Publications - spreading the word

If you use ProteoWizard for your work, please cite us in your publications:

A cross-platform toolkit for mass spectrometry and proteomics. Chambers, M.C., MacLean, B., Burke, R., Amode, D., Ruderman, D.L., Neumann, S., Gatto, L., Fischer, B., Pratt, B., Egertson, J., Hoff, K., Kessner, D., Tasman, N., Shulman, N., Frewen, B., Baker, T.A., Brusniak, M.-Y., Paulse, C., Creasy, D., Flashner, L., Kani, K., Moulding, C., Seymour, S.L., Nuwaysir, L.M., Lefebvre, B., Kuhlmann, F., Roark, J., Rainer, P., Detlev, S., Hemenway, T., Huhmer, A., Langridge, J., Connolly, B., Chadick, T., Holly, K., Eckels, J., Deutsch, E.W., Moritz, R.L., Katz, J.E., Agus, D.B., MacCoss, M., Tabb, D.L. & Mallick, P. Nature Biotechnology 30, 918-920 (2012). Article →

Articles & Papers

  • Kochen MA, Chambers MC, Holman JD, Nesvizhskii AI, Weintraub ST, Belisle JT, Islam MN, Griss J, Tabb DL. Greazy: Open-Source Software for Automated Phospholipid Tandem Mass Spectrometry Identification. Anal Chem. 2016 May 24. [Epub ahead of print] PubMed PMID: 27186799. [abstract] [pdf]
  • Gibbons BC, Chambers MC, Monroe ME, Tabb DL, Payne SH. Correcting systematic bias and instrument measurement drift with mzRefinery. Bioinformatics. 2015 Dec 1;31(23):3838-40. doi: 10.1093/bioinformatics/btv437. Epub 2015 Aug 4. PubMed PMID: 26243018; PubMed Central PMCID: PMC4653383. [pdf]
  • French WR, Zimmerman LJ, Schilling B, Gibson BW, Miller CA, Townsend RR, Sherrod SD, Goodwin CR, McLean JA, Tabb DL. Wavelet-based peak detection and a new charge inference procedure for MS/MS implemented in ProteoWizard's msConvert. J Proteome Res. 2015 Feb 6;14(2):1299-307. doi: 10.1021/pr500886y. Epub 2014 Dec 2. PubMed PMID: 25411686; PubMed Central PMCID: PMC4324452. [abstract] [pdf]
  • Holman JD, Tabb DL, Mallick P. Employing ProteoWizard to Convert Raw Mass Spectrometry Data. Curr Protoc Bioinformatics. 2014 Jun 17;46:13.24.1-9. doi: 10.1002/0471250953.bi1324s46. PubMed PMID: 24939128; PubMed Central PMCID: PMC4113728. [pdf]
  • Wilhelm M, Kirchner M, Steen JA, Steen H. mz5: space- and time-efficient storage of mass spectrometry data sets. Mol Cell Proteomics. 2012 Jan;11(1):O111.011379. doi: 10.1074/mcp.O111.011379. Epub 2011 Sep 29. PubMed PMID: 21960719; PubMed Central PMCID: PMC3270111. [abstract]
  • Eckels J, Hussey P, Nelson EK, Myers T, Rauch A, Bellew M, Connolly B, Law W, Eng JK, Katz J, McIntosh M, Mallick P, Igra M. Installation and use of LabKey Server for proteomics. Curr Protoc Bioinformatics. 2011 Dec;Chapter 13:Unit 13.5.. doi: 10.1002/0471250953.bi1305s36. PubMed PMID: 22161569. [abstract]
  • Effect of Collision Energy Optimization on the Measurement of Peptides by Selected Reaction Monitoring (SRM) Mass Spectrometry [abstract] [pdf]
  • Skyline: An Open Source Document Editor for Creating and Analyzing Targeted Proteomics Experiments. MacLean B, Tomazela DM, Shulman N, Chambers M, Finney GL, Frewen B, Kern R, Tabb DL, Liebler DC, MacCoss MJ. Bioinformatics. 2010 Apr 1;26(7):966-8. [abstract]
  • Expediting the Development of Targeted SRM Assays: Using Data from Shotgun Proteomics to Automate Method Development [abstract] [pdf]
  • Kessner D, Chambers M, Burke R, Agus D, Mallick P. ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics. 2008 Nov 1;24(21):2534-6. doi: 10.1093/bioinformatics/btn323. Epub 2008 Jul 7. PubMed PMID: 18606607; PubMed Central PMCID: PMC2732273. [abstract]
  • Precursor-ion mass re-estimation improves peptide identification on hybrid instruments. Luethy R, Kessner DE, Katz JE, Maclean B, Grothe R, Kani K, Faça V, Pitteri S, Hanash S, Agus DB, Mallick P. J Proteome Res. 2008; 7 (9): 4031-9 [abstract] [pdf]
  • ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323. [abstract] [pdf]


  • HUPO 2009 Toronto poster [pdf]
  • US HUPO 2009 poster [pdf]
  • ASMS 2008 poster for mzML 1.0 [pdf]
  • US HUPO 2008 poster [pdf]
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