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An open source framework for LC-MS based proteomics. OpenMS offers datastructures and algorithms for the processing of mass spectrometry data. The library is written in C++.
The ProteoWizard Library is a set of software libraries and tools for rapid development of proteomics data analysis software. The libraries are cross-platform and built from the ground up using modern C++ techniques.
The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to our open mzXML format.
X!Tandem parser is a parser for X!Tandem xml files. It comes with a small viewer allowing the inspection of the results.
This program presents proteomics data (protein and peptide sequences) in a user-friendly way. Typically, the peptide sequences are found with a mass spectrometer, and the protein sequences are found by sequencing a genome.
Peacock is an application for Mac OS X that can be used to interpret gas-chromatography/mass-spectrometry (GC/MS) data files.