Trans-Proteomic Pipeline


The Trans-Proteomic Pipeline provides a complete workflow to generate spectral libraries suitable for OpenSWATH. Data sets acquired in data-dependent acquisition (DDA) or data-independent acquisition (DIA; preprocessed by DIA-Umpire [2]) can be searched by spectrum-centric scoring against a reference FASTA database using several supported search engines. After statistical validation using PeptideProphet, iProphet & MAYU, a consensus spectral library is generated by SpectraST, which serves as final input for the OpenMS tool TargetedFileConverter.

Contact and Support

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


A comprehensive tutorial [1] describes the individual steps to generate spectral libraries for SWATH-MS using the Trans-Proteomic Pipeline (TPP). Please follow the tutorial until the generation of SpectraST spectral libraries. If you are using DIA data, follow the DIA-Umpire tutorial to generate pseudo-spectra first, which can then be processed using the TPP.

In the last step, import the SpectraST consensus library (format sptxt or splib) and convert it to a MRM transition list:

# This will generate the file db_assays.mrm
spectrast -cNdb_pqp -cICID-QTOF -cM db_consensus.splib

Convert then the MRM transition list to a TraML spectral library and follow the remaining steps in the Generic Transition Lists section.


[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
[2]Tsou CC, Avtonomov D, Larsen B, Tucholska M, Choi H, Gingras AC, Nesvizhskii AI. DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics. Nat Methods. 2015 Mar;12(3):258-64, 7 p following 264. doi: 10.1038/nmeth.3255. Epub 2015 Jan 19. PMID: 25599550