In addition to the libraries, ProteoWizard distributes a number of applications. Many of these operate across Windows, Linux and Macintosh. Because of our reliance upon vendor libraries, some funcionality is only available on Windows. For example, reading vendor-data files. For command-line tools, running the program with no arguments will print usage information.

WinOnly GUI Tools
MSConvertGUI interactive version of the msconvert tool for converting mass spec data files to various formats (Windows only)
SeeMS interactive viewer for mass spec data files (Windows only)
Skyline interactive application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM) methods and analyzing the resulting mass spectrometer data. (Windows only)
Topograph interactive application for working with metabolic labeling and protein metabolism experiments. (Windows only)
General Information
Filters Information on the data filters and transformations provided by the ProteoWizard library, as used in msaccess, msconvert and other tools
Command-Line Tools
chainsaw peptide digest program, takes in sequence files, outputs peptides, masses, etc.
idConvert Reads diverse peptide identification formats and outputs to mzIdentML (or other things)
msaccess command line access to mass spec data files, including spectrum binary data and metadata, selected ion chromatograms, and pseudo-2D gel image creation
msbenchmark ?
msconvert general data format conversion tool
msdiff comparison of two data files, for validation of conversion and preprocessing
msdir ?
msistats ?
mspicture command line pseudo-2D gel image creation with mapped peptide ID info
mscat exports data from a variety of formats into 4 column text format
peakaboo ?
pepcat ?
pepsum ?
qtofpeakpicker peak detection in Q-TOF (quadrupole time-of-flight) raw data
sldout ?
ThermoRawMetaDump extracts methods, tunes, and headers from RAW files as human-readable text. (Windows only)
txt2mzml converts data from 4 column format to mzML
Tools for ProteoWizard Testing
These are mostly for developers to make sure that they haven't broken anything
hello_analyzer ?
hello_analyzer_2 ?
hello_msdata ?
hello_ramp ?
write_example_files ?
write_mzid_example_files ?
write_proteome_example_files ?
write_traml_example_files ?