Trans-Proteomic Pipeline
Overview
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.
Tutorial
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.