ProteoWizard toolkit consists of open-source software libraries and applications for proteomics research. The ProteoWizard toolkit includes the following tools: 1. Skyline: Multiple Reaction Monitoring methods and analysis of mass spectrometer data, 2. Filters, 3. idConvert, 4. msaccess: read M/S data files, spectrum binary and metadata, ion chromatograms, and pseudo-2D gel image creation, 5. msconvert, 6. mspicture: pseudo-2D gel image creation together with mapped peptide ID info, 7. qtofpeakpicker: peak detection in Q-TOF raw data.
Proteomics; Proteomics experiment
Chambers MC, Maclean B, Burke R, Amodei D, Ruderman DL, Neumann S, Gatto L, Fischer B, Pratt B, Egertson J, Hoff K, Kessner D, Tasman N, Shulman N, Frewen B, Baker TA, Brusniak MY, Paulse C, Creasy D, Flashner L, Kani K, Moulding C, Seymour SL, Nuwaysir LM, 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 EW, Moritz RL, Katz JE, Agus DB, MacCoss M, Tabb DL, Mallick P "A cross-platform toolkit for mass spectrometry and proteomics." Nat. Biotechnol. 2012; 30(10):918-20 https://doi.org/10.1038/nbt.2377
PMID: 23051804
PMCID: PMC3471674
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 https://doi.org/10.1002/0471250953.bi1305s36
PMID: 22161569
Holman JD, Tabb DL, Mallick P "Employing ProteoWizard to Convert Raw Mass Spectrometry Data." Curr Protoc Bioinformatics, 2014 https://doi.org/10.1002/0471250953.bi1324s46
PMID: 24939128
PMCID: PMC4113728
Maclean B, Tomazela DM, Abbatiello SE, Zhang S, Whiteaker JR, Paulovich AG, Carr SA, Maccoss MJ "Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry." Anal Chem, 2010 https://doi.org/10.1021/ac102179j
PMID: 21090646
PMCID: PMC3005404
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 https://doi.org/10.1021/pr500886y
PMID: 25411686
PMCID: PMC4324452
Luethy R, Kessner DE, Katz JE, Maclean B, Grothe R, Kani K, Faça V, Pitteri S, Hanash S, Agus DB, Mallick P "Precursor-ion mass re-estimation improves peptide identification on hybrid instruments." J Proteome Res, 2008 https://doi.org/10.1021/pr800307m
PMID: 18707148
PMCID: PMC4673049
Prakash A, Tomazela DM, Frewen B, Maclean B, Merrihew G, Peterman S, Maccoss MJ "Expediting the development of targeted SRM assays: using data from shotgun proteomics to automate method development." J Proteome Res, 2009 https://doi.org/10.1021/pr801028b
PMID: 19326923
PMCID: PMC2743471
Wilhelm M, Kirchner M, Steen JA, Steen H "mz5: space- and time-efficient storage of mass spectrometry data sets." Mol Cell Proteomics, 2012 https://doi.org/10.1074/mcp.O111.011379
PMID: 21960719
PMCID: PMC3270111
Kessner D, Chambers M, Burke R, Agus D, Mallick P "ProteoWizard: open source software for rapid proteomics tools development." Bioinformatics 2008; 24(21):2534-6 https://doi.org/10.1093/bioinformatics/btn323
PMID: 18606607
PMCID: PMC2732273
MacLean B, Tomazela DM, Shulman N, Chambers M, Finney GL, Frewen B, Kern R, Tabb DL, Liebler DC, MacCoss MJ "Skyline: an open source document editor for creating and analyzing targeted proteomics experiments." Bioinformatics 2010; 26(7):966-8 https://doi.org/10.1093/bioinformatics/btq054
PMID: 20147306
PMCID: PMC2844992
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