1000578
 LCQ Fleet: LCQ Fleet.
 MS_MS1_spectrum = 1000579
 MS1 spectrum: Mass spectrum created by a single-stage MS experiment or the first stage of a multi-stage experiment.
 MS_full_spectrum = MS_MS1_spectrum
 full spectrum (MS1 spectrum): Mass spectrum created by a single-stage MS experiment or the first stage of a multi-stage experiment.
 MS_Q1_spectrum = MS_MS1_spectrum
 Q1 spectrum (MS1 spectrum): Mass spectrum created by a single-stage MS experiment or the first stage of a multi-stage experiment.
 MS_Q3_spectrum = MS_MS1_spectrum
 Q3 spectrum (MS1 spectrum): Mass spectrum created by a single-stage MS experiment or the first stage of a multi-stage experiment.
 MS_Single_Stage_Mass_Spectrometry = MS_MS1_spectrum
 Single-Stage Mass Spectrometry (MS1 spectrum): Mass spectrum created by a single-stage MS experiment or the first stage of a multi-stage experiment.
 MS_MSn_spectrum = 1000580
 MSn spectrum: MSn refers to multi-stage MS/MS experiments designed to record product ion spectra where n is the number of product ion stages (progeny ions). For ion traps, sequential MS/MS experiments can be undertaken where n > 2 whereas for a simple triple quadrupole system n= 2.
 MS_multiple_stage_mass_spectrometry_spectrum = MS_MSn_spectrum
 multiple-stage mass spectrometry spectrum (MSn spectrum): MSn refers to multi-stage MS/MS experiments designed to record product ion spectra where n is the number of product ion stages (progeny ions). For ion traps, sequential MS/MS experiments can be undertaken where n > 2 whereas for a simple triple quadrupole system n= 2.
 MS_nth_generation_product_ion_spectrum = MS_MSn_spectrum
 nth generation product ion spectrum (MSn spectrum): MSn refers to multi-stage MS/MS experiments designed to record product ion spectra where n is the number of product ion stages (progeny ions). For ion traps, sequential MS/MS experiments can be undertaken where n > 2 whereas for a simple triple quadrupole system n= 2.
 MS_product_ion_spectrum = MS_MSn_spectrum
 product ion spectrum (MSn spectrum): MSn refers to multi-stage MS/MS experiments designed to record product ion spectra where n is the number of product ion stages (progeny ions). For ion traps, sequential MS/MS experiments can be undertaken where n > 2 whereas for a simple triple quadrupole system n= 2.
 MS_CRM_spectrum = 1000581
 CRM spectrum: Spectrum generated from MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored.
 MS_SIM_spectrum = 1000582
 SIM spectrum: Spectrum obtained with the operation of a mass spectrometer in which the abundances of one ion or several ions of specific m/z values are recorded rather than the entire mass spectrum (Selected Ion Monitoring).
 MS_MIM_spectrum = MS_SIM_spectrum
 MIM spectrum (SIM spectrum): Spectrum obtained with the operation of a mass spectrometer in which the abundances of one ion or several ions of specific m/z values are recorded rather than the entire mass spectrum (Selected Ion Monitoring).
 MS_multiple_ion_monitoring_spectrum = MS_SIM_spectrum
 multiple ion monitoring spectrum (SIM spectrum): Spectrum obtained with the operation of a mass spectrometer in which the abundances of one ion or several ions of specific m/z values are recorded rather than the entire mass spectrum (Selected Ion Monitoring).
 MS_selected_ion_monitoring_spectrum = MS_SIM_spectrum
 selected ion monitoring spectrum (SIM spectrum): Spectrum obtained with the operation of a mass spectrometer in which the abundances of one ion or several ions of specific m/z values are recorded rather than the entire mass spectrum (Selected Ion Monitoring).
 MS_SRM_spectrum = 1000583
 SRM spectrum: Spectrum obtained when data are acquired from specific product ions corresponding to m/z values of selected precursor ions a recorded via two or more stages of mass spectrometry. The precursor/product ion pair is called a transition pair. Data can be obtained for a single transition pair or multiple transition pairs. Multiple time segments of different transition pairs can exist in a single file. Single precursor ions can have multiple product ions consitituting multiple transition pairs. Selected reaction monitoring can be performed as tandem mass spectrometry in time or tandem mass spectrometry in space.
 MS_MRM_spectrum = MS_SRM_spectrum
 MRM spectrum (SRM spectrum): Spectrum obtained when data are acquired from specific product ions corresponding to m/z values of selected precursor ions a recorded via two or more stages of mass spectrometry. The precursor/product ion pair is called a transition pair. Data can be obtained for a single transition pair or multiple transition pairs. Multiple time segments of different transition pairs can exist in a single file. Single precursor ions can have multiple product ions consitituting multiple transition pairs. Selected reaction monitoring can be performed as tandem mass spectrometry in time or tandem mass spectrometry in space.
 MS_multiple_reaction_monitoring_spectrum = MS_SRM_spectrum
 multiple reaction monitoring spectrum (SRM spectrum): Spectrum obtained when data are acquired from specific product ions corresponding to m/z values of selected precursor ions a recorded via two or more stages of mass spectrometry. The precursor/product ion pair is called a transition pair. Data can be obtained for a single transition pair or multiple transition pairs. Multiple time segments of different transition pairs can exist in a single file. Single precursor ions can have multiple product ions consitituting multiple transition pairs. Selected reaction monitoring can be performed as tandem mass spectrometry in time or tandem mass spectrometry in space.
 MS_selected_reaction_monitoring_spectrum = MS_SRM_spectrum
 selected reaction monitoring spectrum (SRM spectrum): Spectrum obtained when data are acquired from specific product ions corresponding to m/z values of selected precursor ions a recorded via two or more stages of mass spectrometry. The precursor/product ion pair is called a transition pair. Data can be obtained for a single transition pair or multiple transition pairs. Multiple time segments of different transition pairs can exist in a single file. Single precursor ions can have multiple product ions consitituting multiple transition pairs. Selected reaction monitoring can be performed as tandem mass spectrometry in time or tandem mass spectrometry in space.
 MS_mzML_file = 1000584
 mzML file: Proteomics Standards Inititative mzML file format.
 MS_contact_attribute = 1000585
 contact attribute: Details about a person or organization to contact in case of concern or discussion about the file.
 MS_contact_name = 1000586
 contact name: Name of the contact person or organization.
 MS_contact_address = 1000587
 contact address: Postal address of the contact person or organization.
 MS_contact_URL = 1000588
 contact URL: Uniform Resource Locator related to the contact person or organization.
 MS_contact_email = 1000589
 contact email: Email address of the contact person or organization.
 MS_contact_organization = 1000590
 contact organization: Home institution of the contact person.
 MS_MzWiff = 1000591
 MzWiff: A software program for converting Applied Biosystems wiff file format to the mzXML or mzML format. MzWiff is currently maintained at the Institute for Systems Biology. It replaces the slower mzStar program.
 MS_smoothing = 1000592
 smoothing: A process of reducing spikes of intensity in order to reduce noise while preserving real peak signal. Many algorithms can be applied for this process.
 MS_baseline_reduction = 1000593
 baseline reduction: A process of removal of varying intensities generated due to variable energy absorption before further processing can take place. Baseline reduction facilitates meaningful comparision between intensities of m/z values.
 MS_low_intensity_data_point_removal = 1000594
 low intensity data point removal: The removal of very low intensity data points that are likely to be spurious noise rather than real signal.
 MS_thresholding = MS_low_intensity_data_point_removal
 thresholding (low intensity data point removal): The removal of very low intensity data points that are likely to be spurious noise rather than real signal.
 MS_time_array = 1000595
 time array: A data array of relative time offset values from a reference time.
 MS_measurement_method = 1000596
 measurement method: An attribute of resolution when recording the detector response in absence of the analyte.
 MS_ion_optics_type = 1000597
 ion optics type: The electrical potential used to impart kinetic energy to ions in a mass spectrometer.
 MS_electron_transfer_dissociation = 1000598
 electron transfer dissociation: A process to fragment ions in a mass spectrometer by inducing fragmentation of cations (e.g. peptides or proteins) by transferring electrons to them.
 MS_ETD = MS_electron_transfer_dissociation
 ETD (electron transfer dissociation): A process to fragment ions in a mass spectrometer by inducing fragmentation of cations (e.g. peptides or proteins) by transferring electrons to them.
 MS_pulsed_q_dissociation = 1000599
 pulsed q dissociation: A process that involves precursor ion activation at high Q, a time delay to allow the precursor to fragment, then a rapid pulse to low Q where all fragment ions are trapped. The product ions can then be scanned out of the ion trap and detected.
 MS_PQD = MS_pulsed_q_dissociation
 PQD (pulsed q dissociation): A process that involves precursor ion activation at high Q, a time delay to allow the precursor to fragment, then a rapid pulse to low Q where all fragment ions are trapped. The product ions can then be scanned out of the ion trap and detected.
 MS_Proteios = 1000600
 Proteios: Database application and analysis platform for proteomics.
 MS_ProteinLynx_Global_Server = 1000601
 ProteinLynx Global Server: Waters software for data analysis.
 MS_Shimadzu_Biotech_instrument_model = 1000602
 Shimadzu Biotech instrument model: Shimadzu Biotech instrument model.
 MS_Shimadzu_Scientific_Instruments_instrument_model = 1000603
 Shimadzu Scientific Instruments instrument model: Shimadzu Scientific Instruments instrument model.
 MS_LCMS_IT_TOF = 1000604
 LCMS-IT-TOF: Shimadzu Scientific Instruments LCMS-IT-TOF MS.
 MS_LCMS_2010EV = 1000605
 LCMS-2010EV: Shimadzu Scientific Instruments LCMS-2010EV MS.
 MS_LCMS_2010A = 1000606
 LCMS-2010A: Shimadzu Scientific Instruments LCMS-2010A MS.
 MS_AXIMA_CFR_MALDI_TOF = 1000607
 AXIMA CFR MALDI-TOF: Shimadzu Biotech AXIMA CFR MALDI-TOF MS.
 MS_AXIMA_QIT = 1000608
 AXIMA-QIT: Shimadzu Biotech AXIMA-QIT MS.
 MS_AXIMA_CFR_plus = 1000609
 AXIMA-CFR plus: Shimadzu Biotech AXIMA-CFR plus MS.
 MS_AXIMA_Performance_MALDI_TOF_TOF = 1000610
 AXIMA Performance MALDI-TOF/TOF: Shimadzu Biotech AXIMA Performance MALDI-TOF/TOF MS.
 MS_AXIMA_Confidence_MALDI_TOF = 1000611
 AXIMA Confidence MALDI-TOF: Shimadzu Biotech AXIMA Confidence MALDI-TOF (curved field reflectron) MS.
 MS_AXIMA_Assurance_Linear_MALDI_TOF = 1000612
 AXIMA Assurance Linear MALDI-TOF: Shimadzu Biotech AXIMA Assurance Linear MALDI-TOF MS.
 MS_DTA_file = 1000613
 DTA file: Sequest DTA file format.
 MS_ProteinLynx_Global_Server_mass_spectrum_XML_file = 1000614
 ProteinLynx Global Server mass spectrum XML file: Peak list file format used by ProteinLynx Global Server.
 MS_ProteoWizard = 1000615
 ProteoWizard: ProteoWizard software for data processing and analysis. Primarily developed by the labs of P. Malick and D. Tabb.
 MS_pwiz = MS_ProteoWizard
 pwiz (ProteoWizard): ProteoWizard software for data processing and analysis. Primarily developed by the labs of P. Malick and D. Tabb.
 MS_preset_scan_configuration = 1000616
 preset scan configuration: A user-defined scan configuration that specifies the instrumental settings in which a spectrum is acquired. An instrument may cycle through a list of preset scan configurations to acquire data. This is a more generic term for the Thermo "scan event", which is defined in the Thermo Xcalibur glossary as: a mass spectrometer scan that is defined by choosing the necessary scan parameter settings. Multiple scan events can be defined for each segment of time.
 MS_wavelength_array = 1000617
 wavelength array: A data array of electromagnetic radiation wavelength values.
 MS_highest_observed_wavelength = 1000618
 highest observed wavelength: Highest wavelength observed in an EMR spectrum.
 MS_lowest_observed_wavelength = 1000619
 lowest observed wavelength: Lowest wavelength observed in an EMR spectrum.
 MS_PDA_spectrum_OBSOLETE = 1000620
 PDA spectrum: Spectrum generated from a photodiode array detector (ultraviolet/visible spectrum).
 MS_photodiode_array_detector = 1000621
 photodiode array detector: An array detector used to record spectra in the ultraviolet and visable region of light.
 MS_PDA = MS_photodiode_array_detector
 PDA (photodiode array detector): An array detector used to record spectra in the ultraviolet and visable region of light.
 MS_Surveyor_PDA = 1000622
 Surveyor PDA: Surveyor PDA.
 MS_Accela_PDA = 1000623
 Accela PDA: Accela PDA.
 MS_inductive_detector = 1000624
 inductive detector: Inductive detector.
 MS_image_current_detector = MS_inductive_detector
 image current detector (inductive detector): Inductive detector.
 MS_chromatogram = 1000625
 chromatogram: The representation of detector response versus time.
 MS_chromatogram_type = 1000626
 chromatogram type: Broad category or type of a chromatogram.
 MS_selected_ion_current_chromatogram = 1000627
 selected ion current chromatogram: Chromatogram created by creating an array of the measurements of a specific single ion current at each time point.
 MS_SIC_chromatogram = MS_selected_ion_current_chromatogram
 SIC chromatogram (selected ion current chromatogram): Chromatogram created by creating an array of the measurements of a specific single ion current at each time point.
 MS_basepeak_chromatogram = 1000628
 basepeak chromatogram: Chromatogram created by creating an array of the most intense peaks at each time point.
 MS_low_intensity_threshold = 1000629
 low intensity threshold: Threshold below which some action is taken.
 MS_data_processing_parameter = 1000630
 data processing parameter: Data processing parameter used in the data processing performed on the data file.
 MS_high_intensity_threshold = 1000631
 high intensity threshold: Threshold above which some action is taken.
 MS_Q_Tof_Premier = 1000632
 Q-Tof Premier: Waters Q-Tof Premier MS.
 MS_possible_charge_state = 1000633
 possible charge state: A possible charge state of the ion in a situation where the charge of an ion is known to be one of several possible values rather than a completely unknown value or determined to be a specific charge with reasonable certainty.
 MS_DSQ = 1000634
 DSQ: ThermoFinnigan DSQ GC-MS.
 MS_ITQ_700 = 1000635
 ITQ 700: Thermo Scientific ITQ 700 GC-MS.
 MS_ITQ_900 = 1000636
 ITQ 900: Thermo Scientific ITQ 900 GC-MS.
 MS_ITQ_1100 = 1000637
 ITQ 1100: Thermo Scientific ITQ 1100 GC-MS.
 MS_LTQ_XL_ETD = 1000638
 LTQ XL ETD: Thermo Scientific LTQ XL MS with ETD.
 MS_LTQ_Orbitrap_XL_ETD = 1000639
 LTQ Orbitrap XL ETD: Thermo Scientific LTQ Orbitrap XL MS with ETD.
 MS_DFS = 1000640
 DFS: Thermo Scientific DFS HR GC-MS.
 MS_DSQ_II = 1000641
 DSQ II: Thermo Scientific DSQ II GC-MS.
 MS_MALDI_LTQ_XL = 1000642
 MALDI LTQ XL: Thermo Scientific MALDI LTQ XL MS.
 MS_MALDI_LTQ_Orbitrap = 1000643
 MALDI LTQ Orbitrap: Thermo Scientific MALDI LTQ Orbitrap MS.
 MS_TSQ_Quantum_Access = 1000644
 TSQ Quantum Access: Thermo Scientific TSQ Quantum Access MS.
 MS_Element_XR = 1000645
 Element XR: Thermo Scientific Element XR HR-ICP-MS.
 MS_Element_2 = 1000646
 Element 2: Thermo Scientific Element 2 HR-ICP-MS.
 MS_Element_GD = 1000647
 Element GD: Thermo Scientific Element GD Glow Discharge MS.
 MS_GC_IsoLink = 1000648
 GC IsoLink: Thermo Scientific GC IsoLink Isotope Ratio MS.
 MS_Exactive = 1000649
 Exactive: Thermo Scientific Exactive MS.
 MS_Proteome_Discoverer = 1000650
 Proteome Discoverer: Thermo Scientific software for data analysis of peptides and proteins.
 MS_3200_QTRAP = 1000651
 3200 QTRAP: AB SCIEX or Applied Biosystems|MDS SCIEX QTRAP 3200.
 MS_4800_Plus_MALDI_TOF_TOF = 1000652
 4800 Plus MALDI TOF/TOF: AB SCIEX or Applied Biosystems|MDS SCIEX 4800 Plus MALDI TOF-TOF Analyzer.
 MS_API_3200 = 1000653
 API 3200: AB SCIEX or Applied Biosystems|MDS SCIEX API 3200 MS.
 MS_API_5000 = 1000654
 API 5000: AB SCIEX or Applied Biosystems|MDS SCIEX API 5000 MS.
 MS_QSTAR_Elite = 1000655
 QSTAR Elite: AB SCIEX or Applied Biosystems|MDS SCIEX QSTAR Elite.
 MS_QSTAR_Pulsar = 1000656
 QSTAR Pulsar: Applied Biosystems|MDS SCIEX QSTAR Pulsar.
 MS_QSTAR_XL = 1000657
 QSTAR XL: Applied Biosystems|MDS SCIEX QSTAR XL.
 MS_4800_Proteomics_Analyzer = 1000658
 4800 Proteomics Analyzer: Applied Biosystems|MDS SCIEX 4800 Proteomics Analyzer.
 MS_4000_Series_Explorer_Software = 1000659
 4000 Series Explorer Software: AB SCIEX or Applied Biosystems software for data acquisition and analysis.
 MS_GPS_Explorer = 1000661
 GPS Explorer: AB SCIEX or Applied Biosystems software for data acquisition and analysis.
 MS_LightSight_Software = 1000662
 LightSight Software: AB SCIEX or Applied Biosystems|MDS SCIEX software metabolite identification.
 MS_ProteinPilot_Software = 1000663
 ProteinPilot Software: AB SCIEX or Applied Biosystems|MDS SCIEX software for protein ID and quant.
 MS_TissueView_Software = 1000664
 TissueView Software: Applied Biosystems|MDS SCIEX software for tissue imaging.
 MS_MarkerView_Software = 1000665
 MarkerView Software: Applied Biosystems|MDS SCIEX software for metabolomics and biomarker profiling.
 MS_MRMPilot_Software = 1000666
 MRMPilot Software: Applied Biosystems|MDS SCIEX software for MRM assay development.
 MS_BioAnalyst = 1000667
 BioAnalyst: Applied Biosystems|MDS SCIEX software for bio-related data exploration.
 MS_Pro_ID = 1000668
 Pro ID: Applied Biosystems|MDS SCIEX software for protein identification.
 MS_Pro_ICAT = 1000669
 Pro ICAT: Applied Biosystems|MDS SCIEX software for protein ID and quant by ICAT.
 MS_Pro_Quant = 1000670
 Pro Quant: Applied Biosystems|MDS SCIEX software for protein ID and quant by iTRAQ.
 MS_Pro_BLAST = 1000671
 Pro BLAST: Applied Biosystems|MDS SCIEX software for MS-BLAST identification.
 MS_Cliquid = 1000672
 Cliquid: AB SCIEX Cliquid software for data analysis and quantitation.
 MS_MIDAS_Workflow_Designer = 1000673
 MIDAS Workflow Designer: Applied Biosystems|MDS SCIEX software for MRM assay development.
 MS_MultiQuant = 1000674
 MultiQuant: Applied Biosystems|MDS SCIEX software for MRM-based quantitation.
 MS_6220_Time_of_Flight_LC_MS = 1000675
 6220 Time-of-Flight LC/MS: The 6220 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources.
 MS_6510_Quadrupole_Time_of_Flight_LC_MS = 1000676
 6510 Quadrupole Time-of-Flight LC/MS: The 6510 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources.
 MS_6520_Quadrupole_Time_of_Flight_LC_MS = 1000677
 6520 Quadrupole Time-of-Flight LC/MS: The 6520 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 26,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources.
 MS_MassHunter_Data_Acquisition = 1000678
 MassHunter Data Acquisition: Software for data acquisition of 6000 series instruments.
 MS_MassHunter_Easy_Access = 1000679
 MassHunter Easy Access: Software for open access data acquisition.
 MS_MassHunter_Qualitative_Analysis = 1000680
 MassHunter Qualitative Analysis: Software for data analysis of data from 6000 series instruments.
 MS_MassHunter_Quantitative_Analysis = 1000681
 MassHunter Quantitative Analysis: Software for quantitation of Triple Quadruople and Quadrupole Time-of-Flight data.
 MS_MassHunter_Metabolite_ID = 1000682
 MassHunter Metabolite ID: Software for identification of metabolites.
 MS_MassHunter_BioConfirm = 1000683
 MassHunter BioConfirm: Software for protein characterization.
 MS_Genespring_MS = 1000684
 Genespring MS: Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data.
 MS_MassHunter_Mass_Profiler = 1000685
 MassHunter Mass Profiler: Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data.
 MS_METLIN = 1000686
 METLIN: Personal Metabolite Database for MassHunter Workstation. Software for identification of human metabolites.
 MS_Spectrum_Mill_for_MassHunter_Workstation = 1000687
 Spectrum Mill for MassHunter Workstation: Software for protein identification and characterization of complex protein digest mixtures.
 MS_6300_Series_Ion_Trap_Data_Analysis_Software = 1000688
 6300 Series Ion Trap Data Analysis Software: Software for data analysis of 6300 series ion trap mass spectrometers.
 MS_Agilent_software = 1000689
 Agilent software: Agilent software for data acquisition and analysis.
 MS_AB_SCIEX_software = 1000690
 AB SCIEX software: AB SCIEX or Applied Biosystems software for data acquisition and analysis.
 MS_Applied_Biosystems_software = 1000691
 Applied Biosystems software: Applied Biosystems|MDS SCIEX software for data acquisition and analysis.
 MS_Bruker_software = 1000692
 Bruker software: Bruker software for data acquisition and analysis.
 MS_Thermo_Finnigan_software = 1000693
 Thermo Finnigan software: Thermo Finnigan software for data acquisition and analysis.
 MS_Waters_software = 1000694
 Waters software: Waters software for data acquisition and analysis.
 MS_apex_ultra = 1000695
 apex ultra: Bruker Daltonics' apex ultra: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR.
 MS_autoflex_III_smartbeam = 1000696
 autoflex III smartbeam: Bruker Daltonics' autoflex III smartbeam: MALDI TOF.
 MS_Bruker_Daltonics_HCT_Series = 1000697
 Bruker Daltonics HCT Series: Bruker Daltonics HCT Series.
 MS_HCTultra = 1000698
 HCTultra: Bruker Daltonics' HCTultra: ESI TOF, Nanospray, APCI, APPI.
 MS_HCTultra_PTM = 1000699
 HCTultra PTM: Bruker Daltonics' HCTultra PTM: ESI TOF, Nanospray, APCI, APPI, PTR.
 MS_HCTultra_ETD_II = 1000700
 HCTultra ETD II: Bruker Daltonics' HCTultra ETD II: ESI Q-TOF, Nanospray, APCI, APPI, ETD.
 MS_microflex_LT = 1000701
 microflex LT: Bruker Daltonics' microflex LT: MALDI TOF.
 MS_micrOTOF = 1000702
 micrOTOF: Bruker Daltonics' micrOTOF: ESI TOF, APCI, APPI.
 MS_micrOTOF_Q = 1000703
 micrOTOF-Q: Bruker Daltonics' micrOTOF-Q: ESI Q-TOF, Nanospray, APCI, APPI.
 MS_micrOTOF_Q_II = 1000704
 micrOTOF-Q II: Bruker Daltonics' micrOTOF-Q II: ESI Q-TOF, Nanospray, APCI, APPI.
 MS_ultraflex_III_TOF_TOF = 1000705
 ultraflex III TOF/TOF: Bruker Daltonics' ultraflex III TOF/TOF: MALDI TOF.
 MS_apexControl = 1000706
 apexControl: Bruker software for data acquisition.
 MS_BioTools = 1000707
 BioTools: Bruker software for data analysis.
 MS_CLINPROT = 1000708
 CLINPROT: Bruker CLINPROT software.
 MS_CLINPROT_micro = 1000709
 CLINPROT micro: Bruker CLINPROT micro software.
 MS_CLINPROT_robot = 1000710
 CLINPROT robot: Bruker CLINPROT robot software.
 MS_ClinProTools = 1000711
 ClinProTools: Bruker ClinProTools software.
 MS_Compass = 1000712
 Compass: Bruker Compass software.
 MS_Compass_for_HCT_esquire = 1000713
 Compass for HCT/esquire: Bruker Compass for HCT/esquire software.
 MS_Compass_for_micrOTOF = 1000714
 Compass for micrOTOF: Bruker Compass for micrOTOF software.
 MS_Compass_OpenAccess = 1000715
 Compass OpenAccess: Bruker compass OpenAccess software.
 MS_Compass_Security_Pack = 1000716
 Compass Security Pack: Bruker compass Security Pack software.
 MS_CompassXport = 1000717
 CompassXport: Bruker stand-alone software for data conversion.
 MS_CompassXtract = 1000718
 CompassXtract: Bruker software library for data access.
 MS_DataAnalysis = 1000719
 DataAnalysis: Bruker software for data analysis.
 MS_dpControl = 1000720
 dpControl: Bruker software for data acquisition.
 MS_esquireControl = 1000721
 esquireControl: Bruker software for data acquisition.
 MS_flexImaging = 1000722
 flexImaging: Bruker software for data analysis.
 MS_GENOLINK = 1000723
 GENOLINK: Bruker GENOLINK software.
 MS_GenoTools = 1000724
 GenoTools: Bruker GenoTools software.
 MS_HCTcontrol = 1000725
 HCTcontrol: Bruker software for data acquisition.
 MS_micrOTOFcontrol = 1000726
 micrOTOFcontrol: Bruker software for data acquisition.
 MS_PolyTools = 1000727
 PolyTools: Bruker PolyTools software.
 MS_ProfileAnalysis = 1000728
 ProfileAnalysis: Bruker software for data analysis.
 MS_PROTEINEER = 1000729
 PROTEINEER: Bruker PROTEINEER software.
 MS_PROTEINEER_dp = 1000730
 PROTEINEER dp: Bruker PROTEINEER dp software.
 MS_PROTEINEER_fc = 1000731
 PROTEINEER fc: Bruker PROTEINEER fc software.
 MS_PROTEINEER_spII = 1000732
 PROTEINEER spII: Bruker PROTEINEER spII software.
 MS_PROTEINEER_LC = 1000733
 PROTEINEER-LC: Bruker PROTEINEER-LC software.
 MS_ProteinScape = 1000734
 ProteinScape: Bruker ProteinScape software.
 MS_PureDisk = 1000735
 PureDisk: BrukerPureDisk software.
 MS_QuantAnalysis = 1000736
 QuantAnalysis: Bruker software for data analysis.
 MS_spControl = 1000737
 spControl: Bruker software for data acquisition.
 MS_TargetAnalysis = 1000738
 TargetAnalysis: Bruker TargetAnalysis software.
 MS_WARP_LC = 1000739
 WARP-LC: Bruker WARP-LC software.
 MS_parameter_file = 1000740
 parameter file: Parameter file used to configure the acquisition of raw data on the instrument.
 MS_Conversion_to_dta = 1000741
 Conversion to dta: Conversion to dta format.
 MS_Bioworks_SRF_file = 1000742
 Bioworks SRF file: Thermo Finnigan SRF file format.
 MS_TSQ_Quantum_Ultra_AM = 1000743
 TSQ Quantum Ultra AM: Thermo Scientific TSQ Quantum Ultra AM.
 MS_selected_ion_m_z = 1000744
 selected ion m/z: Mass-to-charge ratio of the ion selected for fragmentation.
 MS_retention_time_alignment = 1000745
 retention time alignment: The correction of the spectrum scan times, as used e.g. in label-free proteomics.
 MS_high_intensity_data_point_removal = 1000746
 high intensity data point removal: The removal of very high intensity data points.
 MS_completion_time = 1000747
 completion time: The time that a data processing action was finished.
 MS_SSQ_7000 = 1000748
 SSQ 7000: ThermoFinnigan SSQ 7000 MS.
 MS_TSQ_7000 = 1000749
 TSQ 7000: ThermoFinnigan TSQ 7000 MS.
 MS_TSQ = 1000750
 TSQ: ThermoFinnigan TSQ MS.
 MS_TSQ_Quantum_Ultra = 1000751
 TSQ Quantum Ultra: Thermo Scientific TSQ Quantum Ultra.
 MS_TOPP_software = 1000752
 TOPP software: TOPP (The OpenMS proteomics pipeline) software.
 MS_BaselineFilter = 1000753
 BaselineFilter: Removes the baseline from profile spectra using a top-hat filter.
 MS_DBExporter = 1000754
 DBExporter: Exports data from an OpenMS database to a file.
 MS_DBImporter = 1000755
 DBImporter: Imports data to an OpenMS database.
 MS_FileConverter = 1000756
 FileConverter: Converts between different MS file formats.
 MS_FileFilter = 1000757
 FileFilter: Extracts or manipulates portions of data from peak, feature or consensus feature files.
 MS_FileMerger = 1000758
 FileMerger: Merges several MS files into one file.
 MS_InternalCalibration = 1000759
 InternalCalibration: Applies an internal calibration.
 MS_MapAligner = 1000760
 MapAligner: Corrects retention time distortions between maps.
 MS_MapNormalizer = 1000761
 MapNormalizer: Normalizes peak intensities in an MS run.
 MS_NoiseFilter = 1000762
 NoiseFilter: Removes noise from profile spectra by using different smoothing techniques.
 MS_PeakPicker = 1000763
 PeakPicker: Finds mass spectrometric peaks in profile mass spectra.
 MS_Resampler = 1000764
 Resampler: Transforms an LC/MS map into a resampled map or a png image.
 MS_SpectraFilter = 1000765
 SpectraFilter: Applies a filter to peak spectra.
 MS_TOFCalibration = 1000766
 TOFCalibration: Applies time of flight calibration.
 MS_native_spectrum_identifier_format = 1000767
 native spectrum identifier format: Describes how the native spectrum identifiers are formated.
 MS_nativeID_format = MS_native_spectrum_identifier_format
 nativeID format (native spectrum identifier format): Describes how the native spectrum identifiers are formated.
 MS_Thermo_nativeID_format = 1000768
 Thermo nativeID format: controllerType=xsd:nonNegativeInteger controllerNumber=xsd:positiveInteger scan=xsd:positiveInteger.
 MS_Waters_nativeID_format = 1000769
 Waters nativeID format: function=xsd:positiveInteger process=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger.
 MS_WIFF_nativeID_format = 1000770
 WIFF nativeID format: sample=xsd:nonNegativeInteger period=xsd:nonNegativeInteger cycle=xsd:nonNegativeInteger experiment=xsd:nonNegativeInteger.
 MS_Bruker_Agilent_YEP_nativeID_format = 1000771
 Bruker/Agilent YEP nativeID format: scan=xsd:nonNegativeInteger.
 MS_Bruker_BAF_nativeID_format = 1000772
 Bruker BAF nativeID format: scan=xsd:nonNegativeInteger.
 MS_Bruker_FID_nativeID_format = 1000773
 Bruker FID nativeID format: file=xsd:IDREF.
 MS_multiple_peak_list_nativeID_format = 1000774
 multiple peak list nativeID format: index=xsd:nonNegativeInteger.
 MS_single_peak_list_nativeID_format = 1000775
 single peak list nativeID format: file=xsd:IDREF.
 MS_scan_number_only_nativeID_format = 1000776
 scan number only nativeID format: scan=xsd:nonNegativeInteger.
 MS_spectrum_identifier_nativeID_format = 1000777
 spectrum identifier nativeID format: spectrum=xsd:nonNegativeInteger.
 MS_charge_state_calculation = 1000778
 charge state calculation: A process that infers the charge state of an MSn spectrum's precursor(s) by the application of some algorithm.
 MS_below_precursor_intensity_dominance_charge_state_calculation = 1000779
 below precursor intensity dominance charge state calculation: Infers charge state as single or amibiguously multiple by determining the fraction of intensity below the precursor m/z.
 MS_precursor_recalculation = 1000780
 precursor recalculation: A process that recalculates existing precursor selected ions with one or more algorithmically determined precursor selected ions.
 MS_msPrefix_precursor_recalculation = 1000781
 msPrefix precursor recalculation: Recalculates one or more precursor selected ions by peak detection in the isolation windows of high accuracy MS precursor scans.
 MS_Savitzky_Golay_smoothing = 1000782
 Savitzky-Golay smoothing: Reduces intensity spikes by applying local polynomial regression (of degree k) on a distribution (of at least k+1 equally spaced points) to determine the smoothed value for each point. It tends to preserve features of the distribution such as relative maxima, minima and width, which are usually 'flattened' by other adjacent averaging techniques.
 MS_LOWESS_smoothing = 1000783
 LOWESS smoothing: Reduces intensity spikes by applying a modeling method known as locally weighted polynomial regression. At each point in the data set a low-degree polynomial is fit to a subset of the data, with explanatory variable values near the point whose response is being estimated. The polynomial is fit using weighted least squares, giving more weight to points near the point whose response is being estimated and less weight to points further away. The value of the regression function for the point is then obtained by evaluating the local polynomial using the explanatory variable values for that data point. The LOESS fit is complete after regression function values have been computed for each of the n data points. Many of the details of this method, such as the degree of the polynomial model and the weights, are flexible.
 MS_Gaussian_smoothing = 1000784
 Gaussian smoothing: Reduces intensity spikes by convolving the data with a one-dimensional Gaussian function.
 MS_binomial_smoothing = MS_Gaussian_smoothing
 binomial smoothing (Gaussian smoothing): Reduces intensity spikes by convolving the data with a one-dimensional Gaussian function.
 MS_Weierstrass_transform = MS_Gaussian_smoothing
 Weierstrass transform (Gaussian smoothing): Reduces intensity spikes by convolving the data with a one-dimensional Gaussian function.
 MS_moving_average_smoothing = 1000785
 moving average smoothing: Reduces intensity spikes by averaging each point with two or more adjacent points. The more adjacent points that used, the stronger the smoothing effect.
 MS_box_smoothing = MS_moving_average_smoothing
 box smoothing (moving average smoothing): Reduces intensity spikes by averaging each point with two or more adjacent points. The more adjacent points that used, the stronger the smoothing effect.
 MS_boxcar_smoothing = MS_moving_average_smoothing
 boxcar smoothing (moving average smoothing): Reduces intensity spikes by averaging each point with two or more adjacent points. The more adjacent points that used, the stronger the smoothing effect.
 MS_sliding_average_smoothing = MS_moving_average_smoothing
 sliding average smoothing (moving average smoothing): Reduces intensity spikes by averaging each point with two or more adjacent points. The more adjacent points that used, the stronger the smoothing effect.
 MS_non_standard_data_array = 1000786
 non-standard data array: A data array that contains data not covered by any other term in this group. Please do not use this term, if the binary data array type might be commonly used - contact the PSI-MS working group in order to have another CV term added.
 MS_inclusive_low_intensity_threshold = 1000787
 inclusive low intensity threshold: Threshold at or below which some action is taken.
 MS_inclusive_high_intensity_threshold = 1000788
 inclusive high intensity threshold: Threshold at or above which some action is taken.
 MS_enhanced_multiply_charged_spectrum = 1000789
 enhanced multiply charged spectrum: MS1 spectrum that is enriched in multiply-charged ions compared to singly-charged ions.
 MS_time_delayed_fragmentation_spectrum = 1000790
 time-delayed fragmentation spectrum: MSn spectrum in which the product ions are collected after a time delay, which allows the observation of lower energy fragmentation processes after precursor ion activation.
 MS_enhanced_resolution_scan_OBSOLETE = 1000791
 enhanced resolution scan: Scan with enhanced resolution.
 MS_isolation_window_attribute = 1000792
 isolation window attribute: Isolation window parameter.
 MS_isolation_window_upper_limit_OBSOLETE = 1000793
 isolation window upper limit: The highest m/z being isolated in an isolation window.
 MS_isolation_window_lower_limit_OBSOLETE = 1000794
 isolation window lower limit: The lowest m/z being isolated in an isolation window.
 MS_no_combination = 1000795
 no combination: Use this term if only one scan was recorded or there is no information about scans available.
 MS_spectrum_title = 1000796
 spectrum title: A free-form text title describing a spectrum.
 MS_peak_list_scans = 1000797
 peak list scans: A list of scan numbers and or scan ranges associated with a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term.
 MS_peak_list_raw_scans = 1000798
 peak list raw scans: A list of raw scans and or scan ranges used to generate a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term.
 MS_custom_unreleased_software_tool = 1000799
 custom unreleased software tool: A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the PSI-MS working group in order to have another CV term added.
 MS_mass_resolving_power = 1000800
 mass resolving power: The observed mass divided by the difference between two masses that can be separated: m/dm. The procedure by which dm was obtained and the mass at which the measurement was made should be reported.
 MS_area_peak_picking = 1000801
 area peak picking: Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The area defined by all raw data points that belong to the peak is reported.
 MS_sum_peak_picking = MS_area_peak_picking
 sum peak picking (area peak picking): Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The area defined by all raw data points that belong to the peak is reported.
 MS_height_peak_picking = 1000802
 height peak picking: Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The maximum intensity of all raw data points that belong to the peak is reported.
 MS_max_peak_picking = MS_height_peak_picking
 max peak picking (height peak picking): Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The maximum intensity of all raw data points that belong to the peak is reported.
 MS_analyzer_scan_offset = 1000803
 analyzer scan offset: Offset between two analyzers in a constant neutral loss or neutral gain scan. The value corresponds to the neutral loss or neutral gain value.
 MS_electromagnetic_radiation_spectrum = 1000804
 electromagnetic radiation spectrum: A plot of the relative intensity of electromagnetic radiation as a function of the wavelength.
 MS_EMR_spectrum = MS_electromagnetic_radiation_spectrum
 EMR spectrum (electromagnetic radiation spectrum): A plot of the relative intensity of electromagnetic radiation as a function of the wavelength.
 MS_emission_spectrum = 1000805
 emission spectrum: A plot of the relative intensity of electromagnetic radiation emitted by atoms or molecules when excited.
 MS_absorption_spectrum = 1000806
 absorption spectrum: A plot of the relative intensity of electromagnetic radiation absorbed by atoms or molecules when excited.
 MS_Th_s = 1000807
 Th/s: Unit describing the scan rate of a spectrum in Thomson per second.
 MS_chromatogram_attribute = 1000808
 chromatogram attribute: Chromatogram properties that are associated with a value.
 MS_chromatogram_title = 1000809
 chromatogram title: A free-form text title describing a chromatogram.
 MS_mass_chromatogram = 1000810
 mass chromatogram: A plot of the relative abundance of a beam or other collection of ions as a function of the retention time.
 MS_electromagnetic_radiation_chromatogram = 1000811
 electromagnetic radiation chromatogram: The measurement of electromagnetic properties as a function of the retention time.
 MS_EMR_radiation_chromatogram = MS_electromagnetic_radiation_chromatogram
 EMR radiation chromatogram (electromagnetic radiation chromatogram): The measurement of electromagnetic properties as a function of the retention time.
 MS_absorption_chromatogram = 1000812
 absorption chromatogram: The measurement of light absorbed by the sample as a function of the retention time.
 MS_emission_chromatogram = 1000813
 emission chromatogram: The measurement of light emitted by the sample as a function of the retention time.
 MS_counts_per_second = 1000814
 counts per second: The number of counted events observed per second in one or a group of elements of a detector.
 MS_Bruker_BAF_file = 1000815
 Bruker BAF file: Bruker BAF raw file format.
 MS_Bruker_U2_file = 1000816
 Bruker U2 file: Bruker HyStar U2 file format.
 MS_HyStar = 1000817
 HyStar: Bruker software for hyphenated experiments.
 MS_Acquity_UPLC_PDA = 1000818
 Acquity UPLC PDA: Acquity UPLC Photodiode Array Detector.
 MS_Acquity_UPLC_FLR = 1000819
 Acquity UPLC FLR: Acquity UPLC Fluorescence Detector.
 MS_flow_rate_array = 1000820
 flow rate array: A data array of flow rate measurements.
 MS_pressure_array = 1000821
 pressure array: A data array of pressure measurements.
 MS_temperature_array = 1000822
 temperature array: A data array of temperature measurements.
 MS_Bruker_U2_nativeID_format = 1000823
 Bruker U2 nativeID format: declaration=xsd:nonNegativeInteger collection=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger.
 MS_no_nativeID_format = 1000824
 no nativeID format: No nativeID format indicates that the file tagged with this term does not contain spectra that can have a nativeID format.
 MS_Bruker_FID_file = 1000825
 Bruker FID file: Bruker FID file format.
 MS_elution_time = 1000826
 elution time: The time of elution from a chromatographic column, relative to the start of the chromatography.
 MS_isolation_window_target_m_z = 1000827
 isolation window target m/z: The primary or reference m/z about which the isolation window is defined.
 MS_isolation_window_lower_offset = 1000828
 isolation window lower offset: The extent of the isolation window in m/z below the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z.
 MS_isolation_window_upper_offset = 1000829
 isolation window upper offset: The extent of the isolation window in m/z above the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z.
 MS_sample_preparation = 1000831
 sample preparation: Properties of the preparation steps which took place before the measurement was performed.
 MS_MALDI_matrix_application = 1000832
 MALDI matrix application: Attributes to describe the technique how the sample is prepared with the matrix solution.
 MS_matrix_application_type = 1000833
 matrix application type: Describes the technique how the matrix is put on the sample target.
 MS_matrix_solution = 1000834
 matrix solution: Describes the chemical solution used as matrix.
 MS_matrix_solution_concentration = 1000835
 matrix solution concentration: Concentration of the chemical solution used as matrix.
 MS_dried_droplet_MALDI_matrix_preparation = 1000836
 dried droplet MALDI matrix preparation: Dried droplet in MALDI matrix preparation.
 MS_printed_MALDI_matrix_preparation = 1000837
 printed MALDI matrix preparation: Printed MALDI matrix preparation.
 MS_sprayed_MALDI_matrix_preparation = 1000838
 sprayed MALDI matrix preparation: Sprayed MALDI matrix preparation.
 MS_precoated_MALDI_sample_plate = 1000839
 precoated MALDI sample plate: Precoated MALDI sample plate.
 MS_laser = 1000840
 laser: Device that emits light (electromagnetic radiation) through a process called stimulated emission. The term is an acronym for Light Amplification by Stimulated Emission of Radiation.
 MS_laser_attribute = 1000841
 laser attribute: Laser properties that are associated with a value.
 MS_laser_type = 1000842
 laser type: Type of laser used used for desorption purpose.
 MS_wavelength = 1000843
 wavelength: The distance between two peaks of the emitted laser beam.
 MS_focus_diameter_x = 1000844
 focus diameter x: Describes the diameter of the laser beam in x direction.
 MS_focus_diameter_y = 1000845
 focus diameter y: Describes the diameter of the laser beam in y direction.
 MS_pulse_energy = 1000846
 pulse energy: Describes output energy of the laser system. May be attenuated by filters or other means.
 MS_pulse_duration = 1000847
 pulse duration: Describes how long the laser beam was emitted from the laser device.
 MS_attenuation = 1000848
 attenuation: Describes the reduction of the intensity of the laser beam energy.
 MS_impact_angle = 1000849
 impact angle: Describes the angle between the laser beam and the sample target.
 MS_gas_laser = 1000850
 gas laser: Laser which is powered by a gaseous medium.
 MS_solid_state_laser = 1000851
 solid-state laser: Solid state laser materials are commonly made by doping a crystalline solid host with ions that provide the required energy states.
 MS_dye_laser = 1000852
 dye-laser: Dye lasers use an organic dye as the gain medium.
 MS_free_electron_laser = 1000853
 free electron laser: Free electron laser uses a relativistic electron beam as the lasing medium which move freely through a magnetic structure, hence the term.
 MS_LTQ_XL = 1000854
 LTQ XL: Thermo Scientific LTQ XL MS.
 MS_LTQ_Velos = 1000855
 LTQ Velos: Thermo Scientific LTQ Velos MS.
 MS_LTQ_Velos_ETD = 1000856
 LTQ Velos ETD: Thermo Scientific LTQ Velos MS with ETD.
 MS_run_attribute = 1000857
 run attribute: Properties of the described run.
 MS_fraction_identifier = 1000858
 fraction identifier: Identier string that describes the sample fraction. This identifer should contain the fraction number(s) or similar information.
 MS_molecule = 1000859
 molecule: A molecules is a fundamental component of a chemical compound that is the smallest part of the compound that can participate in a chemical reaction.
 MS_peptide = 1000860
 peptide: A compound of low molecular weight that is composed of two or more amino acids.
 MS_chemical_compound_attribute = 1000861
 chemical compound attribute: A describable property of a chemical compound.
 MS_isoelectric_point = 1000862
 isoelectric point: The pH of a solution at which a charged molecule does not migrate in an electric field.
 MS_pI = MS_isoelectric_point
 pI (isoelectric point): The pH of a solution at which a charged molecule does not migrate in an electric field.
 MS_predicted_isoelectric_point = 1000863
 predicted isoelectric point: The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm.
 MS_predicted_pI = MS_predicted_isoelectric_point
 predicted pI (predicted isoelectric point): The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm.
 MS_chemical_compound_formula = 1000864
 chemical compound formula: A combination of symbols used to express the chemical composition of a compound.
 MS_empirical_formula = 1000865
 empirical formula: A chemical formula which expresses the proportions of the elements present in a substance.
 MS_molecular_formula = 1000866
 molecular formula: A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked.
 MS_structural_formula = 1000867
 structural formula: A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other.
 MS_SMILES_string = 1000868
 SMILES string: The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string.
 MS_collision_gas_pressure = 1000869
 collision gas pressure: The gas pressure of the collision gas used for collisional excitation.
 MS_4000_QTRAP_OBSOLETE = 1000870
 4000 QTRAP: AB SCIEX or Applied Biosystems|MDS SCIEX QTRAP 4000.
 MS_SRM_software = 1000871
 SRM software: Software used to predict, select, or optimize transitions or analyze the results of selected reaction monitoring runs.
 MS_MaRiMba = 1000872
 MaRiMba: Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology.
 MS_peptide_attribute_calculation_software = 1000873
 peptide attribute calculation software: Software used to predict or calculate numberical attributes of peptides.
 MS_SSRCalc = 1000874
 SSRCalc: Sequence Specific Retention Calculator esimates the retention time of peptides based on their sequence.
 MS_declustering_potential = 1000875
 declustering potential: Potential difference between the orifice and the skimmer in volts.
 MS_cone_voltage = 1000876
 cone voltage: Potential difference between the sampling cone/orifice in volts.
 MS_tube_lens_voltage = 1000877
 tube lens voltage: Potential difference setting of the tube lens in volts.
 MS_external_reference_identifier = 1000878
 external reference identifier: An identifier/accession number to an external reference database.
 MS_PubMed_identifier = 1000879
 PubMed identifier: A unique identifier for a publication in the PubMed database (MIR:00000015).
 MS_interchannel_delay = 1000880
 interchannel delay: The duration of intervals between scanning, during which the instrument configuration is switched.
 MS_chemical_compound = 1000881
 chemical compound: A substance formed by chemical union of two or more elements or ingredients in definite proportion by weight.
 MS_protein = 1000882
 protein: A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA coding for the protein.
 MS_protein_short_name = 1000883
 protein short name: A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN).
 MS_protein_attribute = 1000884
 protein attribute: An nonphysical attribute describing a specific protein.
 MS_protein_accession = 1000885
 protein accession: Accession number for a specific protein in a database.
 MS_protein_name = 1000886
 protein name: A long name describing the function of the protein.
 MS_peptide_attribute = 1000887
 peptide attribute: An nonphysical attribute that can be used to describe a peptide.
 MS_unmodified_peptide_sequence = 1000888
 unmodified peptide sequence: A sequence of letter symbols denoting the order of amino acids that compose the peptide, without encoding any amino acid mass modifications that might be present.
 MS_modified_peptide_sequence = 1000889
 modified peptide sequence: A sequence of letter symbols denoting the order of amino acids that compose the peptide plus the encoding any amino acid modifications that are present.
 MS_peptide_labeling_state = 1000890
 peptide labeling state: A state description of how a peptide might be isotopically or isobarically labelled.
 MS_heavy_labeled_peptide = 1000891
 heavy labeled peptide: A peptide that has been created or labeled with some heavier-than-usual isotopes.
 MS_unlabeled_peptide = 1000892
 unlabeled peptide: A peptide that has not been labeled with heavier-than-usual isotopes. This is often referred to as "light" to distinguish from "heavy".
 MS_light_labeled_peptide = MS_unlabeled_peptide
 light labeled peptide (unlabeled peptide): A peptide that has not been labeled with heavier-than-usual isotopes. This is often referred to as "light" to distinguish from "heavy".
 MS_peptide_group_label = 1000893
 peptide group label: An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label.
 MS_retention_time = 1000894
 retention time: A measure of the interval relative to the beginning of a mass spectrometric run when a peptide will exit the chromatographic column.
 MS_local_retention_time = 1000895
 local retention time: A measure of the interval relative to the beginning of a mass spectrometric run when a peptide will exit an unspecified local chromatographic column and instrumental setup.
 MS_normalized_retention_time = 1000896
 normalized retention time: A measure of the interval relative to the beginning of a mass spectrometric run when a peptide will exit a standardized reference chromatographic column and instrumental setup.
 MS_predicted_retention_time = 1000897
 predicted retention time: A time interval relative to the beginning of a mass spectrometric run when a peptide will exit a chromatographic column as predicted by a referenced software application.
 MS_standard = 1000898
 standard: Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence.
 MS_de_facto_standard = 1000899
 de facto standard: A practice or product that has become a standard not because it has been approved by a standards organization but because it is widely used and recognized by the industry as being standard.
 MS_minimum_information_standard = 1000900
 minimum information standard: A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result.
 MS_retention_time_normalization_standard = 1000901
 retention time normalization standard: A standard providing the retention times at which a set of reference compounds exit the reference chromatographic column.
 MS_H_PINS_retention_time_normalization_standard = 1000902
 H-PINS retention time normalization standard: The de facto standard providing the retention times at which a set of halogenated reference peptides exit the reference chromatographic column.
 MS_product_ion_series_ordinal = 1000903
 product ion series ordinal: The ordinal of the fragment within a specified ion series. (e.g. 8 for a y8 ion).
 MS_product_ion_m_z_delta = 1000904
 product ion m/z delta: The difference in m/z of the predicted m/z based on the assigned product ion minus the actual observed peak m/z.
 MS_percent_of_base_peak_times_100 = 1000905
 percent of base peak times 100: The magnitude of a peak expressed in terms of the percentage of the magnitude of the base peak intensity multiplied by 100. The base peak is therefore 10000. This unit is common in normalized spectrum libraries.
 MS_peak_intensity_rank = 1000906
 peak intensity rank: Ordinal specifying the rank in intensity of a peak in a spectrum. Base peak is 1. The next most intense peak is 2, etc.
 MS_peak_targeting_suitability_rank = 1000907
 peak targeting suitability rank: Ordinal specifying the rank of a peak in a spectrum in terms of suitability for targeting. The most suitable peak is 1. The next most suitability peak is 2, etc. Suitability is algorithm and context dependant.
 MS_transition = 1000908
 transition: A set of two m/z values corresponding to the precursor m/z and a fragment m/z that in combination can be used to identify or quantify a specific ion, although not necessarily uniquely.
 MS_reaction = MS_transition
 reaction (transition): A set of two m/z values corresponding to the precursor m/z and a fragment m/z that in combination can be used to identify or quantify a specific ion, although not necessarily uniquely.
 MS_transition_validation_method = 1000909
 transition validation method: The strategy used to validate that a transition is effective.
 MS_transition_optimized_on_specified_instrument = 1000910
 transition optimized on specified instrument: The transition has been optimized by direct injection of the peptide into an instrument specified in a separate term, and the optimum voltages and fragmentation energies have been determined.
 MS_transition_validated_with_an_MS_MS_spectrum_on_specified_instrument = 1000911
 transition validated with an MS/MS spectrum on specified instrument: The transition has been validated by obtaining an MS/MS spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term.
 MS_transition_purported_from_an_MS_MS_spectrum_on_a_different__specified_instrument = 1000912
 transition purported from an MS/MS spectrum on a different, specified instrument: The transition has been purported by obtaining an MS/MS spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term. However, the detecting instrument is of a different type (e.g. ion trap) than the instrument that the transition will eventually be used on (e.g. triple quad).
 MS_transition_predicted_by_informatic_analysis = 1000913
 transition predicted by informatic analysis: The transition has been predicted by informatics software without any direct spectral evidence.
 MS_tab_delimited_text_file = 1000914
 tab delimited text file: A file that has two or more columns of tabular data where each column is separated by a TAB character.
 MS_retention_time_window_attribute = 1000915
 retention time window attribute: An attribute of a window in time about which a peptide might elute from the column.
 MS_retention_time_window_lower_offset = 1000916
 retention time window lower offset: The extent of the retention time window in time units below the target retention time. The lower and upper offsets may be asymetric about the target time.
 MS_retention_time_window_upper_offset = 1000917
 retention time window upper offset: The extent of the retention time window in time units above the target retention time. The lower and upper offsets may be asymetric about the target time.
 MS_target_list = 1000918
 target list: A list of peptides or compounds and their expected m/z coordinates that can be used to cause a mass spectrometry to obtain spectra of those molecules specifically.
 MS_target_inclusion_exclusion_priority = 1000919
 target inclusion exclusion priority: A priority setting specifying whether included or excluded targets have priority over the other.
 MS_includes_supersede_excludes = 1000920
 includes supersede excludes: A priority setting specifying that included targets have priority over the excluded targets if there is a conflict.
 MS_excludes_supersede_includes = 1000921
 excludes supersede includes: A priority setting specifying that excluded targets have priority over the included targets if there is a conflict.
 MS_Skyline = 1000922
 Skyline: Software used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the MacCoss lab at the University of Washington. https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=default.
 MS_TIQAM = 1000923
 TIQAM: Software used to predict, select, and optimize transitions for selected reaction monitoring experiments developed and distributed by the Institute for Systems Biology.
 MS_MaRiMba_OBSOLETE = 1000924
 MaRiMba: Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology.
 MS_ATAQS = 1000925
 ATAQS: Software suite used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the Institute for Systems Biology.
 MS_product_interpretation_rank = 1000926
 product interpretation rank: The integer rank given an interpretation of an observed product ion. For example, if y8 is selected as the most likely interpretation of a peak, then it is assigned a rank of 1.
 MS_ion_injection_time = 1000927
 ion injection time: The length of time spent filling an ion trapping device.
 MS_calibration_spectrum = 1000928
 calibration spectrum: A spectrum derived from a special calibration source, rather than from the primary injected sample. A calibration spectrum is typically derived from a substance that can be used to correct systematic shift in m/z for spectra of the primary inject sample.
 MS_Shimadzu_Biotech_nativeID_format = 1000929
 Shimadzu Biotech nativeID format: source=xsd:string start=xsd:nonNegativeInteger end=xsd:nonNegativeInteger.
 MS_Shimadzu_Biotech_database_entity = 1000930
 Shimadzu Biotech database entity: Shimadzu Biotech format.
 MS_QTRAP_5500 = 1000931
 QTRAP 5500: Applied Biosystems|MDS SCIEX QTRAP 5500.
 MS_TripleTOF_5600 = 1000932
 TripleTOF 5600: AB SCIEX TripleTOF 5600, a quadrupole - quadrupole - time-of-flight mass spectrometer.
 MS_protein_modifications = 1000933
 protein modifications: Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation.
 MS_gene_name = 1000934
 gene name: Name of the gene from which the protein is translated.
 MS_spectrum_interpretation = 1001000
 spectrum interpretation: Collection of terms from the PSI Proteome Informatics standards describing the interpretation of spectra.
 MS_Sequest_CleavesAt = 1001005
 Sequest:CleavesAt:
 MS_Sequest_ViewCV = 1001006
 Sequest:ViewCV: Branch containing the CV terms for Sequest View Input Parameters.
 MS_Sequest_OutputLines = 1001007
 Sequest:OutputLines:
 MS_Sequest_DescriptionLines = 1001009
 Sequest:DescriptionLines:
 MS_de_novo_search = 1001010
 de novo search: A de novo sequencing search (without database).
 MS_search_database_details = 1001011
 search database details: Details about the database searched.
 MS_database_source = 1001012
 database source: The organisation, project or laboratory from where the database is obtained (uniprot, ncbi, ebi, other).
 MS_database_name = 1001013
 database name: The name of the search database (nr, SwissProt or est_human).
 MS_database_local_file_path_OBSOLETE = 1001014
 database local file path: OBSOLETE: Use attribute in mzIdentML instead. Local file path of the search database from the search engine's point of view.
 MS_database_original_uri = 1001015
 database original uri: URI, from where the search database was originally downloaded.
 MS_database_version_OBSOLETE = 1001016
 database version: OBSOLETE: Use attribute in mzIdentML instead. Version of the search database .
 MS_database_release_date_OBSOLETE = 1001017
 database release date: OBSOLETE: Use attribute in mzIdentML instead. Release date of the search database.
 MS_database_type = 1001018
 database type: Database containing amino acid or nucleic acid sequences.
 MS_database_filtering = 1001019
 database filtering: Was there filtering used on the database.
 MS_DB_filter_taxonomy = 1001020
 DB filter taxonomy: A taxonomy filter was to the database search.
 MS_DB_filter_on_accession_numbers = 1001021
 DB filter on accession numbers: Filtering applied specifically by accession number pattern.
 MS_DB_MW_filter = 1001022
 DB MW filter: Filtering applied specifically by protein molecular weight, specified as either a range or above/below a threshold value.
 MS_DB_PI_filter = 1001023
 DB PI filter: Filtering applied specifically by predicted protein isoelectric focussing point (pI), specified as either a range or above/below a threshold value.
 MS_translation_frame_OBSOLETE = 1001024
 translation frame: OSBOLETE: use attribute in mzIdentML instead. The translated open reading frames from a nucleotide database considered in the search (range: 1-6).
 MS_translation_table = 1001025
 translation table: The translation table used to translate the nucleotides to amino acids.
 MS_Sequest_NormalizeXCorrValues = 1001026
 Sequest:NormalizeXCorrValues:
 MS_DB_filter_on_sequence_pattern = 1001027
 DB filter on sequence pattern: Filtering applied specifically by amino acid sequence pattern.
 MS_Sequest_SequenceHeaderFilter = 1001028
 Sequest:SequenceHeaderFilter:
 MS_number_of_sequences_searched = 1001029
 number of sequences searched: The number of sequences (proteins / nucleotides) from the database search after filtering.
 MS_number_of_peptide_seqs_compared_to_each_spectrum = 1001030
 number of peptide seqs compared to each spectrum: Number of peptide seqs compared to each spectrum.
 MS_spectral_library_search = 1001031
 spectral library search: A search using a library of spectra.
 MS_Sequest_SequencePartialFilter = 1001032
 Sequest:SequencePartialFilter:
 MS_date___time_search_performed_OBSOLETE = 1001035
 date / time search performed: OBSOLETE: use attribute in mzIdentML instead. Date and time of the actual search run.
 MS_search_time_taken = 1001036
 search time taken: The time taken to complete the search in seconds.
 MS_Sequest_ShowFragmentIons = 1001037
 Sequest:ShowFragmentIons:
 MS_Sequest_Consensus = 1001038
 Sequest:Consensus: Specify depth as value of the CVParam!
 MS_intermediate_analysis_format = 1001040
 intermediate analysis format: Type of the source file, the mzIdentML was created from.
 MS_Sequest_sortCV = 1001041
 Sequest:sortCV: Branch containing the CV terms for Sequest View / Sort Input Parameters.
 MS_Sequest_LimitTo = 1001042
 Sequest:LimitTo: Specify "number of dtas shown" as value of the CVParam!
 MS_cleavage_agent_details = 1001044
 cleavage agent details: Details of cleavage agent (enzyme).
 MS_cleavage_agent_name = 1001045
 cleavage agent name: The name of the cleavage agent.
 MS_Sequest_sort_by_dCn = 1001046
 Sequest:sort_by_dCn:
 MS_Sequest_sort_by_dM = 1001047
 Sequest:sort_by_dM:
 MS_Sequest_sort_by_Ions = 1001048
 Sequest:sort_by_Ions:
 MS_Sequest_sort_by_MH_ = 1001049
 Sequest:sort_by_MH+:
 MS_Sequest_sort_by_P = 1001050
 Sequest:sort_by_P:
 MS_multiple_enzyme_combination_rules_OBSOLETE = 1001051
 multiple enzyme combination rules: OBSOLETE: use attribute independent in mzIdentML instead. Description of multiple enzyme digestion protocol, if any.
 MS_Sequest_sort_by_PreviousAminoAcid = 1001052
 Sequest:sort_by_PreviousAminoAcid:
 MS_Sequest_sort_by_Ref = 1001053
 Sequest:sort_by_Ref:
 MS_modification_parameters = 1001055
 modification parameters: Modification parameters for the search engine run.
 MS_modification_specificity_rule = 1001056
 modification specificity rule: The specificity rules for the modifications applied by the search engine.
 MS_tolerance_on_types_OBSOLETE = 1001057
 tolerance on types: OBSOLETE: Tolerance on types.
 MS_quality_estimation_by_manual_validation = 1001058
 quality estimation by manual validation: The quality estimation was done manually.
 MS_Sequest_sort_by_RSp = 1001059
 Sequest:sort_by_RSp:
 MS_quality_estimation_method_details = 1001060
 quality estimation method details: Method for quality estimation (manually or with decoy database).
 MS_neutral_loss_OBSOLETE = 1001061
 neutral loss: OBSOLETE: replaced by MS:1000336 (neutral loss): Leave this to PSI-MOD?
 MS_Mascot_MGF_file = 1001062
 Mascot MGF file:
 MS_TODOscoring_model_OBSOLETE = 1001065
 TODOscoring model: OBSOLETE: There is Phenyx:ScoringModel for Phenyx! Scoring model (more detailed granularity). TODO: add some child terms!
 MS_ions_series_considered_in_search = 1001066
 ions series considered in search: The description of the ion fragment series (including charges and neutral losses) that are considered by the search engine.
 MS_Sequest_sort_by_Sp = 1001068
 Sequest:sort_by_Sp:
 MS_Sequest_sort_by_TIC = 1001069
 Sequest:sort_by_TIC:
 MS_Sequest_sort_by_Scan = 1001070
 Sequest:sort_by_Scan:
 MS_Sequest_sort_by_Sequence = 1001071
 Sequest:sort_by_Sequence:
 MS_Sequest_sort_by_Sf = 1001072
 Sequest:sort_by_Sf:
 MS_database_type_amino_acid = 1001073
 database type amino acid: Database contains amino acid sequences.
 MS_database_type_nucleotide = 1001079
 database type nucleotide: Database contains nucleid acid sequences.
 MS_search_type = 1001080
 search type: Enumeration of type of search value (i.e. from PMF, sequence tag, MS-MS).
 MS_pmf_search = 1001081
 pmf search: A peptide mass fingerprint search.
 MS_tag_search = 1001082
 tag search: A sequence tag search.
 MS_ms_ms_search = 1001083
 ms-ms search: An ms/ms search (with fragment ions).
 MS_database_nr = 1001084
 database nr:
 MS_protein_result_details = 1001085
 protein result details: Protein level information.
 MS_Sequest_sort_by_XCorr = 1001086
 Sequest:sort_by_XCorr:
 MS_Sequest_ProcessCV = 1001087
 Sequest:ProcessCV: Branch containing the CV terms for Sequest View / Process Input Parameters.
 MS_protein_description = 1001088
 protein description: The protein description line from the sequence entry in the source database FASTA file.
 MS_molecule_taxonomy = 1001089
 molecule taxonomy: The taxonomy of the resultant molecule from the search.
 MS_taxonomy_nomenclature_OBSOLETE = 1001090
 taxonomy nomenclature: OBSOLETE: The system used to indicate taxonomy. There should be an enumerated list of options: latin name, NCBI TaxID, common name, Swiss-Prot species ID (ex. RABIT from the full protein ID ALBU_RABIT).
 MS_NoEnzyme_OBSOLETE = 1001091
 NoEnzyme:
 MS_peptide_identification_confidence_metric = 1001092
 peptide identification confidence metric: Peptide identification confidence metric for a peptide (p-value, Expect value, confidence, local FDR).
 MS_sequence_coverage = 1001093
 sequence coverage: The percent coverage for the protein based upon the matched peptide sequences (can be calculated).
 MS_Sequest_sort_by_z = 1001094
 Sequest:sort_by_z:
 MS_Sequest_ProcessAll = 1001095
 Sequest:ProcessAll:
 MS_Sequest_TopPercentMostIntense = 1001096
 Sequest:TopPercentMostIntense: Specify "percentage" as value of the CVParam!
 MS_distinct_peptide_sequences = 1001097
 distinct peptide sequences: This counts distinct sequences hitting the protein without regard to a minimal confidence threshold.
 MS_confident_distinct_peptide_sequences = 1001098
 confident distinct peptide sequences: This counts the number of distinct peptide sequences. Multiple charge states and multiple modification states do NOT count as multiple sequences. The definition of 'confident' must be qualified elsewhere.
 MS_confident_peptide_qualification = 1001099
 confident peptide qualification: The point of this entry is to define what is meant by confident for the term Confident distinct peptide sequence and/or Confident peptides. Example 1 - metric=Paragon:Confidence value=95 sense=greater than Example 2 - metric=Mascot:Eval value=0.05 sense=less than.
 MS_confident_peptide_sequence_number = 1001100
 confident peptide sequence number: This counts the number of peptide sequences without regard to whether they are distinct. Multiple charges states and multiple modification states DO count as multiple peptides. The definition of 'confident' must be qualified elsewhere.
 MS_protein_group_subset_relationship = 1001101
 protein group/subset relationship: Branch containing protein group/subset relationships.
 MS_Sequest_Chromatogram = 1001102
 Sequest:Chromatogram:
 MS_Sequest_InfoAndLog = 1001103
 Sequest:InfoAndLog:
 MS_database_SwissProt = 1001104
 database SwissProt:
 MS_peptide_result_details = 1001105
 peptide result details: Peptide level information.
 MS_Sequest_TopNumber = 1001106
 Sequest:TopNumber: Specify "number" as value of the CVParam!
 MS_data_stored_in_database = 1001107
 data stored in database: Source file for this mzIdentML was a data set in a database.
 MS_param__a_ion = 1001108
 param: a ion:
 MS_Sequest_CullTo = 1001109
 Sequest:CullTo: Specify cull string as value of the CVParam!
 MS_Sequest_modeCV = 1001110
 Sequest:modeCV: Branch containing the CV terms for Sequest Mode Input Parameters.
 MS_Sequest_Full = 1001111
 Sequest:Full:
 MS_n_terminal_flanking_residue = 1001112
 n-terminal flanking residue: The residue preceeding the first amino acid in the peptide sequence as it occurs in the protein. Use 'N-term' to denote if the peptide starts at the N terminus of the protein.
 MS_c_terminal_flanking_residue = 1001113
 c-terminal flanking residue: The residue following the last amino acid in the peptide sequence as it occurs in the protein. Use 'C-term' to denote if the peptide ends at the C terminus of the protein.
 MS_retention_time_s_ = 1001114
 retention time(s): Retention time of the spectrum from the source file.
 MS_scan_number_s__OBSOLETE = 1001115
 scan number(s): OBSOLETE: use spectrumID attribute of SpectrumIdentificationResult. Take from mzData.
 MS_single_protein_result_details = 1001116
 single protein result details: Results specific for one protein as part of a protein ambiguity group (a result not valid for all the other proteins in the protein ambiguity group).
 MS_theoretical_mass = 1001117
 theoretical mass: The theoretical mass of the molecule (e.g. the peptide sequence and its modifications).
 MS_param__b_ion = 1001118
 param: b ion:
 MS_param__c_ion = 1001119
 param: c ion:
 MS_Sequest_FormatAndLinks = 1001120
 Sequest:FormatAndLinks:
 MS_number_of_matched_peaks = 1001121
 number of matched peaks: The number of peaks that were matched as qualified by the ion series considered field. If a peak matches multiple ions then only 1 would be added the count.
 MS_ions_series_considered = 1001122
 ions series considered: The ion series that were used during the calculation of the count (e.g. b, y, a, b, c, y, z, b, b-NH3, b-H20, b+, z, z-, z+, y-H3PO4, immonium).
 MS_number_of_peaks_used = 1001123
 number of peaks used: The number of peaks from the original peak list that are used to calculate the scores for a particular search engine. All ions that have the opportunity to match or be counted even if they don't.
 MS_number_of_peaks_submitted = 1001124
 number of peaks submitted: The number of peaks from the original peaks listed that were submitted to the search engine.
 MS_manual_validation = 1001125
 manual validation: Result of quality estimation: decision of a manual validation.
 MS_Sequest_Fast = 1001126
 Sequest:Fast:
 MS_peptide_sharing_details = 1001127
 peptide sharing details: Accessions Containing Sequence - Accessions for each protein containing this peptide.
 MS_Sequest_selectCV = 1001128
 Sequest:selectCV: Branch containing the CV terms for Sequest Select Input Parameters.
 MS_quantification_information = 1001129
 quantification information: Quantification information.
 MS_peptide_raw_area = 1001130
 peptide raw area: Peptide raw area.
 MS_error_on_peptide_area = 1001131
 error on peptide area: Error on peptide area.
 MS_peptide_ratio = 1001132
 peptide ratio: Peptide ratio.
 MS_error_on_peptide_ratio = 1001133
 error on peptide ratio: Error on peptide ratio.
 MS_protein_ratio = 1001134
 protein ratio: Protein ratio.
 MS_error_on_protein_ratio = 1001135
 error on protein ratio: Error on protein ratio.
 MS_p_value__protein_diff_from_1_randomly_ = 1001136
 p-value (protein diff from 1 randomly): P-value (protein diff from 1 randomly).
 MS_absolute_quantity = 1001137
 absolute quantity: Absolute quantity in terms of real concentration or molecule copy number in sample.
 MS_error_on_absolute_quantity = 1001138
 error on absolute quantity: Error on absolute quantity.
 MS_quantitation_software_name = 1001139
 quantitation software name: Quantitation software name.
 MS_quantitation_software_version_OBSOLETE = 1001140
 quantitation software version: Quantitation software version.
 MS_intensity_of_precursor_ion = 1001141
 intensity of precursor ion: The intensity of the precursor ion.
 MS_database_IPI_human = 1001142
 database IPI_human:
 MS_search_engine_specific_score_for_peptides = 1001143
 search engine specific score for peptides:
 MS_Sequest_SelectDefault = 1001144
 Sequest:SelectDefault:
 MS_Sequest_SelectAdvancedCV = 1001145
 Sequest:SelectAdvancedCV: Branch containing the CV terms for Sequest Select Advanced Input Parameters.
 MS_param__a_ion_NH3 = 1001146
 param: a ion-NH3:
 MS_protein_ambiguity_group_result_details = 1001147
 protein ambiguity group result details:
 MS_param__a_ion_H2O = 1001148
 param: a ion-H2O: Ion a - H2O if a significant and fragment includes STED.
 MS_param__b_ion_NH3 = 1001149
 param: b ion-NH3:
 MS_param__b_ion_H2O = 1001150
 param: b ion-H2O: Ion b - H2O if b significant and fragment includes STED.
 MS_param__y_ion_NH3 = 1001151
 param: y ion-NH3:
 MS_param__y_ion_H2O = 1001152
 param: y ion-H2O: Ion y - H2O if y significant and fragment includes STED.
 MS_search_engine_specific_score = 1001153
 search engine specific score: Search engine specific scores.
 MS_Sequest_probability = 1001154
 Sequest:probability: The SEQUEST result 'Probability'.
 MS_Sequest_xcorr = 1001155
 Sequest:xcorr: The SEQUEST result 'XCorr'.
 MS_Sequest_deltacn = 1001156
 Sequest:deltacn: The SEQUEST result 'DeltaCn'.
 MS_Sequest_sp = 1001157
 Sequest:sp: The SEQUEST result 'Sp' (protein).
 MS_Sequest_Uniq = 1001158
 Sequest:Uniq:
 MS_Sequest_expectation_value = 1001159
 Sequest:expectation value: The SEQUEST result 'Expectation value'.
 MS_Sequest_sf = 1001160
 Sequest:sf: The SEQUEST result 'Sf'.
 MS_Sequest_matched_ions = 1001161
 Sequest:matched ions: The SEQUEST result 'Matched Ions'.
 MS_Sequest_total_ions = 1001162
 Sequest:total ions: The SEQUEST result 'Total Ions'.
 MS_Sequest_consensus_score = 1001163
 Sequest:consensus score: The SEQUEST result 'Consensus Score'.
 MS_Paragon_unused_protscore = 1001164
 Paragon:unused protscore: The Paragon result 'Unused ProtScore'.
 MS_Paragon_total_protscore = 1001165
 Paragon:total protscore: The Paragon result 'Total ProtScore'.
 MS_Paragon_score = 1001166
 Paragon:score: The Paragon result 'Score'.
 MS_Paragon_confidence = 1001167
 Paragon:confidence: The Paragon result 'Confidence'.
 MS_Paragon_expression_error_factor = 1001168
 Paragon:expression error factor: The Paragon result 'Expression Error Factor'.
 MS_Paragon_expression_change_p_value = 1001169
 Paragon:expression change p-value: The Paragon result 'Expression change P-value'.
 MS_Paragon_contrib = 1001170
 Paragon:contrib: The Paragon result 'Contrib'.
 MS_Mascot_score = 1001171
 Mascot:score: The Mascot result 'Score'.
 MS_Mascot_expectation_value = 1001172
 Mascot:expectation value: The Mascot result 'expectation value'.
 MS_Mascot_matched_ions = 1001173
 Mascot:matched ions: The Mascot result 'Matched ions'.
 MS_Mascot_total_ions = 1001174
 Mascot:total ions: The Mascot result 'Total ions'.
 MS_peptide_shared_in_multiple_proteins = 1001175
 peptide shared in multiple proteins:
 MS______KR_____P_ = 1001176
 (?<=[KR])(?!P):
 MS_number_of_molecular_hypothesis_considered = 1001177
 number of molecular hypothesis considered: Number of Molecular Hypothesis Considered - This is the number of molecules (e.g. peptides for proteomics) considered for a particular search.
 MS_database_EST = 1001178
 database EST:
 MS_Cleavage_agent_regular_expression = 1001180
 Cleavage agent regular expression: Branch containing regular expressions for cleavage enzymes.
 MS_search_statistics = 1001184
 search statistics: The details of the actual run of the search.
 MS_modification_specificity_N_term = 1001189
 modification specificity N-term: As parameter for search engine: apply the modification only N-terminal.
 MS_modification_specificity_C_term = 1001190
 modification specificity C-term: As parameter for search engine: apply the modification only C-terminal.
 MS_p_value_OBSOLETE = 1001191
 p-value: Quality estimation by p-value.
 MS_Expect_value = 1001192
 Expect value: Result of quality estimation: Expect value.
 MS_confidence_score = 1001193
 confidence score: Result of quality estimation: confidence score.
 MS_quality_estimation_with_decoy_database = 1001194
 quality estimation with decoy database: Quality estimation by decoy database.
 MS_decoy_DB_type_reverse = 1001195
 decoy DB type reverse: Decoy type: Amino acids of protein sequences are used in reverse order.
 MS_decoy_DB_type_randomized = 1001196
 decoy DB type randomized: Decoy type: Amino acids of protein sequences are randomized (keeping the original protein mass).
 MS_DB_composition_target_decoy = 1001197
 DB composition target+decoy: Decoy database composition: database contains original (target) and decoy entries.
 MS_protein_identification_confidence_metric = 1001198
 protein identification confidence metric: Protein identification confidence metric (p-value, Expect value, confidence, local FDR).
 MS_Mascot_DAT_file = 1001199
 Mascot DAT file: Source file for this mzIdentML was a Mascot DAT file.
 MS_Sequest_out_file = 1001200
 Sequest out file: Source file for this mzIdentML was ONE Sequest out file.
 MS_DB_MW_filter_maximum = 1001201
 DB MW filter maximum:
 MS_DB_MW_filter_minimum = 1001202
 DB MW filter minimum:
 MS_DB_PI_filter_maximum = 1001203
 DB PI filter maximum:
 MS_DB_PI_filter_minimum = 1001204
 DB PI filter minimum:
 MS_Mascot = 1001207
 Mascot:
 MS_Sequest = 1001208
 Sequest:
 MS_Phenyx = 1001209
 Phenyx:
 MS_mass_type_settings = 1001210
 mass type settings: The type of mass difference value to be considered by the search engine (monoisotopic or average).
 MS_parent_mass_type_mono = 1001211
 parent mass type mono: Mass type setting for parent mass was monoisotopic.
 MS_parent_mass_type_average = 1001212
 parent mass type average: Mass type setting for parent mass was average isotopic.
 MS_search_result_details_OBSOLETE = 1001213
 search result details: OBSOLETE: Scores and global result characteristics.
 MS_prot_global_FDR = 1001214
 prot:global FDR: Estimation of global false discovery rate of the proteins.
 MS_Sequest_PeptideSp = 1001215
 Sequest:PeptideSp: The SEQUEST result 'Sp' in out file (peptide).
 MS_Sequest_PeptideRankSp = 1001217
 Sequest:PeptideRankSp: The SEQUEST result 'Sp' of 'Rank/Sp' in out file (peptide). Also called 'rsp'.
 MS_Sequest_PeptideNumber = 1001218
 Sequest:PeptideNumber: The SEQUEST result '#' in out file (peptide).
 MS_Sequest_PeptideIdnumber = 1001219
 Sequest:PeptideIdnumber: The SEQUEST result 'Id#' in out file (peptide).
 MS_frag__y_ion = 1001220
 frag: y ion: Fragmentation information, type of product: y ion.
 MS_fragmentation_information = 1001221
 fragmentation information: Fragmentation information like ion types.
 MS_frag__b_ion___H2O = 1001222
 frag: b ion - H2O: Fragmentation information, type of product: b ion without water.
 MS_frag__y_ion___H2O = 1001223
 frag: y ion - H2O: Fragmentation information, type of product: y ion without water.
 MS_frag__b_ion = 1001224
 frag: b ion: Fragmentation information, type of product: b ion.
 MS_product_ion_m_z = 1001225
 product ion m/z: The m/z of the product ion.
 MS_fragment_ion_m_z = MS_product_ion_m_z
 fragment ion m/z (product ion m/z): The m/z of the product ion.
 MS_product_ion_intensity = 1001226
 product ion intensity: The intensity of the product ion.
 MS_fragment_ion_intensity = MS_product_ion_intensity
 fragment ion intensity (product ion intensity): The intensity of the product ion.
 MS_product_ion_m_z_error = 1001227
 product ion m/z error: The product ion m/z error.
 MS_frag__x_ion = 1001228
 frag: x ion: Fragmentation information, type of product: x ion.
 MS_frag__a_ion = 1001229
 frag: a ion: Fragmentation information, type of product: a ion.
 MS_frag__z_ion = 1001230
 frag: z ion: Fragmentation information, type of product: z ion.
 MS_frag__c_ion = 1001231
 frag: c ion: Fragmentation information, type of product: c ion.
 MS_frag__b_ion___NH3 = 1001232
 frag: b ion - NH3: Fragmentation information, type of product: b ion without ammonium ion.
 MS_frag__y_ion___NH3 = 1001233
 frag: y ion - NH3: Fragmentation information, type of product: y ion without ammonium ion.
 MS_frag__a_ion___H2O = 1001234
 frag: a ion - H2O: Fragmentation information, type of product: a ion without water.
 MS_frag__a_ion___NH3 = 1001235
 frag: a ion - NH3: Fragmentation information, type of product: a ion without ammonium.
 MS_frag__d_ion = 1001236
 frag: d ion: Fragmentation information, type of product: d ion.
 MS_frag__v_ion = 1001237
 frag: v ion: Fragmentation information, type of product: v ion.
 MS_frag__w_ion = 1001238
 frag: w ion: Fragmentation information, type of product: w ion.
 MS_frag__immonium_ion = 1001239
 frag: immonium ion: Fragmentation information, type of product: immonium ion.
 MS_non_identified_ion = 1001240
 non-identified ion: Non-identified ion.
 MS_co_eluting_ion = 1001241
 co-eluting ion: Co-eluting ion.
 MS_Sequest_out_folder = 1001242
 Sequest out folder: Source file for this mzIdentML was a Sequest folder with its out files.
 MS_Sequest_summary = 1001243
 Sequest summary: Source file for this mzIdentML was a Sequest summary page (proteins).
 MS_PerSeptive_PKS_file = 1001245
 PerSeptive PKS file:
 MS_Sciex_API_III_file = 1001246
 Sciex API III file:
 MS_Bruker_XML_file = 1001247
 Bruker XML file: Bruker data exchange xml.
 MS_search_input_details = 1001249
 search input details:
 MS_local_FDR = 1001250
 local FDR: Result of quality estimation: the local FDR at the current position of a sorted list.
 MS_Trypsin = 1001251
 Trypsin:
 MS_DB_source_EBI = 1001252
 DB source EBI:
 MS_DB_source_NCBI = 1001253
 DB source NCBI:
 MS_DB_source_UniProt = 1001254
 DB source UniProt:
 MS_fragment_mass_type_average = 1001255
 fragment mass type average: Mass type setting for fragment mass was average isotopic.
 MS_fragment_mass_type_mono = 1001256
 fragment mass type mono: Mass type setting for fragment mass was monoisotopic.
 MS_param__v_ion = 1001257
 param: v ion:
 MS_param__d_ion = 1001258
 param: d ion:
 MS_param__immonium_ion = 1001259
 param: immonium ion:
 MS_param__w_ion = 1001260
 param: w ion:
 MS_param__x_ion = 1001261
 param: x ion:
 MS_param__y_ion = 1001262
 param: y ion:
 MS_param__z_ion = 1001263
 param: z ion:
 MS_role_type = 1001266
 role type: Role of a Person or Organization.
 MS_software_vendor = 1001267
 software vendor:
 MS_programmer = 1001268
 programmer:
 MS_instrument_vendor = 1001269
 instrument vendor:
 MS_lab_personnel = 1001270
 lab personnel:
 MS_researcher = 1001271
 researcher:
 MS_____R____P_ = 1001272
 (?<=R)(?!P):
 MS_____BD__ = 1001273
 (?=[BD]):
 MS_____DE__ = 1001274
 (?=[DE]):
 MS_ProteinScape_SearchEvent = 1001275
 ProteinScape SearchEvent: Source data for this mzIdentML was a ProteinScape SearchEvent.
 MS_ProteinScape_Gel = 1001276
 ProteinScape Gel: Source data for this mzIdentML was a ProteinScape Gel.
 MS_decoy_DB_accession_regexp = 1001283
 decoy DB accession regexp: Specify the regular expression for decoy accession numbers.
 MS_decoy_DB_derived_from = 1001284
 decoy DB derived from: The name of the database, the search database was derived from.
 MS_database_IPI_mouse = 1001285
 database IPI_mouse:
 MS_database_IPI_rat = 1001286
 database IPI_rat:
 MS_database_IPI_zebrafish = 1001287
 database IPI_zebrafish:
 MS_database_IPI_chicken = 1001288
 database IPI_chicken:
 MS_database_IPI_cow = 1001289
 database IPI_cow:
 MS_database_IPI_arabidopsis = 1001290
 database IPI_arabidopsis:
 MS_decoy_DB_from_nr = 1001291
 decoy DB from nr:
 MS_decoy_DB_from_IPI_rat = 1001292
 decoy DB from IPI_rat:
 MS_decoy_DB_from_IPI_mouse = 1001293
 decoy DB from IPI_mouse:
 MS_decoy_DB_from_IPI_arabidopsis = 1001294
 decoy DB from IPI_arabidopsis:
 MS_decoy_DB_from_EST = 1001295
 decoy DB from EST:
 MS_decoy_DB_from_IPI_zebrafish = 1001296
 decoy DB from IPI_zebrafish:
 MS_decoy_DB_from_SwissProt = 1001297
 decoy DB from SwissProt:
 MS_decoy_DB_from_IPI_chicken = 1001298
 decoy DB from IPI_chicken:
 MS_decoy_DB_from_IPI_cow = 1001299
 decoy DB from IPI_cow:
 MS_decoy_DB_from_IPI_human = 1001300
 decoy DB from IPI_human:
 MS_protein_rank = 1001301
 protein rank: The rank of the protein in a list sorted by the search engine.
 MS_search_engine_specific_input_parameter = 1001302
 search engine specific input parameter: This branch contains search engine specific input parameters (e.g. Mascot Sig Threshold).
 MS_Arg_C = 1001303
 Arg-C: Endoproteinase Arg-C.
 MS_Clostripain = MS_Arg_C
 Clostripain (Arg-C): Endoproteinase Arg-C.
 MS_Asp_N = 1001304
 Asp-N:
 MS_Asp_N_ambic = 1001305
 Asp-N_ambic:
 MS_Chymotrypsin = 1001306
 Chymotrypsin:
 MS_CNBr = 1001307
 CNBr: Cyanogen bromide.
 MS_Formic_acid = 1001308
 Formic_acid:
 MS_Lys_C = 1001309
 Lys-C:
 MS_Lys_C_P = 1001310
 Lys-C/P:
 MS_PepsinA = 1001311
 PepsinA:
 MS_TrypChymo = 1001312
 TrypChymo:
 MS_Trypsin_P = 1001313
 Trypsin/P:
 MS_V8_DE = 1001314
 V8-DE:
 MS_V8_E = 1001315
 V8-E:
 MS_Mascot_SigThreshold = 1001316
 Mascot:SigThreshold:
 MS_Mascot_MaxProteinHits = 1001317
 Mascot:MaxProteinHits:
 MS_Mascot_ProteinScoringMethod = 1001318
 Mascot:ProteinScoringMethod:
 MS_Mascot_MinMSMSThreshold = 1001319
 Mascot:MinMSMSThreshold:
 MS_Mascot_ShowHomologousProteinsWithSamePeptides = 1001320
 Mascot:ShowHomologousProteinsWithSamePeptides:
 MS_Mascot_ShowHomologousProteinsWithSubsetOfPeptides = 1001321
 Mascot:ShowHomologousProteinsWithSubsetOfPeptides:
 MS_Mascot_RequireBoldRed = 1001322
 Mascot:RequireBoldRed:
 MS_Mascot_UseUnigeneClustering = 1001323
 Mascot:UseUnigeneClustering:
 MS_Mascot_IncludeErrorTolerantMatches = 1001324
 Mascot:IncludeErrorTolerantMatches:
 MS_Mascot_ShowDecoyMatches = 1001325
 Mascot:ShowDecoyMatches:
 MS_add_others_OBSOLETE = 1001326
 add_others:
 MS_OMSSA_evalue = 1001328
 OMSSA:evalue: OMSSA E-value.
 MS_OMSSA_pvalue = 1001329
 OMSSA:pvalue: OMSSA p-value.
 MS_X_Tandem_expect = 1001330
 X!Tandem:expect: The X!Tandem expectation value.
 MS_X_Tandem_hyperscore = 1001331
 X!Tandem:hyperscore: The X!Tandem hyperscore.
 MS______FYWL_____P_ = 1001332
 (?<=[FYWL])(?!P):
 MS_____M_ = 1001333
 (?<=M):
 MS______D_______D__ = 1001334
 ((?<=D))|((?=D)):
 MS_____K____P_ = 1001335
 (?<=K)(?!P):
 MS_____K_ = 1001336
 (?<=K):
 MS______FL__ = 1001337
 (?<=[FL]):
 MS______FYWLKR_____P_ = 1001338
 (?<=[FYWLKR])(?!P):
 MS______KR__ = 1001339
 (?<=[KR]):
 MS______BDEZ_____P_ = 1001340
 (?<=[BDEZ])(?!P):
 MS______EZ_____P_ = 1001341
 (?<=[EZ])(?!P):
 MS_database_sequence_details = 1001342
 database sequence details: Details about a single database sequence.
 MS_NA_sequence = 1001343
 NA sequence: The sequence is a nucleic acid sequence.
 MS_AA_sequence = 1001344
 AA sequence: The sequence is a amino acid sequence.
 MS_mass_table_source = 1001345
 mass table source: Children of this term specify the source of the mass table used.
 MS_AAIndex_mass_table = 1001346
 AAIndex mass table: The masses used in the mass table are taken from AAIndex.
 MS_database_file_formats = 1001347
 database file formats: The children of this term define file formats of the sequence database used.
 MS_FASTA_format = 1001348
 FASTA format: The sequence database was stored in the FASTA format.
 MS_ASN_1 = 1001349
 ASN.1: The sequence database was stored in the ASN.1 format.
 MS_NCBI___p_ = 1001350
 NCBI *.p*: The sequence database was stored in the NCBI formatdb (*.p*) format.
 MS_clustal_aln = 1001351
 clustal aln: ClustalW ALN (multiple alignment) format.
 MS_embl_em = 1001352
 embl em: EMBL entry format.
 MS_NBRF_PIR = 1001353
 NBRF PIR: The NBRF PIR was used as format.
 MS_mass_table_options = 1001354
 mass table options: Root node for options for the mass table used.
 MS_peptide_descriptions = 1001355
 peptide descriptions: Descriptions of peptides.
 MS_spectrum_descriptions = 1001356
 spectrum descriptions: Descriptions of the input spectra.
 MS_spectrum_quality_descriptions = 1001357
 spectrum quality descriptions: Description of the quality of the input spectrum.
 MS_msmsEval_quality = 1001358
 msmsEval quality: This term reports the quality of the spectrum assigned by msmsEval.
 MS_ambiguous_residues = 1001359
 ambiguous residues: Children of this term describe abiguous residues.
 MS_alternate_single_letter_codes = 1001360
 alternate single letter codes: List of standard residue one letter codes which are used to replace a non-standard.
 MS_alternate_mass = 1001361
 alternate mass: List of masses a non-standard letter code is replaced with.
 MS_number_of_unmatched_peaks = 1001362
 number of unmatched peaks: The number of unmatched peaks.
 MS_peptide_unique_to_one_protein = 1001363
 peptide unique to one protein:
 MS_pep_global_FDR = 1001364
 pep:global FDR: Estimation of global false discovery rate of the peptides.
 MS_frag__internal_yb_ion = 1001365
 frag: internal yb ion:
 MS_frag__internal_ya_ion = 1001366
 frag: internal ya ion:
 MS_frag__z_1_ion = 1001367
 frag: z+1 ion:
 MS_frag__z_2_ion = 1001368
 frag: z+2 ion:
 MS_text_file = 1001369
 text file: Simple text file of "m/z [intensity]" values for a PMF (or single MS-MS) search.
 MS_Mascot_homology_threshold = 1001370
 Mascot:homology threshold: The Mascot result 'homology threshold'.
 MS_Mascot_identity_threshold = 1001371
 Mascot:identity threshold: The Mascot result 'identity threshold'.
 MS_Sequest_Sequences = 1001372
 Sequest:Sequences:
 MS_Sequest_TIC = 1001373
 Sequest:TIC:
 MS_Sequest_Sum = 1001374
 Sequest:Sum:
 MS_Phenyx_Instrument_Type = 1001375
 Phenyx:Instrument Type:
 MS_Phenyx_Scoring_Model = 1001376
 Phenyx:Scoring Model:
 MS_Phenyx_Default_Parent_Charge = 1001377
 Phenyx:Default Parent Charge:
 MS_Phenyx_Trust_Parent_Charge = 1001378
 Phenyx:Trust Parent Charge:
 MS_Phenyx_Turbo = 1001379
 Phenyx:Turbo:
 MS_Phenyx_Turbo_ErrorTol = 1001380
 Phenyx:Turbo:ErrorTol:
 MS_Phenyx_Turbo_Coverage = 1001381
 Phenyx:Turbo:Coverage:
 MS_Phenyx_Turbo_Series = 1001382
 Phenyx:Turbo:Series:
 MS_Phenyx_MinPepLength = 1001383
 Phenyx:MinPepLength:
 MS_Phenyx_MinPepzscore = 1001384
 Phenyx:MinPepzscore:
 MS_Phenyx_MaxPepPvalue = 1001385
 Phenyx:MaxPepPvalue:
 MS_Phenyx_AC_Score = 1001386
 Phenyx:AC Score:
 MS_Phenyx_Conflict_Resolution = 1001387
 Phenyx:Conflict Resolution:
 MS_Phenyx_AC = 1001388
 Phenyx:AC:
 MS_Phenyx_ID = 1001389
 Phenyx:ID:
 MS_Phenyx_Score = 1001390
 Phenyx:Score:
 MS_Phenyx_Peptides1 = 1001391
 Phenyx:Peptides1: First number of phenyx result "#Peptides".
 MS_Phenyx_Peptides2 = 1001392
 Phenyx:Peptides2: Second number of phenyx result "#Peptides".
 MS_Phenyx_Auto = 1001393
 Phenyx:Auto:
 MS_Phenyx_User = 1001394
 Phenyx:User:
 MS_Phenyx_Pepzscore = 1001395
 Phenyx:Pepzscore:
 MS_Phenyx_PepPvalue = 1001396
 Phenyx:PepPvalue:
 MS_Phenyx_NumberOfMC = 1001397
 Phenyx:NumberOfMC:
 MS_Phenyx_Modif = 1001398
 Phenyx:Modif:
 MS_OMSSA_csv_file = 1001399
 OMSSA csv file: Source file for this mzIdentML was an OMSSA csv file.
 MS_OMSSA_xml_file = 1001400
 OMSSA xml file: Source file for this mzIdentML was an OMSSA xml file.
 MS_X_Tandem_xml_file = 1001401
 X!Tandem xml file: Source file for this mzIdentML was an X!Tandem xml file.
 MS_spectrum_identification_result_details = 1001405
 spectrum identification result details: This subsection describes terms which can describe details of spectrum identification results.
 MS_param__internal_yb_ion = 1001406
 param: internal yb ion:
 MS_param__internal_ya_ion = 1001407
 param: internal ya ion:
 MS_param__z_1_ion = 1001408
 param: z+1 ion:
 MS_param__z_2_ion = 1001409
 param: z+2 ion:
 MS_translation_start_codons = 1001410
 translation start codons: The translation start codons used to translate the nucleotides to amino acids.
 MS_search_tolerance_specification = 1001411
 search tolerance specification:
 MS_search_tolerance_plus_value = 1001412
 search tolerance plus value:
 MS_search_tolerance_minus_value = 1001413
 search tolerance minus value:
 MS_MGF_scans_OBSOLETE = 1001414
 MGF scans: OBSOLETE: replaced by MS:1000797 (peak list scans): This term can hold the scans attribute from an MGF input file.
 MS_MGF_raw_scans_OBSOLETE = 1001415
 MGF raw scans: OBSOLETE: replaced by MS:1000798 (peak list raw scans): This term can hold the raw scans attribute from an MGF input file.
 MS_spectrum_title_OBSOLETE = 1001416
 spectrum title: OBSOLETE: replaced by MS:1000796 (spectrum title): Holds the spectrum title from different input file formats, e.g. MGF TITLE.
 MS_SpectraST_dot = 1001417
 SpectraST:dot: SpectraST dot product of two spectra, measuring spectral similarity.
 MS_SpectraST_dot_bias = 1001418
 SpectraST:dot_bias: SpectraST measure of how much of the dot product is dominated by a few peaks.
 MS_SpectraST_discriminant_score_F = 1001419
 SpectraST:discriminant score F: SpectraST spectrum score.
 MS_SpectraST_delta = 1001420
 SpectraST:delta: SpectraST normalised difference between dot product of top hit and runner-up.
 MS_pepXML_file = 1001421
 pepXML file: Source file for this mzIdentML was a pepXML file.
 MS_protXML_file = 1001422
 protXML file: Source file for this mzIdentML was a protXML file.
 MS_translation_table_description = 1001423
 translation table description: A URL that describes the translation table used to translate the nucleotides to amino acids.
 MS_ProteinExtractor_Methodname = 1001424
 ProteinExtractor:Methodname:
 MS_ProteinExtractor_GenerateNonRedundant = 1001425
 ProteinExtractor:GenerateNonRedundant:
 MS_ProteinExtractor_IncludeIdentified = 1001426
 ProteinExtractor:IncludeIdentified:
 MS_ProteinExtractor_MaxNumberOfProteins = 1001427
 ProteinExtractor:MaxNumberOfProteins:
 MS_ProteinExtractor_MaxProteinMass = 1001428
 ProteinExtractor:MaxProteinMass:
 MS_ProteinExtractor_MinNumberOfPeptides = 1001429
 ProteinExtractor:MinNumberOfPeptides:
 MS_ProteinExtractor_UseMascot = 1001430
 ProteinExtractor:UseMascot:
 MS_ProteinExtractor_MascotPeptideScoreThreshold = 1001431
 ProteinExtractor:MascotPeptideScoreThreshold:
 MS_ProteinExtractor_MascotUniqueScore = 1001432
 ProteinExtractor:MascotUniqueScore:
 MS_ProteinExtractor_MascotUseIdentityScore = 1001433
 ProteinExtractor:MascotUseIdentityScore:
 MS_ProteinExtractor_MascotWeighting = 1001434
 ProteinExtractor:MascotWeighting:
 MS_ProteinExtractor_UseSequest = 1001435
 ProteinExtractor:UseSequest:
 MS_ProteinExtractor_SequestPeptideScoreThreshold = 1001436
 ProteinExtractor:SequestPeptideScoreThreshold:
 MS_ProteinExtractor_SequestUniqueScore = 1001437
 ProteinExtractor:SequestUniqueScore:
 MS_ProteinExtractor_SequestWeighting = 1001438
 ProteinExtractor:SequestWeighting:
 MS_ProteinExtractor_UseProteinSolver = 1001439
 ProteinExtractor:UseProteinSolver:
 MS_ProteinExtractor_ProteinSolverPeptideScoreThreshold = 1001440
 ProteinExtractor:ProteinSolverPeptideScoreThreshold:
 MS_ProteinExtractor_ProteinSolverUniqueScore = 1001441
 ProteinExtractor:ProteinSolverUniqueScore:
 MS_ProteinExtractor_ProteinSolverWeighting = 1001442
 ProteinExtractor:ProteinSolverWeighting:
 MS_ProteinExtractor_UsePhenyx = 1001443
 ProteinExtractor:UsePhenyx:
 MS_ProteinExtractor_PhenyxPeptideScoreThreshold = 1001444
 ProteinExtractor:PhenyxPeptideScoreThreshold:
 MS_ProteinExtractor_PhenyxUniqueScore = 1001445
 ProteinExtractor:PhenyxUniqueScore:
 MS_ProteinExtractor_PhenyxWeighting = 1001446
 ProteinExtractor:PhenyxWeighting:
 MS_prot_FDR_threshold = 1001447
 prot:FDR threshold: False-discovery rate threshold for proteins.
 MS_pep_FDR_threshold = 1001448
 pep:FDR threshold: False-discovery rate threshold for peptides.
 MS_OMSSA_e_value_threshold = 1001449
 OMSSA e-value threshold: Threshold for OMSSA e-value for quality estimation.
 MS_decoy_DB_details = 1001450
 decoy DB details: Details of decoy generation and database structure.
 MS_decoy_DB_generation_algorithm = 1001451
 decoy DB generation algorithm: Name of algorithm used for decoy generation.
 MS_decoy_DB_type_shuffle = 1001452
 decoy DB type shuffle: Decoy type: Amino acids of protein sequences are used in a random order.
 MS_DB_composition_only_decoy = 1001453
 DB composition only decoy: Decoy database composition: database contains only decoy entries.
 MS_quality_estimation_with_implicite_decoy_sequences = 1001454
 quality estimation with implicite decoy sequences: Decoy entries are generated during the search, not explicitly stored in a database (like Mascot Decoy).
 MS_acquisition_software = 1001455
 acquisition software: Acquisition software.
 MS_analysis_software = 1001456
 analysis software: Analysis software.
 MS_data_processing_software = 1001457
 data processing software: Conversion software.
 MS_spectrum_generation_information = 1001458
 spectrum generation information: Vocabularies describing the spectrum generation information.
 MS_file_format = 1001459
 file format: Format of data files.
 MS_unknown_modification = 1001460
 unknown modification: This term should be given if the modification was unknown.
 MS_greylag = 1001461
 greylag: Greylag identification software, see greylag.org.
 MS_PEFF_format = 1001462
 PEFF format: The sequence database was stored in the PEFF (PSI enhanced FastA file) format.
 MS_Phenyx_XML_format = 1001463
 Phenyx XML format:
 MS_DTASelect_file = 1001464
 DTASelect file:
 MS_MS2_file = 1001466
 MS2 file: MS2 file.
 MS_taxonomy__NCBI_TaxID = 1001467
 taxonomy: NCBI TaxID: This term is used if a NCBI TaxID is specified, e.g. 9606 for Homo sapiens.
 MS_taxonomy__common_name = 1001468
 taxonomy: common name: This term is used if a common name is specified, e.g. human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible.
 MS_taxonomy__scientific_name = 1001469
 taxonomy: scientific name: This term is used if a scientific name is specified, e.g. Homo sapiens. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible.
 MS_taxonomy__Swiss_Prot_ID = 1001470
 taxonomy: Swiss-Prot ID: This term is used if a swiss prot taxonomy id is specified, e.g. Human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible.
 MS_peptide_modification_details = 1001471
 peptide modification details: The children of this term can be used to describe modifications.
 MS_selected_ion_monitoring_chromatogram = 1001472
 selected ion monitoring chromatogram: Chromatogram created by creating an array of the measurements of a selectively monitored ion at each time point.
 MS_SIM_chromatogram = MS_selected_ion_monitoring_chromatogram
 SIM chromatogram (selected ion monitoring chromatogram): Chromatogram created by creating an array of the measurements of a selectively monitored ion at each time point.
 MS_selected_reaction_monitoring_chromatogram = 1001473
 selected reaction monitoring chromatogram: Chromatogram created by creating an array of the measurements of a selectively monitored reaction at each time point.
 MS_SRM_chromatogram = MS_selected_reaction_monitoring_chromatogram
 SRM chromatogram (selected reaction monitoring chromatogram): Chromatogram created by creating an array of the measurements of a selectively monitored reaction at each time point.
 MS_consecutive_reaction_monitoring_chromatogram_OBSOLETE = 1001474
 consecutive reaction monitoring chromatogram: Chromatogram created by creating an array of the measurements of a series of monitored reactions at each time point.
 MS_CRM_chromatogram_OBSOLETE = MS_consecutive_reaction_monitoring_chromatogram_OBSOLETE
 CRM chromatogram (consecutive reaction monitoring chromatogram): Chromatogram created by creating an array of the measurements of a series of monitored reactions at each time point.
 MS_OMSSA = 1001475
 OMSSA: Open Mass Spectrometry Search Algorithm was used to analyze the spectra.
 MS_X_Tandem = 1001476
 X!Tandem: X!Tandem was used to analyze the spectra.
 MS_SpectraST = 1001477
 SpectraST: SpectraST was used to analyze the spectra.
 MS_Mascot_Parser = 1001478
 Mascot Parser: Mascot Parser was used to analyze the spectra.
 MS_null_terminated_ASCII_string = 1001479
 null-terminated ASCII string: Sequence of zero or more non-zero ASCII characters terminated by a single null (0) byte.
 MS_AB_SCIEX_TOF_TOF_nativeID_format = 1001480
 AB SCIEX TOF/TOF nativeID format: jobRun=xsd:nonNegativeInteger spotLabel=xsd:string spectrum=xsd:nonNegativeInteger.
 MS_AB_SCIEX_TOF_TOF_database = 1001481
 AB SCIEX TOF/TOF database: Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument database.
 MS_TOF_TOF_5800 = 1001482
 TOF/TOF 5800: AB SCIEX or Applied Biosystems|MDS Analytical Technologies AB SCIEX TOF/TOF 5800 Analyzer.
 MS_AB_SCIEX_TOF_TOF_Series_Explorer_Software = 1001483
 AB SCIEX TOF/TOF Series Explorer Software: AB SCIEX or Applied Biosystems software for TOF/TOF data acquisition and analysis.
 MS_intensity_normalization = 1001484
 intensity normalization: Normalization of data point intensities.
 MS_m_z_calibration = 1001485
 m/z calibration: Calibration of data point m/z positions.
 MS_data_filtering = 1001486
 data filtering: Filtering out part of the data.
 MS_ProteinExtractor = 1001487
 ProteinExtractor: An algorithm for protein determination/assembly integrated into Bruker's ProteinScape.
 MS_Mascot_Distiller = 1001488
 Mascot Distiller: Mascot Distiller.
 MS_Mascot_Integra = 1001489
 Mascot Integra: Mascot Integra.
 MS_Percolator = 1001490
 Percolator: Percolator.
 MS_percolator_Q_value = 1001491
 percolator:Q value: Percolator:Q value.
 MS_percolator_score = 1001492
 percolator:score: Percolator:score.
 MS_percolator_PEP = 1001493
 percolator:PEP: Posterior error probability.
 MS_no_threshold = 1001494
 no threshold: In case no threshold was used.
 MS_ProteinScape_SearchResultId = 1001495
 ProteinScape:SearchResultId: The SearchResultId of this peptide as SearchResult in the ProteinScape database.
 MS_ProteinScape_SearchEventId = 1001496
 ProteinScape:SearchEventId: The SearchEventId of the SearchEvent in the ProteinScape database.
 MS_ProteinScape_ProfoundProbability = 1001497
 ProteinScape:ProfoundProbability: The Profound probability score stored by ProteinScape.
 MS_Profound_z_value = 1001498
 Profound:z value: The Profound z value.
 MS_Profound_Cluster = 1001499
 Profound:Cluster: The Profound cluster score.
 MS_Profound_ClusterRank = 1001500
 Profound:ClusterRank: The Profound cluster rank.
 MS_MSFit_Mowse_score = 1001501
 MSFit:Mowse score: The MSFit Mowse score.
 MS_Sonar_Score = 1001502
 Sonar:Score: The Sonar score.
 MS_ProteinScape_PFFSolverExp = 1001503
 ProteinScape:PFFSolverExp: The ProteinSolver exp value stored by ProteinScape.
 MS_ProteinScape_PFFSolverScore = 1001504
 ProteinScape:PFFSolverScore: The ProteinSolver score stored by ProteinScape.
 MS_ProteinScape_IntensityCoverage = 1001505
 ProteinScape:IntensityCoverage: The intensity coverage of the identified peaks in the spectrum calculated by ProteinScape.
 MS_ProteinScape_SequestMetaScore = 1001506
 ProteinScape:SequestMetaScore: The Sequest meta score calculated by ProteinScape from the original Sequest scores.
 MS_ProteinExtractor_Score = 1001507
 ProteinExtractor:Score: The score calculated by ProteinExtractor.
 MS_Agilent_MassHunter_nativeID_format = 1001508
 Agilent MassHunter nativeID format: scanId=xsd:nonNegativeInteger.
 MS_Agilent_MassHunter_file = 1001509
 Agilent MassHunter file: A data file found in an Agilent MassHunter directory which contains raw data acquired by an Agilent mass spectrometer.
 MS_TSQ_Vantage = 1001510
 TSQ Vantage: TSQ Vantage.
 MS_Sequence_database_filter_types = 1001511
 Sequence database filter types: Filter types which are used to filter a sequence database.
 MS_Sequence_database_filters = 1001512
 Sequence database filters: Sequence database filters which actually can contains values, e.g. to limit PI value of the sequences used to search.
 MS_DB_sequence_filter_pattern = 1001513
 DB sequence filter pattern:
 MS_DB_accession_filter_string = 1001514
 DB accession filter string:
 MS_frag__c_ion___H2O = 1001515
 frag: c ion - H2O: Fragmentation information, type of product: c ion without water.
 MS_frag__c_ion___NH3 = 1001516
 frag: c ion - NH3: Fragmentation information, type of product: c ion without ammonia.
 MS_frag__z_ion___H2O = 1001517
 frag: z ion - H2O: Fragmentation information, type of product: z ion without water.
 MS_frag__z_ion___NH3 = 1001518
 frag: z ion - NH3: Fragmentation information, type of product: z ion without ammonia.
 MS_frag__x_ion___H2O = 1001519
 frag: x ion - H2O: Fragmentation information, type of product: x ion without water.
 MS_frag__x_ion___NH3 = 1001520
 frag: x ion - NH3: Fragmentation information, type of product: x ion without ammonia.
 MS_frag__precursor_ion___H2O = 1001521
 frag: precursor ion - H2O: Fragmentation information, type of product: precursor ion without water.
 MS_frag__precursor_ion___NH3 = 1001522
 frag: precursor ion - NH3: Fragmentation information, type of product: precursor ion without ammonia.
 MS_frag__precursor_ion = 1001523
 frag: precursor ion: Fragmentation information, type of product: precursor ion.
 MS_fragment_neutral_loss = 1001524
 fragment neutral loss: This term can describe a neutral loss m/z value that is lost from an ion.
 MS_precursor_neutral_loss = 1001525
 precursor neutral loss: This term can describe a neutral loss m/z value that is lost from an ion.
 MS_spectrum_from_database_integer_nativeID_format = 1001526
 spectrum from database integer nativeID format: databasekey=xsd:long.
 MS_Proteinscape_spectra = 1001527
 Proteinscape spectra: Spectra from Bruker/Protagen Proteinscape database.
 MS_Mascot_query_number = 1001528
 Mascot query number: query=xsd:nonNegativeInteger.
 MS_spectra_data_details = 1001529
 spectra data details: Child-terms contain information to map the results back to spectra.
 MS_mzML_unique_identifier = 1001530
 mzML unique identifier: mzMLid=xsd:IDREF.
 MS_spectrum_from_ProteinScape_database_nativeID_format = 1001531
 spectrum from ProteinScape database nativeID format: databasekey=xsd:long.
 MS_spectrum_from_database_string_nativeID_format = 1001532
 spectrum from database string nativeID format: databasekey=xsd:string.
 MS_Bruker_Daltonics_esquire_series = 1001533
 Bruker Daltonics esquire series:
 MS_Bruker_Daltonics_flex_series = 1001534
 Bruker Daltonics flex series:
 MS_Bruker_Daltonics_BioTOF_series = 1001535
 Bruker Daltonics BioTOF series:
 MS_Bruker_Daltonics_micrOTOF_series = 1001536
 Bruker Daltonics micrOTOF series:
 MS_BioTOF = 1001537
 BioTOF: Bruker Daltonics' BioTOF: ESI TOF.
 MS_BioTOF_III = 1001538
 BioTOF III: Bruker Daltonics' BioTOF III: ESI TOF.
 MS_UltroTOF_Q = 1001539
 UltroTOF-Q: Bruker Daltonics' UltroTOF-Q: ESI Q-TOF (MALDI optional).
 MS_micrOTOF_II = 1001540
 micrOTOF II: Bruker Daltonics' micrOTOF II: ESI TOF, Nanospray, APCI, APPI.
 MS_maXis = 1001541
 maXis: Bruker Daltonics' maXis: ESI Q-TOF, Nanospray, APCI, APPI.
 MS_amaZon_ETD = 1001542
 amaZon ETD: Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR.
 MS_microflex_LRF = 1001543
 microflex LRF: Bruker Daltonics' microflex LRF: MALDI TOF.
 MS_ultrafleXtreme = 1001544
 ultrafleXtreme: Bruker Daltonics' ultrafleXtreme: MALDI TOF.
 MS_Bruker_Daltonics_amaZon_series = 1001545
 Bruker Daltonics amaZon series:
 MS_amaZon_X = 1001546
 amaZon X: Bruker Daltonics' amaZon X: ESI quadrupole ion trap, APCI, APPI, ETD, PTR.
 MS_Bruker_Daltonics_maXis_series = 1001547
 Bruker Daltonics maXis series:
 MS_Bruker_Daltonics_solarix_series = 1001548
 Bruker Daltonics solarix series: Bruker Daltonics' solarix: ESI quadrupole ion trap, APCI, APPI, ETD, PTR.
 MS_solariX = 1001549
 solariX: Bruker Daltonics' solariX: ESI, MALDI, Qh-FT_ICR.
 MS_microflex_II = 1001550
 microflex II: Bruker Daltonics' microflex II: MALDI TOF.
 MS_autoflex_II_TOF_TOF = 1001553
 autoflex II TOF/TOF: Bruker Daltonics' autoflex II TOF/TOF: MALDI TOF.
 MS_autoflex_III_TOF_TOF_smartbeam = 1001554
 autoflex III TOF/TOF smartbeam: Bruker Daltonics' autoflex III TOF/TOF smartbeam: MALDI TOF.
 MS_autoflex = 1001555
 autoflex: Bruker Daltonics' autoflex: MALDI TOF.
 MS_Bruker_Daltonics_apex_series = 1001556
 Bruker Daltonics apex series:
 MS_Shimadzu_Biotech_software = 1001557
 Shimadzu Biotech software:
 MS_MALDI_Solutions = 1001558
 MALDI Solutions: Shimadzu Biotech software for data acquisition, processing, and analysis.
 MS_AB_SCIEX_TOF_TOF_T2D_nativeID_format = 1001559
 AB SCIEX TOF/TOF T2D nativeID format: file=xsd:IDREF.
 MS_AB_SCIEX_TOF_TOF_T2D_file = 1001560
 AB SCIEX TOF/TOF T2D file: Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument export format.
 MS_Scaffold = 1001561
 Scaffold: Scaffold analysis software, see www.proteomesoftware.com.
 MS_Scaffold_nativeID_format = 1001562
 Scaffold nativeID format: Scaffold native ID format.
 MS_Sequest_SQT = 1001563
 Sequest SQT: Source file for this mzIdentML was a Sequest SQT.
 MS_Discoverer_MSF = 1001564
 Discoverer MSF: Source file for this mzIdentML was in Thermo Scientific Discoverer MSF format.
 MS_IdentityE_XML = 1001565
 IdentityE XML: Source file for this mzIdentML was in Waters IdentityE XML format.
 MS_ProteinLynx_XML = 1001566
 ProteinLynx XML: Source file for this mzIdentML was in Waters ProteinLynx XML format.
 MS_SpectrumMill_directories = 1001567
 SpectrumMill directories: Source file for this mzIdentML was in Agilent SpectrumMill directory format.
 MS_Scaffold_Peptide_Probability = 1001568
 Scaffold:Peptide Probability: Scaffold peptide probability score.
 MS_IdentityE_Score = 1001569
 IdentityE Score: Waters IdentityE peptide score.
 MS_ProteinLynx_Log_Likelihood = 1001570
 ProteinLynx:Log Likelihood: ProteinLynx log likelihood score.
 MS_ProteinLynx_Ladder_Score = 1001571
 ProteinLynx:Ladder Score: Waters ProteinLynx Ladder score.
 MS_SpectrumMill_Score = 1001572
 SpectrumMill:Score: Spectrum mill peptide score.
 MS_SpectrumMill_SPI = 1001573
 SpectrumMill:SPI: SpectrumMill SPI score (%).
 MS_report_only_spectra_assigned_to_identified_proteins = 1001574
 report only spectra assigned to identified proteins: .
 MS_Scaffold__Minimum_Peptide_Count = 1001575
 Scaffold: Minimum Peptide Count: Minimum number of peptides a protein must have to be accepted.
 MS_Scaffold__Minimum_Protein_Probability = 1001576
 Scaffold: Minimum Protein Probability: Minimum protein probability a protein must have to be accepted.
 MS_Scaffold__Minimum_Peptide_Probability = 1001577
 Scaffold: Minimum Peptide Probability: Minimum probability a peptide must have to be accepted for protein scoring.
 MS_minimum_number_of_enzymatic_termini = 1001578
 minimum number of enzymatic termini: Minimum number of enzymatic termini a pepide must have to be accepted.
 MS_Scaffold_Protein_Probability = 1001579
 Scaffold:Protein Probability: Scaffold protein probability score.
 MS_SpectrumMill_Discriminant_Score = 1001580
 SpectrumMill:Discriminant Score: Discriminant score from Agilent SpectrumMill software.
 MS_FAIMS_compensation_voltage = 1001581
 FAIMS compensation voltage: The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion.
 MS_FAIMS_CV = MS_FAIMS_compensation_voltage
 FAIMS CV (FAIMS compensation voltage): The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion.
 MS_XCMS = 1001582
 XCMS: Bioconductor package XCMS for preprocessing high-throughput, untargeted analyte profiling data.
 MS_MaxQuant = 1001583
 MaxQuant: MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. It is specifically aimed at high resolution MS data.
 MS_combined_pmf___ms_ms_search = 1001584
 combined pmf + ms-ms search: Search that includes data from Peptide Mass Fingerprint (PMF) and MS/MS (aka Peptide Fragment Fingerprint - PFF).
 MS_MyriMatch = 1001585
 MyriMatch: Tabb Lab software for directly comparing peptides in a database to tandem mass spectra.
 MS_DirecTag = 1001586
 DirecTag: Tabb Lab software for generating sequence tags from tandem mass spectra.
 MS_TagRecon = 1001587
 TagRecon: Tabb Lab software for reconciling sequence tags to a protein database.
 MS_Pepitome = 1001588
 Pepitome: Tabb Lab software for spectral library searches on tandem mass spectra.
 MS_MyriMatch_MVH = 1001589
 MyriMatch:MVH: Using the multivariate hypergeometric distribution and a peak list divided into several intensity classes, this score is the negative natural log probability that the predicted peaks matched to experimental peaks by random chance.
 MS_Pepitome_MVH = MS_MyriMatch_MVH
 Pepitome:MVH (MyriMatch:MVH): Using the multivariate hypergeometric distribution and a peak list divided into several intensity classes, this score is the negative natural log probability that the predicted peaks matched to experimental peaks by random chance.
 MS_TagRecon_MVH = MS_MyriMatch_MVH
 TagRecon:MVH (MyriMatch:MVH): Using the multivariate hypergeometric distribution and a peak list divided into several intensity classes, this score is the negative natural log probability that the predicted peaks matched to experimental peaks by random chance.
 MS_MyriMatch_mzFidelity = 1001590
 MyriMatch:mzFidelity: The negative natural log probability that predicted peaks match to experimental peaks by random chance by scoring the m/z delta of the matches in a multinomial distribution.
 MS_Pepitome_mzFidelity = MS_MyriMatch_mzFidelity
 Pepitome:mzFidelity (MyriMatch:mzFidelity): The negative natural log probability that predicted peaks match to experimental peaks by random chance by scoring the m/z delta of the matches in a multinomial distribution.
 MS_TagRecon_mzFidelity = MS_MyriMatch_mzFidelity
 TagRecon:mzFidelity (MyriMatch:mzFidelity): The negative natural log probability that predicted peaks match to experimental peaks by random chance by scoring the m/z delta of the matches in a multinomial distribution.
 MS_anchor_protein = 1001591
 anchor protein: A representative protein selected from a set of sequence same-set or spectrum same-set proteins.
 MS_family_member_protein = 1001592
 family member protein: A protein with significant homology to another protein, but some distinguishing peptide matches.
 MS_group_member_with_undefined_relationship_OR_ortholog_protein = 1001593
 group member with undefined relationship OR ortholog protein: TO ENDETAIL: a really generic relationship OR ortholog protein.
 MS_sequence_same_set_protein = 1001594
 sequence same-set protein: A protein which is indistinguishable or equivalent to another protein, having matches to an identical set of peptide sequences.
 MS_spectrum_same_set_protein = 1001595
 spectrum same-set protein: A protein which is indistinguishable or equivalent to another protein, having matches to a set of peptide sequences that cannot be distinguished using the evidence in the mass spectra.
 MS_sequence_sub_set_protein = 1001596
 sequence sub-set protein: A protein with a sub-set of the peptide sequence matches for another protein, and no distinguishing peptide matches.
 MS_spectrum_sub_set_protein = 1001597
 spectrum sub-set protein: A protein with a sub-set of the matched spectra for another protein, where the matches cannot be distinguished using the evidence in the mass spectra, and no distinguishing peptide matches.
 MS_sequence_subsumable_protein = 1001598
 sequence subsumable protein: A sequence same-set or sequence sub-set protein where the matches are distributed across two or more proteins.
 MS_spectrum_subsumable_protein = 1001599
 spectrum subsumable protein: A spectrum same-set or spectrum sub-set protein where the matches are distributed across two or more proteins.
 MS_Protein_Inference_Confidence_Category = 1001600
 Protein Inference Confidence Category: Confidence category of inferred protein (conclusive, non conclusive, ambiguous group or indistinguishable).
 MS_ProteomeDiscoverer_Spectrum_Files_Raw_File_names_OBSOLETE = 1001601
 ProteomeDiscoverer:Spectrum Files:Raw File names: Name and location of the .raw file or files.
 MS_ProteomeDiscoverer_SRF_File_Selector_SRF_File_Path_OBSOLETE = 1001602
 ProteomeDiscoverer:SRF File Selector:SRF File Path: Path and name of the .srf (Sequest Result Format) file.
 MS_ProteomeDiscoverer_Spectrum_Selector_Ionization_Source_OBSOLETE = 1001603
 ProteomeDiscoverer:Spectrum Selector:Ionization Source: Ionization source (electro-, nano-, thermospray, electron impact, APCI, MALDI, FAB etc).
 MS_ProteomeDiscoverer_Activation_Type_OBSOLETE = 1001604
 ProteomeDiscoverer:Activation Type: Fragmentation method used (CID, MPD, ECD, PQD, ETD, HCD, Any).
 MS_ProteomeDiscoverer_Spectrum_Selector_Lower_RT_Limit = 1001605
 ProteomeDiscoverer:Spectrum Selector:Lower RT Limit: Lower retention-time limit.
 MS_ProteomeDiscoverer_Mass_Analyzer_OBSOLETE = 1001606
 ProteomeDiscoverer:Mass Analyzer: Type of mass spectrometer used (ITMS, FTMS, TOFMS, SQMS, TQMS, SectorMS).
 MS_ProteomeDiscoverer_Max_Precursor_Mass = 1001607
 ProteomeDiscoverer:Max Precursor Mass: Maximum mass limit of a singly charged precursor ion.
 MS_ProteomeDiscoverer_Min_Precursor_Mass = 1001608
 ProteomeDiscoverer:Min Precursor Mass: Minimum mass limit of a singly charged precursor ion.
 MS_ProteomeDiscoverer_Minimum_Peak_Count = 1001609
 ProteomeDiscoverer:Minimum Peak Count: Minimum number of peaks in a tandem mass spectrum that is allowed to pass the filter and to be subjected to further processing in the workflow.
 MS_ProteomeDiscoverer_MS_Order_OBSOLETE = 1001610
 ProteomeDiscoverer:MS Order: Level of the mass spectrum (MS/MS=MS2 ... MS10).
 MS_ProteomeDiscoverer_Polarity_Mode_OBSOLETE = 1001611
 ProteomeDiscoverer:Polarity Mode: Polarity mode (positive or negative).
 MS_ProteomeDiscoverer_Spectrum_Selector_Precursor_Selection = 1001612
 ProteomeDiscoverer:Spectrum Selector:Precursor Selection: Determines which precursor mass to use for a given MSn scan. This option applies only to higher-order MSn scans (n >= 3).
 MS_ProteomeDiscoverer_SN_Threshold = 1001613
 ProteomeDiscoverer:SN Threshold: Signal-to-Noise ratio below which peaks are removed.
 MS_ProteomeDiscoverer_Scan_Type_OBSOLETE = 1001614
 ProteomeDiscoverer:Scan Type: Scan type for the precursor ion (full, Single Ion Monitoring (SIM), Single Reaction Monitoring (SRM)).
 MS_ProteomeDiscoverer_Total_Intensity_Threshold = 1001615
 ProteomeDiscoverer:Total Intensity Threshold: Used to filter out tandem mass spectra that have a total intensity current(sum of the intensities of all peaks in a spectrum) below the specified value.
 MS_ProteomeDiscoverer_Spectrum_Selector_Unrecognized_Activation_Type_Replacements = 1001616
 ProteomeDiscoverer:Spectrum Selector:Unrecognized Activation Type Replacements: Specifies the fragmentation method to use in the search algorithm if it is not included in the scan header.
 MS_ProteomeDiscoverer_Spectrum_Selector_Unrecognized_Charge_Replacements = 1001617
 ProteomeDiscoverer:Spectrum Selector:Unrecognized Charge Replacements: Specifies the charge state of the precursor ions, if it is not defined in the scan header.
 MS_ProteomeDiscoverer_Spectrum_Selector_Unrecognized_Mass_Analyzer_Replacements = 1001618
 ProteomeDiscoverer:Spectrum Selector:Unrecognized Mass Analyzer Replacements: Specifies the mass spectrometer to use to produce the spectra, if it is not included in the scan header.
 MS_ProteomeDiscoverer_Spectrum_Selector_Unrecognized_MS_Order_Replacements = 1001619
 ProteomeDiscoverer:Spectrum Selector:Unrecognized MS Order Replacements: Specifies the MS scan order used to produce the product spectra, if it is not included in the scan header.
 MS_ProteomeDiscoverer_Spectrum_Selector_Unrecognized_Polarity_Replacements = 1001620
 ProteomeDiscoverer:Spectrum Selector:Unrecognized Polarity Replacements: Specifies the polarity of the ions monitored if it is not included in the scan header.
 MS_ProteomeDiscoverer_Spectrum_Selector_Upper_RT_Limit = 1001621
 ProteomeDiscoverer:Spectrum Selector:Upper RT Limit: Upper retention-time limit.
 MS_ProteomeDiscoverer_Non_Fragment_Filter_Mass_Window_Offset = 1001622
 ProteomeDiscoverer:Non-Fragment Filter:Mass Window Offset: Specifies the size of the mass-to-charge ratio (m/z) window in daltons used to remove precursors.
 MS_ProteomeDiscoverer_Non_Fragment_Filter_Maximum_Neutral_Loss_Mass = 1001623
 ProteomeDiscoverer:Non-Fragment Filter:Maximum Neutral Loss Mass: Maximum allowed mass of a neutral loss.
 MS_ProteomeDiscoverer_Non_Fragment_Filter_Remove_Charge_Reduced_Precursor = 1001624
 ProteomeDiscoverer:Non-Fragment Filter:Remove Charge Reduced Precursor: Determines whether the charge-reduced precursor peaks found in an ETD or ECD spectrum are removed.
 MS_ProteomeDiscoverer_Non_Fragment_Filter_Remove_Neutral_Loss_Peaks = 1001625
 ProteomeDiscoverer:Non-Fragment Filter:Remove Neutral Loss Peaks: Determines whether neutral loss peaks are removed from ETD and ECD spectra.
 MS_ProteomeDiscoverer_Non_Fragment_Filter_Remove_Only_Known_Masses = 1001626
 ProteomeDiscoverer:Non-Fragment Filter:Remove Only Known Masses: Determines whether overtone peaks are removed from LTQ FT or LTQ FT Ultra ECD spectra.
 MS_ProteomeDiscoverer_Non_Fragment_Filter_Remove_Precursor_Overtones = 1001627
 ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Overtones: Determines whether precursor overtone peaks in the spectrum are removed from the input spectrum.
 MS_ProteomeDiscoverer_Non_Fragment_Filter_Remove_Precursor_Peak = 1001628
 ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Peak: Determines whether precursor artifact peaks from the MS/MS input spectra are removed.
 MS_ProteomeDiscoverer_Spectrum_Grouper_Allow_Mass_Analyzer_Mismatch = 1001629
 ProteomeDiscoverer:Spectrum Grouper:Allow Mass Analyzer Mismatch: Determines whether the fragment spectrum for scans with the same precursor mass is grouped, regardless of mass analyzer and activation type.
 MS_ProteomeDiscoverer_Spectrum_Grouper_Allow_MS_Order_Mismatch = 1001630
 ProteomeDiscoverer:Spectrum Grouper:Allow MS Order Mismatch: Determines whether spectra from different MS order scans can be grouped together.
 MS_ProteomeDiscoverer_Spectrum_Grouper_Max_RT_Difference_OBSOLETE = 1001631
 ProteomeDiscoverer:Spectrum Grouper:Max RT Difference: Chromatographic window where precursors to be grouped must reside to be considered the same species.
 MS_ProteomeDiscoverer_Spectrum_Grouper_Precursor_Mass_Criterion = 1001632
 ProteomeDiscoverer:Spectrum Grouper:Precursor Mass Criterion: Groups spectra measured within the given mass and retention-time tolerances into a single spectrum for analysis.
 MS_ProteomeDiscoverer_Xtract_Highest_Charge = 1001633
 ProteomeDiscoverer:Xtract:Highest Charge: Highest charge state that is allowed for the deconvolution of multiply charged data.
 MS_ProteomeDiscoverer_Xtract_Highest_MZ_OBSOLETE = 1001634
 ProteomeDiscoverer:Xtract:Highest MZ: Highest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract.
 MS_ProteomeDiscoverer_Xtract_Lowest_Charge = 1001635
 ProteomeDiscoverer:Xtract:Lowest Charge: Lowest charge state that is allowed for the deconvolution of multiply charged data.
 MS_ProteomeDiscoverer_Xtract_Lowest_MZ_OBSOLETE = 1001636
 ProteomeDiscoverer:Xtract:Lowest MZ: Lowest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract.
 MS_ProteomeDiscoverer_Xtract_Monoisotopic_Mass_Only = 1001637
 ProteomeDiscoverer:Xtract:Monoisotopic Mass Only: Determines whether the isotopic pattern, i.e. all isotopes of a mass are removed from the spectrum.
 MS_ProteomeDiscoverer_Xtract_Overlapping_Remainder = 1001638
 ProteomeDiscoverer:Xtract:Overlapping Remainder: Fraction of the more abundant peak that an overlapping multiplet must exceed in order to be processed (deconvoluted).
 MS_ProteomeDiscoverer_Xtract_Required_Fitting_Accuracy = 1001639
 ProteomeDiscoverer:Xtract:Required Fitting Accuracy: Accuracy required for a pattern fit to be considered valid.
 MS_ProteomeDiscoverer_Xtract_Resolution_At_400 = 1001640
 ProteomeDiscoverer:Xtract:Resolution At 400: Resolution at mass 400.
 MS_ProteomeDiscoverer_Lowest_Charge_State = 1001641
 ProteomeDiscoverer:Lowest Charge State: Minimum charge state below which peptides are filtered out.
 MS_ProteomeDiscoverer_Highest_Charge_State = 1001642
 ProteomeDiscoverer:Highest Charge State: Maximum charge above which peptides are filtered out.
 MS_ProteomeDiscoverer_Spectrum_Score_Filter_Let_Pass_Above_Scores = 1001643
 ProteomeDiscoverer:Spectrum Score Filter:Let Pass Above Scores: Determines whether spectra with scores above the threshold score are retained rather than filtered out.
 MS_ProteomeDiscoverer_Dynamic_Modifications = 1001644
 ProteomeDiscoverer:Dynamic Modifications: Determine dynamic post-translational modifications (PTMs).
 MS_ProteomeDiscoverer_Static_Modifications = 1001645
 ProteomeDiscoverer:Static Modifications: Static Modification to all occurrences of a named amino acid.
 MS_ProteomeDiscoverer_Mascot_Decoy_Search_OBSOLETE = 1001646
 ProteomeDiscoverer:Mascot:Decoy Search: Determines whether the Proteome Discoverer application searches an additional decoy database.
 MS_ProteomeDiscoverer_Mascot_Error_tolerant_Search = 1001647
 ProteomeDiscoverer:Mascot:Error tolerant Search: Determines whether to search error-tolerant.
 MS_ProteomeDiscoverer_Mascot_Max_MGF_File_Size = 1001648
 ProteomeDiscoverer:Mascot:Max MGF File Size: Maximum size of the .mgf (Mascot Generic Format) file in MByte.
 MS_ProteomeDiscoverer_Mascot_Mascot_Server_URL = 1001649
 ProteomeDiscoverer:Mascot:Mascot Server URL: URL (Uniform resource Locator) of the Mascot server.
 MS_ProteomeDiscoverer_Mascot_Number_of_attempts_to_submit_the_search = 1001650
 ProteomeDiscoverer:Mascot:Number of attempts to submit the search: Number of attempts to submit the Mascot search.
 MS_ProteomeDiscoverer_Mascot_X_Static_Modification = 1001651
 ProteomeDiscoverer:Mascot:X Static Modification: Number of attempts to submit the Mascot search.
 MS_ProteomeDiscoverer_Mascot_User_Name_OBSOLETE = 1001652
 ProteomeDiscoverer:Mascot:User Name: Name of the user submitting the Mascot search.
 MS_ProteomeDiscoverer_Mascot_Time_interval_between_attempts_to_submit_a_search = 1001653
 ProteomeDiscoverer:Mascot:Time interval between attempts to submit a search: Time interval between attempts to submit a search in seconds.
 MS_ProteomeDiscoverer_Enzyme_Name_OBSOLETE = 1001654
 ProteomeDiscoverer:Enzyme Name: Specifies the enzyme reagent used for protein digestion.
 MS_ProteomeDiscoverer_Fragment_Mass_Tolerance_OBSOLETE = 1001655
 ProteomeDiscoverer:Fragment Mass Tolerance: Mass tolerance used for matching fragment peaks in Da or mmu.
 MS_Mascot_Instrument = 1001656
 Mascot:Instrument: Type of instrument used to acquire the data in the raw file.
 MS_ProteomeDiscoverer_Maximum_Missed_Cleavage_Sites = 1001657
 ProteomeDiscoverer:Maximum Missed Cleavage Sites: Maximum number of missed cleavage sites to consider during the digest.
 MS_ProteomeDiscoverer_Mascot_Peptide_CutOff_Score = 1001658
 ProteomeDiscoverer:Mascot:Peptide CutOff Score: Minimum score in the IonScore column that each peptide must exceed in order to be reported.
 MS_ProteomeDiscoverer_Precursor_Mass_Tolerance_OBSOLETE = 1001659
 ProteomeDiscoverer:Precursor Mass Tolerance: Mass window for which precursor ions are considered to be the same species.
 MS_ProteomeDiscoverer_Mascot_Protein_CutOff_Score = 1001660
 ProteomeDiscoverer:Mascot:Protein CutOff Score: Minimum protein score in the IonScore column that each protein must exceed in order to be reported.
 MS_ProteomeDiscoverer_Protein_Database_OBSOLETE = 1001661
 ProteomeDiscoverer:Protein Database: Database to use in the search (configured on the Mascot server).
 MS_ProteomeDiscoverer_Mascot_Protein_Relevance_Factor = 1001662
 ProteomeDiscoverer:Mascot:Protein Relevance Factor: Specifies a factor that is used in calculating a threshold that determines whether a protein appears in the results report.
 MS_ProteomeDiscoverer_Target_FDR_Relaxed = 1001663
 ProteomeDiscoverer:Target FDR Relaxed: Specifies the relaxed target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with moderate confidence.
 MS_ProteomeDiscoverer_Target_FDR_Strict = 1001664
 ProteomeDiscoverer:Target FDR Strict: Specifies the strict target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with high confidence.
 MS_ProteomeDiscoverer_Mascot_Taxonomy_OBSOLETE = 1001665
 ProteomeDiscoverer:Mascot:Taxonomy: Limits searches to entries from a particular species or group of species.
 MS_ProteomeDiscoverer_Use_Average_Precursor_Mass_OBSOLETE = 1001666
 ProteomeDiscoverer:Use Average Precursor Mass: Use average mass for the precursor.
 MS_Mascot_use_MudPIT_scoring_OBSOLETE = 1001667
 Mascot:use MudPIT scoring: Determines whether to use MudPIT or normal scoring.
 MS_ProteomeDiscoverer_Absolute_XCorr_Threshold = 1001668
 ProteomeDiscoverer:Absolute XCorr Threshold: Minimum cross-correlation threshold that determines whether peptides in an .srf file are imported.
 MS_ProteomeDiscoverer_SEQUEST_Calculate_Probability_Score = 1001669
 ProteomeDiscoverer:SEQUEST:Calculate Probability Score: Determines whether to calculate a probability score for every peptide match.
 MS_ProteomeDiscoverer_SEQUEST_CTerminal_Modification = 1001670
 ProteomeDiscoverer:SEQUEST:CTerminal Modification: Dynamic C-terminal modification that is used during the search.
 MS_ProteomeDiscoverer_SEQUEST_Fragment_Ion_Cutoff_Percentage = 1001671
 ProteomeDiscoverer:SEQUEST:Fragment Ion Cutoff Percentage: Percentage of the theoretical ions that must be found in order for a peptide to be scored and retained.
 MS_ProteomeDiscoverer_SEQUEST_Max_Identical_Modifications_Per_Peptide = 1001672
 ProteomeDiscoverer:SEQUEST:Max Identical Modifications Per Peptide: Maximum number of identical modifications that a single peptide can have.
 MS_ProteomeDiscoverer_Max_Modifications_Per_Peptide = 1001673
 ProteomeDiscoverer:Max Modifications Per Peptide: Maximum number of different modifications that a peptide can have, e.g. because of steric hindrance.
 MS_ProteomeDiscoverer_SEQUEST_Maximum_Peptides_Considered = 1001674
 ProteomeDiscoverer:SEQUEST:Maximum Peptides Considered: Maximum number of peptides that are searched and scored per spectrum.
 MS_ProteomeDiscoverer_Maximum_Peptides_Output = 1001675
 ProteomeDiscoverer:Maximum Peptides Output: Maximum number of peptide matches reported per spectrum.
 MS_ProteomeDiscoverer_Maximum_Protein_References_Per_Peptide = 1001676
 ProteomeDiscoverer:Maximum Protein References Per Peptide: Maximum number of proteins that a single identified peptide can be associated with during protein assembly.
 MS_ProteomeDiscoverer_SEQUEST_NTerminal_Modification = 1001677
 ProteomeDiscoverer:SEQUEST:NTerminal Modification: Dynamic N-terminal modification that is used during the search.
 MS_ProteomeDiscoverer_Peptide_CTerminus = 1001678
 ProteomeDiscoverer:Peptide CTerminus: Static modification for the C terminal of the peptide used during the search.
 MS_ProteomeDiscoverer_Peptide_NTerminus = 1001679
 ProteomeDiscoverer:Peptide NTerminus: Static modification for the N terminal of the peptide used during the search.
 MS_ProteomeDiscoverer_SEQUEST_Peptide_Relevance_Factor = 1001680
 ProteomeDiscoverer:SEQUEST:Peptide Relevance Factor: Specifies a factor to apply to the protein score.
 MS_ProteomeDiscoverer_Protein_Relevance_Threshold = 1001681
 ProteomeDiscoverer:Protein Relevance Threshold: Specifies a peptide threshold that determines whether the protein that it is a part of is scored and retained in the report.
 MS_ProteomeDiscoverer_Search_Against_Decoy_Database_OBSOLETE = 1001682
 ProteomeDiscoverer:Search Against Decoy Database: Determines whether the Proteome Discoverer application searches against a decoy database.
 MS_ProteomeDiscoverer_SEQUEST_Use_Average_Fragment_Masses = 1001683
 ProteomeDiscoverer:SEQUEST:Use Average Fragment Masses: Use average masses for the fragments.
 MS_ProteomeDiscoverer_Use_Neutral_Loss_a_Ions = 1001684
 ProteomeDiscoverer:Use Neutral Loss a Ions: Determines whether a ions with neutral loss are used for spectrum matching.
 MS_ProteomeDiscoverer_Use_Neutral_Loss_b_Ions = 1001685
 ProteomeDiscoverer:Use Neutral Loss b Ions: Determines whether b ions with neutral loss are used for spectrum matching.
 MS_ProteomeDiscoverer_Use_Neutral_Loss_y_Ions = 1001686
 ProteomeDiscoverer:Use Neutral Loss y Ions: Determines whether y ions with neutral loss are used for spectrum matching.
 MS_ProteomeDiscoverer_Use_Neutral_Loss_z_Ions = 1001687
 ProteomeDiscoverer:Use Neutral Loss z Ions: Determines whether z ions with neutral loss are used for spectrum matching.
 MS_ProteomeDiscoverer_SEQUEST_Weight_of_a_Ions = 1001688
 ProteomeDiscoverer:SEQUEST:Weight of a Ions: Uses a ions for spectrum matching with this relative factor.
 MS_ProteomeDiscoverer_SEQUEST_Weight_of_b_Ions = 1001689
 ProteomeDiscoverer:SEQUEST:Weight of b Ions: Uses b ions for spectrum matching with this relative factor.
 MS_ProteomeDiscoverer_SEQUEST_Weight_of_c_Ions = 1001690
 ProteomeDiscoverer:SEQUEST:Weight of c Ions: Uses c ions for spectrum matching with this relative factor.
 MS_ProteomeDiscoverer_SEQUEST_Weight_of_d_Ions = 1001691
 ProteomeDiscoverer:SEQUEST:Weight of d Ions: Uses c ions for spectrum matching with this relative factor.
 MS_ProteomeDiscoverer_SEQUEST_Weight_of_v_Ions = 1001692
 ProteomeDiscoverer:SEQUEST:Weight of v Ions: Uses c ions for spectrum matching with this relative factor.
 MS_ProteomeDiscoverer_SEQUEST_Weight_of_w_Ions = 1001693
 ProteomeDiscoverer:SEQUEST:Weight of w Ions: Uses c ions for spectrum matching with this relative factor.
 MS_ProteomeDiscoverer_SEQUEST_Weight_of_x_Ions = 1001694
 ProteomeDiscoverer:SEQUEST:Weight of x Ions: Uses x ions for spectrum matching with this relative factor.
 MS_ProteomeDiscoverer_SEQUEST_Weight_of_y_Ions = 1001695
 ProteomeDiscoverer:SEQUEST:Weight of y Ions: Uses y ions for spectrum matching with this relative factor.
 MS_ProteomeDiscoverer_SEQUEST_Weight_of_z_Ions = 1001696
 ProteomeDiscoverer:SEQUEST:Weight of z Ions: Uses z ions for spectrum matching with this relative factor.
 MS_ProteomeDiscoverer_ZCore_Protein_Score_Cutoff = 1001697
 ProteomeDiscoverer:ZCore:Protein Score Cutoff: Sets a minimum protein score that each protein must exceed in order to be reported.
 MS_ProteomeDiscoverer_Reporter_Ions_Quantizer_Integration_Method = 1001698
 ProteomeDiscoverer:Reporter Ions Quantizer:Integration Method: Specifies which peak to select if more than one peak is found inside the integration window.
 MS_ProteomeDiscoverer_Reporter_Ions_Quantizer_Integration_Window_Tolerance = 1001699
 ProteomeDiscoverer:Reporter Ions Quantizer:Integration Window Tolerance: Specifies the mass-to-charge window that enables one to look for the reporter peaks.
 MS_ProteomeDiscoverer_Reporter_Ions_Quantizer_Quantitation_Method = 1001700
 ProteomeDiscoverer:Reporter Ions Quantizer:Quantitation Method: Quantitation method for isobarically labeled quantitation.
 MS_ProteomeDiscoverer_Spectrum_Exporter_Export_Format_OBSOLETE = 1001701
 ProteomeDiscoverer:Spectrum Exporter:Export Format: Format of the exported spectra (dta, mgf or mzData).
 MS_ProteomeDiscoverer_Spectrum_Exporter_File_name = 1001702
 ProteomeDiscoverer:Spectrum Exporter:File name: Name of the output file that contains the exported data.
 MS_ProteomeDiscoverer_Search_Modifications_Only_For_Identified_Proteins = 1001703
 ProteomeDiscoverer:Search Modifications Only For Identified Proteins: Influences the modifications search.
 MS_ProteomeDiscoverer_SEQUEST_Std_High_Confidence_XCorr_Charge1 = 1001704
 ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge1: Standard high confidence XCorr parameter for charge = 1.
 MS_ProteomeDiscoverer_SEQUEST_Std_High_Confidence_XCorr_Charge2 = 1001705
 ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge2: Standard high confidence XCorr parameter for charge = 2.
 MS_ProteomeDiscoverer_SEQUEST_Std_High_Confidence_XCorr_Charge3 = 1001706
 ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge3: Standard high confidence XCorr parameter for charge = 3.
 MS_ProteomeDiscoverer_SEQUEST_Std_High_Confidence_XCorr_Charge4 = 1001707
 ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge4: Standard high confidence XCorr parameter for charge >= 4.
 MS_ProteomeDiscoverer_SEQUEST_Std_Medium_Confidence_XCorr_Charge1 = 1001708
 ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge1: Standard medium confidence XCorr parameter for charge = 1.
 MS_ProteomeDiscoverer_SEQUEST_Std_Medium_Confidence_XCorr_Charge2 = 1001709
 ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge2: Standard medium confidence XCorr parameter for charge = 2.
 MS_ProteomeDiscoverer_SEQUEST_Std_Medium_Confidence_XCorr_Charge3 = 1001710
 ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge3: Standard medium confidence XCorr parameter for charge = 3.
 MS_ProteomeDiscoverer_SEQUEST_Std_Medium_Confidence_XCorr_Charge4 = 1001711
 ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge4: Standard medium confidence XCorr parameter for charge >= 4.
 MS_ProteomeDiscoverer_SEQUEST_FT_High_Confidence_XCorr_Charge1 = 1001712
 ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge1: FT high confidence XCorr parameter for charge = 1.
 MS_ProteomeDiscoverer_SEQUEST_FT_High_Confidence_XCorr_Charge2 = 1001713
 ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge2: FT high confidence XCorr parameter for charge = 2.
 MS_ProteomeDiscoverer_SEQUEST_FT_High_Confidence_XCorr_Charge3 = 1001714
 ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge3: FT high confidence XCorr parameter for charge = 3.
 MS_ProteomeDiscoverer_SEQUEST_FT_High_Confidence_XCorr_Charge4 = 1001715
 ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge4: FT high confidence XCorr parameter for charge >= 4.
 MS_ProteomeDiscoverer_SEQUEST_FT_Medium_Confidence_XCorr_Charge1 = 1001716
 ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge1: FT medium confidence XCorr parameter for charge = 1.
 MS_ProteomeDiscoverer_SEQUEST_FT_Medium_Confidence_XCorr_Charge2 = 1001717
 ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge2: FT medium confidence XCorr parameter for charge = 2.
 MS_ProteomeDiscoverer_SEQUEST_FT_Medium_Confidence_XCorr_Charge3 = 1001718
 ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge3: FT medium confidence XCorr parameter for charge = 3.
 MS_ProteomeDiscoverer_SEQUEST_FT_Medium_Confidence_XCorr_Charge4 = 1001719
 ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge4: FT medium confidence XCorr parameter for charge >= 4.
 MS_ProteomeDiscoverer_1__Dynamic_Modification = 1001720
 ProteomeDiscoverer:1. Dynamic Modification: Determine 1st dynamic post-translational modifications (PTMs).
 MS_ProteomeDiscoverer_2__Dynamic_Modification = 1001721
 ProteomeDiscoverer:2. Dynamic Modification: Determine 2nd dynamic post-translational modifications (PTMs).
 MS_ProteomeDiscoverer_3__Dynamic_Modification = 1001722
 ProteomeDiscoverer:3. Dynamic Modification: Determine 3rd dynamic post-translational modifications (PTMs).
 MS_ProteomeDiscoverer_4__Dynamic_Modification = 1001723
 ProteomeDiscoverer:4. Dynamic Modification: Determine 4th dynamic post-translational modifications (PTMs).
 MS_ProteomeDiscoverer_Static_Modification_for_X = 1001724
 ProteomeDiscoverer:Static Modification for X: Static Modification for X.
 MS_ProteomeDiscoverer_Initial_minimal_peptide_probability = 1001725
 ProteomeDiscoverer:Initial minimal peptide probability: Minimal initial peptide probability to contribute to analysis.
 MS_ProteomeDiscoverer_Minimal_peptide_probability = 1001726
 ProteomeDiscoverer:Minimal peptide probability: Minimum adjusted peptide probability contributing to protein probability.
 MS_ProteomeDiscoverer_Minimal_peptide_weight = 1001727
 ProteomeDiscoverer:Minimal peptide weight: Minimum peptide weight contributing to protein probability.
 MS_ProteomeDiscoverer_Number_of_input1_spectra = 1001728
 ProteomeDiscoverer:Number of input1 spectra: Number of spectra from 1+ precursor ions.
 MS_ProteomeDiscoverer_Number_of_input2_spectra = 1001729
 ProteomeDiscoverer:Number of input2 spectra: Number of spectra from 2+ precursor ions.
 MS_ProteomeDiscoverer_Number_of_input3_spectra = 1001730
 ProteomeDiscoverer:Number of input3 spectra: Number of spectra from 3+ precursor ions.
 MS_ProteomeDiscoverer_Number_of_input4_spectra = 1001731
 ProteomeDiscoverer:Number of input4 spectra: Number of spectra from 4+ precursor ions.
 MS_ProteomeDiscoverer_Number_of_input5_spectra = 1001732
 ProteomeDiscoverer:Number of input5 spectra: Number of spectra from 5+ precursor ions.
 MS_ProteomeDiscoverer_Number_of_predicted_correct_proteins = 1001733
 ProteomeDiscoverer:Number of predicted correct proteins: Total number of predicted correct protein ids (sum of probabilities).
 MS_ProteomeDiscoverer_Organism_OBSOLETE = 1001734
 ProteomeDiscoverer:Organism: Sample organism (used for annotation purposes).
 MS_ProteomeDiscoverer_Reference_Database_OBSOLETE = 1001735
 ProteomeDiscoverer:Reference Database: Full path database name.
 MS_ProteomeDiscoverer_Residue_substitution_list = 1001736
 ProteomeDiscoverer:Residue substitution list: Residues considered equivalent when comparing peptides.
 MS_ProteomeDiscoverer_Source_file_extension_OBSOLETE = 1001737
 ProteomeDiscoverer:Source file extension: File type (if not pepXML).
 MS_ProteomeDiscoverer_Source_Files_OBSOLETE = 1001738
 ProteomeDiscoverer:Source Files: Input pepXML files.
 MS_ProteomeDiscoverer_Source_Files_old_OBSOLETE = 1001739
 ProteomeDiscoverer:Source Files old: Input pepXML files (old).
 MS_ProteomeDiscoverer_WinCyg_reference_database = 1001740
 ProteomeDiscoverer:WinCyg reference database: Windows full path for database.
 MS_ProteomeDiscoverer_WinCyg_source_files = 1001741
 ProteomeDiscoverer:WinCyg source files: Windows pepXML file names.
 MS_LTQ_Orbitrap_Velos = 1001742
 LTQ Orbitrap Velos: Finnigan LTQ Orbitrap Velos MS.
 MS_ProteomeDiscoverer_Mascot_Weight_of_A_Ions = 1001743
 ProteomeDiscoverer:Mascot:Weight of A Ions: Determines if to use A ions for spectrum matching.
 MS_ProteomeDiscoverer_Mascot_Weight_of_B_Ions = 1001744
 ProteomeDiscoverer:Mascot:Weight of B Ions: Determines if to use B ions for spectrum matching.
 MS_ProteomeDiscoverer_Mascot_Weight_of_C_Ions = 1001745
 ProteomeDiscoverer:Mascot:Weight of C Ions: Determines if to use C ions for spectrum matching.
 MS_ProteomeDiscoverer_Mascot_Weight_of_D_Ions = 1001746
 ProteomeDiscoverer:Mascot:Weight of D Ions: Determines if to use D ions for spectrum matching.
 MS_ProteomeDiscoverer_Mascot_Weight_of_V_Ions = 1001747
 ProteomeDiscoverer:Mascot:Weight of V Ions: Determines if to use V ions for spectrum matching.
 MS_ProteomeDiscoverer_Mascot_Weight_of_W_Ions = 1001748
 ProteomeDiscoverer:Mascot:Weight of W Ions: Determines if to use W ions for spectrum matching.
 MS_ProteomeDiscoverer_Mascot_Weight_of_X_Ions = 1001749
 ProteomeDiscoverer:Mascot:Weight of X Ions: Determines if to use X ions for spectrum matching.
 MS_ProteomeDiscoverer_Mascot_Weight_of_Y_Ions = 1001750
 ProteomeDiscoverer:Mascot:Weight of Y Ions: Determines if to use Y ions for spectrum matching.
 MS_ProteomeDiscoverer_Mascot_Weight_of_Z_Ions = 1001751
 ProteomeDiscoverer:Mascot:Weight of Z Ions: Determines if to use z ions for spectrum matching.
 MS_ProteomeDiscoverer_Spectrum_Selector_Use_New_Precursor_Reevaluation = 1001752
 ProteomeDiscoverer:Spectrum Selector:Use New Precursor Reevaluation: Determines if to use precursor reevaluation.
 MS_ProteomeDiscoverer_Spectrum_Selector_SN_Threshold_FTonly = 1001753
 ProteomeDiscoverer:Spectrum Selector:SN Threshold FTonly: Signal-to-Noise ratio below which peaks are removed (in FT mode only).
 MS_ProteomeDiscoverer_Mascot_Please_Do_not_Touch_this = 1001754
 ProteomeDiscoverer:Mascot:Please Do not Touch this: Unknown Mascot parameter which ProteomeDiscoverer uses for mascot searches.
 MS_contact_phone_number = 1001755
 contact phone number: Phone number of the contact person or organization.
 MS_contact_fax_number = 1001756
 contact fax number: Fax number for the contact person or organization.
 MS_contact_toll_free_phone_number = 1001757
 contact toll-free phone number: Toll-free phone number of the contact person or organization.