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,...