Welcome to the downloads page.
Here you will find software tools developed by the SFCAP, links to recent publications, Collaborator protocols and forms.
Software
For previous versions of software, please contact the developers directly. Utility tools are available under the Apache license. Published scientific-applications are available under a permissive open-source license.
Subversion Repository All our utility tools are available from our ProteoWizard sourceforge site [http://proteowizard.sourceforge.net/]. Or you can download them directly here [ src | win | linux | osx ]
The ProteoWizard Libraries are a set of HUPO-PSI formats (mzML!) compatible software libraries that provide a basic proteomics analysis framework, including data file access, chemistry computations, and LCMS dataset analysis. Although the computations are in common use throughout the proteomics community, there has not been a single, cross-platform, modular and extensible software package.
A variety of tools exist there including:
msConvert: general data format conversion tool. Writes mzML or mzXML. Currently reads mzML, mzXML, Thermo RAW (Windows), with more vendor formats in the near future.
msDiff: comparison of two data files, for validation of conversion and preprocessing
msAccess: command line access to mass spec data files, including spectrum binary data and metadata, selected ion chromatograms, and pseudo-2D gel image creation.
msPicture: reads pepXML and draws pseudo-2D gel images.
msCat: reads mzML, mzXML, RAW and writes out in 4 column text format.
SOPs, Protocols & Forms
Sample Collection Form[download doc]
Selected Publications
deVera IE, Katz JE, Agus DB. Clinical proteomics: the promises and challenges of mass spectrometry-based biomarker discovery. Clin Adv Hematol Oncol. 2006 Jul;4(7):541-9. [download pdf]
Katz JE, Mallick P, Agus DB. A perspective on protein profiling of blood. BJU Int. 2005 Sep;96(4):477-82. [download pdf]
Mallick P, Schirle M, Chen SS, Flory MR, Lee H, Martin D, Ranish J, Raught B, Schmitt R, Werner T, Kuster B, Aebersold R. Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol. 2007 Jan;25(1):125-31. [download pdf]
Desiere F, Deutsch EW, King NL, Nesvizhskii AI, Mallick P, Eng J, Chen S, Eddes J, Loevenich SN, Aebersold R. The PeptideAtlas project. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D655-8. [download pdf]
Kuster B, Schirle M, Mallick P, Aebersold R. Scoring proteomes with proteotypic peptide probes. Nat Rev Mol Cell Biol. 2005 Jul;6(7):577-83. [download pdf]
All SFCAP Publications
Related Publications, Primers and Tutorials