cancel
Showing results for 
Search instead for 
Did you mean: 
Orbitrap_SciLib
Reputable Mentor II
Reputable Mentor II
Beausoleil SA, Villén J, Gerber SA, Rush J, Gygi SP.
Nat Biotechnol. 2006 Oct;24(10):1285-92.
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 our methods in a fully automated fashion to nocodazole-arrested HeLa cell lysate where we identified 1,761 nonredundant phosphorylation sites from 491 proteins with a peptide false-positive rate of 1.3%.

http://www.nature.com/nbt/journal/v24/n10/pdf/nbt1240.pdf
Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, Massachusetts 02115, USA.
Version history
Last update:
3 weeks ago
Updated by:
Contributors