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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.
A tool for extracting and preprocessing spectral count data for label-free quantitative proteomic analysis. This program is designed to be used with the Trans-Proteomic Pipeline (TPP).