Trans-Proteomic Pipeline


A tutorial [1] describes individual steps to generate spectral libraries for SWATH-MS using the Trans-Proteomic Pipeline (TPP).

Contact and Support

We provide support separately for the TPP, the msproteomicstools and the OpenMS components of the workflow.


[1]Schubert OT, Gillet LC, Collins BC, Navarro P, Rosenberger G, Wolski WE, Lam H, Amodei D, Mallick P, MacLean B, Aebersold R. Building high-quality assay libraries for targeted analysis of SWATH MS data. Nat Protoc. 2015 Mar;10(3):426-41. doi: 10.1038/nprot.2015.015. Epub 2015 Feb 12. PMID: 25675208