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The Trans-Proteomic Pipeline (TPP) is a suite of software tools that enables start-to-finish analysis of mass spectrometry (MS) proteomics datasets, originally and continually developed at the Institute for Systems Biology in Seattle, USA. While several of the component tools such as PepideProphet1  and ProteinProphet2  predated the TPP as an entity itself, the TPP was first presented in 2005 by Keller et al.3  as a uniform analysis platform comprising a set of tools that were all interoperable on account of a shared set of open file formats. Since then the TPP has grown to encompass many additional tools,...

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