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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 front end for several popular open source proteomics tools
APP automates and allows distributed computing of common proteomics tasks using a java-front end to provide both GUI and server parts. It is highly recommended for use with the Trans Proteomic Pipeline but this is not a requirement.