Computational Libraries

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Name Paper Programming Language(s) PIs / Affiliations Description
Coon OMSSA Proteomic Analysis Software Suite (COMPASS) paper C# .NET Joshua Coon
University of Wisconsin–Madison
A software suite designed around OMSSA for Thermo .raw files.
msInspect paper Java Martin McIntosh
Fred Hutchinson Cancer Research Center
A useful set of libraries and tools for Java.
ProteoWizard paper C++ Parag Mallick
Stanford University / University of Southern California
A nearly comprenhensive set of libraries and tools for proteomics. Excellent for reading vendor formats and reading/writing open formats.
The OpenMS Proteomics Pipeline (TOPP) paper C++ Knut Reinert / Oliver Kohlbacher / Andreas Hildebrandt
Free University Berlin / University of TĂĽbingen / Saarland University
A full pipeline for proteomics written using modern principles.
Trans-Proteomic Pipeline (TPP) paper C++ Ruedi Aebersold
Institute for Systems Biology
A comprehensive suite of tools for beginning-to-end proteomics data analysis.