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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...
The Maltcms - Modular Application Toolkit for Chromatography Mass-Spectrometry is a JAVA API for preprocessing, alignment, analysis and visualization of data stored in open file formats used in Proteomics and Metabolomics research.
Spectre for mass spectrometry. (Quantitiave) analysis of multiple ls-ms(ms) runs, using mzXML import of raw data. (working on mzDATA). Provides filters, alignment- and export tools.
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PARPs database is a web-based tool whose features include experiment annotation, protein database searching, protein sequence management.Statistical validation, , visualization, and converters from raw MS data open mzXML mzData format