ProteoWizard

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.

Topic

Proteomics;Proteomics experiment

Detail

  • Operation: Parsing;Formatting;Spectral library search;Data handling;Mass spectrum visualisation;MRM/SRM

  • Software interface: Command-line user interface

  • Language: C#

  • License: Apache License v2

  • Cost: Free

  • Version name: -

  • Credit: The Wunderkinder Foundation, Redstone Family Foundation, National Cancer Institute, National Institutes of Health, National Science Foundation, the European Union 7th Framework Program PRIME-XS.

  • Input: -

  • Output: -

  • Contact: support@proteowizard.org | matt.chambers@proteowizard.org | parag@proteowizard.org

  • Collection: -

  • Maturity: -

Publications

  • Installation and use of LabKey Server for proteomics.
  • Eckels J, Hussey P, Nelson EK, Myers T, Rauch A, et al. (2011). Installation and use of LabKey Server for proteomics. Curr Protoc Bioinformatics Chapter 13: Unit 13.5..
  • https://doi.org/10.1002/0471250953.bi1305s36
  • PMID: 22161569
  • PMC: -
  • Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry.
  • Maclean B, Tomazela DM, Abbatiello SE, Zhang S, Whiteaker JR, et al. (2010). Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry. Anal Chem 82(24): 10116-24.
  • https://doi.org/10.1021/ac102179j
  • PMID: 21090646
  • PMC: PMC3005404
  • Wavelet-based peak detection and a new charge inference procedure for MS/MS implemented in ProteoWizard's msConvert.
  • French WR, Zimmerman LJ, Schilling B, Gibson BW, Miller CA, et al. (2015). Wavelet-based peak detection and a new charge inference procedure for MS/MS implemented in ProteoWizard's msConvert. J Proteome Res 14(2): 1299-307.
  • https://doi.org/10.1021/pr500886y
  • PMID: 25411686
  • PMC: PMC4324452
  • Precursor-ion mass re-estimation improves peptide identification on hybrid instruments.
  • Luethy R, Kessner DE, Katz JE, Maclean B, Grothe R, et al. (2008). Precursor-ion mass re-estimation improves peptide identification on hybrid instruments. J Proteome Res 7(9): 4031-9.
  • https://doi.org/10.1021/pr800307m
  • PMID: 18707148
  • PMC: PMC4673049
  • Expediting the development of targeted SRM assays: using data from shotgun proteomics to automate method development.
  • Prakash A, Tomazela DM, Frewen B, Maclean B, Merrihew G, et al. (2009). Expediting the development of targeted SRM assays: using data from shotgun proteomics to automate method development. J Proteome Res 8(6): 2733-9.
  • https://doi.org/10.1021/pr801028b
  • PMID: 19326923
  • PMC: PMC2743471
  • A cross-platform toolkit for mass spectrometry and proteomics.
  • Chambers MC, et al. A cross-platform toolkit for mass spectrometry and proteomics. A cross-platform toolkit for mass spectrometry and proteomics. 2012; 30:918-20. doi: 10.1038/nbt.2377
  • https://doi.org/10.1038/nbt.2377
  • PMID: 23051804
  • PMC: PMC3471674
  • mz5: space- and time-efficient storage of mass spectrometry data sets.
  • Wilhelm M, Kirchner M, Steen JA, Steen H (2012). mz5: space- and time-efficient storage of mass spectrometry data sets. Mol Cell Proteomics 11(1): O111.011379.
  • https://doi.org/10.1074/mcp.O111.011379
  • PMID: 21960719
  • PMC: PMC3270111
  • ProteoWizard: open source software for rapid proteomics tools development.
  • Kessner D, et al. ProteoWizard: open source software for rapid proteomics tools development. ProteoWizard: open source software for rapid proteomics tools development. 2008; 24:2534-6. doi: 10.1093/bioinformatics/btn323
  • https://doi.org/10.1093/bioinformatics/btn323
  • PMID: 18606607
  • PMC: PMC2732273
  • Skyline: an open source document editor for creating and analyzing targeted proteomics experiments.
  • MacLean B, et al. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. 2010; 26:966-8. doi: 10.1093/bioinformatics/btq054
  • https://doi.org/10.1093/bioinformatics/btq054
  • PMID: 20147306
  • PMC: PMC2844992

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