Authors
Sean A Beausoleil, Judit Villén, Scott A Gerber, John Rush, Steven P Gygi
Publication date
2006/10
Journal
Nature biotechnology
Volume
24
Issue
10
Pages
1285-1292
Publisher
Nature Publishing Group US
Description
Data analysis and interpretation remain major logistical challenges when attempting to identify large numbers of protein phosphorylation sites by nanoscale reverse-phase liquid chromatography/tandem mass spectrometry (LC-MS/MS) (Supplementary Figure 1 online). In this report we address challenges that are often only addressable by laborious manual validation, including data set error, data set sensitivity and phosphorylation site localization. We provide a large-scale phosphorylation data set with a measured error rate as determined by the target-decoy approach, we demonstrate an approach to maximize data set sensitivity by efficiently distracting incorrect peptide spectral matches (PSMs), and we present a probability-based score, the Ascore, that measures the probability of correct phosphorylation site localization based on the presence and intensity of site-determining ions in MS/MS spectra. We applied …
Total citations
Scholar articles
SA Beausoleil, J Villén, SA Gerber, J Rush, SP Gygi - Nature biotechnology, 2006