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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 the open mzML/mzXML formats.
Comet open source tandem mass spectrometry (MS/MS) search engine.
September 2021: the code repository has migrate to https://github.com/UWPR/Comet
Comet is an open source tandem mass spectrometry (MS/MS) sequence database search engine. It identifies peptides by searching MS/MS spectra against sequences present in protein sequence databases.
Comet currently exists as a simple Windows or Linux command line binary that only does MS/MS database search. Supported input formats are mzXML, mzML, ms2, and Thermo RAW files. Supported output formats are tab...
A library for reading Mass Spectometry files. Reuse mzXML converter code but compile with gcc and Qt instead of MSVC. Some features have been added, e.g. UV scan reading