PT  - JOURNAL ARTICLE
AU  - David D. Shteynberg
AU  - Eric W. Deutsch
AU  - David S. Campbell
AU  - Michael R. Hoopmann
AU  - Ulrike Kusebauch
AU  - Dave Lee
AU  - Luis Mendoza
AU  - Mukul K. Midha
AU  - Zhi Sun
AU  - Anthony D. Whetton
AU  - Robert L. Moritz
TI  - PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline
AID  - 10.1101/679845
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 679845
4099  - http://biorxiv.org/content/early/2019/06/27/679845.short
4100  - http://biorxiv.org/content/early/2019/06/27/679845.full
AB  - Spectral matching sequence database search engines commonly used on mass spectrometry-based proteomics experiments excel at identifying peptide sequence ions, and in addition, possible sequence ions carrying post-translational modifications (PTMs), but most do not provide confidence metrics for the exact localization of those PTMs when several possible sites are available. Localization is absolutely required for downstream molecular cell biology analysis of PTM function in vitro and in vivo. Therefore, we developed PTMProphet, a free and open-source software tool integrated into the Trans-Proteomic Pipeline, which reanalyzes identified spectra from any search engine for which pepXML output is available to provide localization confidence to enable appropriate further characterization of biologic events. Localization of any type of mass modification (e.g., phosphorylation) is supported. PTMProphet applies Bayesian mixture models to compute probabilities for each site/peptide spectrum match where a PTM has been identified. These probabilities can be combined to compute a global false localization rate at any threshold to guide downstream analysis. We describe the PTMProphet tool, its underlying algorithms and demonstrate its performance on ground-truth synthetic peptide reference datasets, one previously published small dataset, one new larger dataset, and also on a previously published phospho-enriched dataset where the correct sites of modification are unknown. Data have been deposited to ProteomeXchange with identifier PXD013210.