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

Katz JE. Deploying Mass Spectrometric Data Analysis in the Amazon AWS Cloud Computing Environment. Methods Mol Biol. 2021;2271:375-397. doi: 10.1007/978-1-0716-1241-5_26. PMID: 33908021.
Pino LK, Searle BC, Bollinger JG, Nunn B, MacLean B, MacCoss MJ. The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics. Mass Spectrom Rev. 2020 May;39(3):229-244. doi: 10.1002/mas.21540. Epub 2017 Jul 9. PMID: 28691345; PMCID: PMC5799042.
Adams KJ, Pratt B, Bose N, Dubois LG, St John-Williams L, Perrott KM, Ky K, Kapahi P, Sharma V, MacCoss MJ, Moseley MA, Colton CA, MacLean BX, Schilling B, Thompson JW; Alzheimer’s Disease Metabolomics Consortium. Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics. J Proteome Res. 2020 Apr 3;19(4):1447-1458. doi: 10.1021/acs.jproteome.9b00640. Epub 2020 Mar 26. PMID: 31984744; PMCID: PMC7127945.
Amodei D, Egertson J, MacLean BX, Johnson R, Merrihew GE, Keller A, Marsh D, Vitek O, Mallick P, MacCoss MJ. Improving Precursor Selectivity in Data- Independent Acquisition Using Overlapping Windows. J Am Soc Mass Spectrom. 2019 Apr;30(4):669-684. doi: 10.1007/s13361-018-2122-8. Epub 2019 Jan 22. PMID: 30671891; PMCID: PMC6445824.
MacLean BX, Pratt BS, Egertson JD, MacCoss MJ, Smith RD, Baker ES. Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions. J Am Soc Mass Spectrom. 2018 Nov;29(11):2182-2188. doi: 10.1007/s13361-018-2028-5. Epub 2018 Jul 25. PMID: 30047074; PMCID: PMC6191345.
Adusumilli R, Mallick P. Data Conversion with ProteoWizard msConvert. Methods Mol Biol. 2017;1550:339-368. doi: 10.1007/978-1-4939-6747-6_23. PMID: 28188540.
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. 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]
Egertson JD, Kuehn A, Merrihew GE, Bateman NW, MacLean BX, Ting YS, Canterbury JD, Marsh DM, Kellmann M, Zabrouskov V, Wu CC, MacCoss MJ. Multiplexed MS/MS for improved data-independent acquisition. Nat Methods. 2013 Aug;10(8):744-6. doi: 10.1038/nmeth.2528. Epub 2013 Jun 23. PMID: 23793237; PMCID: PMC3881977.
Wilhelm M, Kirchner M, Steen JAJ, 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. PMID: 21960719; PMCID: PMC3270111.
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]