The TPP is a complete and mature suite of free and open-source software tools for MS data representation, MS data visualization, peptide identification and validation, protein identification, quantification, and annotation, data storage and mining, and biological inference.
The TPP is available on Linux and Windows systems and builds on Mac OS X as well, and supports a well-established worldwide user community.
The latest TPP version is 6.1.0, released June 2022.
Read the Release Notes and Installation Notes for the latest version.
Download directly from Sourceforge.
Deutsch et.al. "Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics." Proteomics Clin Appl. 2015 Aug;9(7-8):745-54.
To cite other TPP components, please refer to this page.
Development of the TPP is currently supported by the National Institute Of General Medical Sciences of the National Institutes of Health under award number R01GM087221.
- ProteoMapper
- A set of tools to index and map peptides to proteome databases, including PEFF modifications
