PhosphoScore: an open-source phosphorylation site assignment tool for MSn data

Correct phosphorylation site assignment is a critical aspect of phosphoproteomic analysis. Large-scale phosphopeptide data sets that are generated through liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) analysis often contain hundreds or thousands of phosphorylation sites that requ...

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Bibliographic Details
Published in:Journal of proteome research 2008-07, Vol.7 (7), p.3054-3059
Main Authors: Ruttenberg, Brian E, Pisitkun, Trairak, Knepper, Mark A, Hoffert, Jason D
Format: Article
Language:English
Subjects:
Algorithms
Animals
Aquaporin 2 - metabolism
Chromatography, Liquid
Databases, Factual
HeLa Cells
Humans
Kidney Tubules, Collecting - chemistry
Markov Chains
Monte Carlo Method
Phosphopeptides - analysis
Phosphorylation
Proteomics
Rats
Software
Spectrometry, Mass, Electrospray Ionization
Tandem Mass Spectrometry
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Description
Summary:Correct phosphorylation site assignment is a critical aspect of phosphoproteomic analysis. Large-scale phosphopeptide data sets that are generated through liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) analysis often contain hundreds or thousands of phosphorylation sites that require validation. To this end, we have created PhosphoScore, an open-source assignment program that is compatible with phosphopeptide data from multiple MS levels (MS(n)). The algorithm takes into account both the match quality and normalized intensity of observed spectral peaks compared to a theoretical spectrum. PhosphoScore produced >95% correct MS(2) assignments from known synthetic data, > 98% agreement with an established MS(2) assignment algorithm (Ascore), and >92% agreement with visual inspection of MS(3) and MS(4) spectra.
ISSN:1535-3893
1535-3907
DOI:10.1021/pr800169k