Prophossi: automating expert validation of phosphopeptide-spectrum matches from tandem mass spectrometry.

Bioinformatics
David M A MartinMichael A J Ferguson

Abstract

Complex patterns of protein phosphorylation mediate many cellular processes. Tandem mass spectrometry (MS/MS) is a powerful tool for identifying these post-translational modifications. In high-throughput experiments, mass spectrometry database search engines, such as MASCOT provide a ranked list of peptide identifications based on hundreds of thousands of MS/MS spectra obtained in a mass spectrometry experiment. These search results are not in themselves sufficient for confident assignment of phosphorylation sites as identification of characteristic mass differences requires time-consuming manual assessment of the spectra by an experienced analyst. The time required for manual assessment has previously rendered high-throughput confident assignment of phosphorylation sites challenging. We have developed a knowledge base of criteria, which replicate expert assessment, allowing more than half of cases to be automatically validated and site assignments verified with a high degree of confidence. This was assessed by comparing automated spectral interpretation with careful manual examination of the assignments for 501 peptides above the 1% false discovery rate (FDR) threshold corresponding to 259 putative phosphorylation sites in 74 ...Continue Reading

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Citations

Mar 28, 2012·Analytical and Bioanalytical Chemistry·Caroline EvansPhillip C Wright
Sep 21, 2011·Analytical Chemistry·Fangjun WangHanfa Zou
Mar 13, 2016·Journal of Experimental Botany·Sacha Baginsky
Mar 19, 2013·Methods : a Companion to Methods in Enzymology·Timothy G CurranForest M White
Feb 6, 2015·Advances in Bioinformatics·Alessandra TiengoPaolo Magni
Aug 6, 2015·Plant Physiology·Qintao LuSacha Baginsky

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Methods Mentioned

BETA
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Software Mentioned

SEQUEST
SLRV
Analyst QS
MASCOT Large Results Viewer ( MLRV )
Star
PostgreSQL
DB
SEQUEST Prophet
TransProteomicsPipeline ( TPP )
TryPP

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