Trans-proteomic-pipeline like ('TTPish') workflow for MASSyPup64

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.