JUMP-ptm | JUMPptm aims to identify PTM events

JUMP-ptm is a Perl library. JUMP-ptm has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

JUMPptm aims to identify PTM events from unmatched spectra after conventional peptide analysis of the whole proteome. By default, JUMPptm assumes that the whole proteome data has been analyzed by the JUMP suite, which outputs the identification of peptides/proteins, and the high-quality (HQ) unmatched spectra with de novo tags. Such HQ spectra (input #1) are taken as JUMPptm input, and searched against a list of PTMs specified by the user (input #2) using the multi-stage database search strategy using Comet. The PTM list can be guided by the results from an open search using MSFragger. JUMPptm exports the PTM peptide identification with TMT-based quantification. NOTE : Please use ptm_pipeline2.py script to run the entire pipeline for the standalone version. Similarly, ptm_pipeline.py script run entire pipeline for Platform LSF to schedule jobs on the computational cluster. As the list of PTMs gets larger or number of mzXML files increases, is is better to use cluster rather than standalone version. For other platform, users may edit the job submission functions. Note that JUMPptm only supports 64-bit macOS and Linux.