TTPish workflow for MASSyPup64 with text search

This proteomics workflow performs a comet search and subsequently a validation of the results with PeptideProphet/Protein Prophet. Results are exported in various formats, to facilitate the downstream evaluation in other programs and the sharing of data (EXCEL, csv, mzIdentML).

Contrary to a standard Trans-Proteomic-Pipeline (TPP) installation, the workflow can be to mass spectrometry data in whatever localization (i.e. the files do not have to be uploaded/ copied to a special directory).

The workflow was described in the article: Winkler R. An evolving computational platform for biological mass spectrometry: workflows, statistics and data mining with MASSyPup64. PeerJ. 2015 (https://peerj.com/articles/1401/).

Since all dependencies (comet, TPP, ..) are installed on MASSyPup64, this m64 workflow should run without any further configuration.

Additionally to my previously uploaded protein identifcation workflow, the validated results are searched for a text pattern (e.g. protein name containing "xxx") and matching results are written into a separate csv file.