Integrated data management and validation platform for phosphorylated tandem mass spectrometry data.
Integrated data management and validation platform for phosphorylated tandem mass spectrometry data.
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DOI：
10.1002/pmic.200900727
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发表时间：
2010-10
期刊：
影响因子：
3.4
通讯作者：
Hautaniemi, Sampsa
中科院分区：
文献类型：
--
作者：
Lahesmaa-Korpinen, Anna-Maria;Carlson, Scott M.;White, Forest M.;Hautaniemi, Sampsa
Tandem mass spectrometry (MS/MS) is a widely used method for proteome-wide analysis of protein expression and post-translational modifications (PTMs). The thousands of MS/MS spectra produced from a single experiment pose a major challenge for downstream analysis. Standard programs, such as Mascot, provide peptide assignments for many of the spectra, including identification of PTM sites, but these results are plagued by false positive identifications. In phosphoproteomics experiments only a single peptide assignment is typically available to support identification of each phosphorylation site, so minimizing false positives is critical. Thus, tedious manual validation is often required to increase confidence in the spectral assignments. We have developed phoMSVal, an open-source platform for managing MS/MS data and automatically validating identified phosphopeptides. We tested five classification algorithms with 17 extracted features to separate correct peptide assignments from incorrect ones using over 3000 manually curated spectra. The naive Bayes algorithm was among the best classifiers with an area under the ROC curve value of 97% and positive predictive value of 97% for phosphotyrosine data. This classifier required only three features to achieve a 76% decrease in false positives as compared to Mascot while retaining 97% of true positives. This algorithm was able to classify an independent phosphoserine/threonine dataset with area under ROC curve value of 93% and positive predictive value of 91%, demonstrating the applicability of this method for all types of phospho-MS/MS data. PhoMSVal is available at http://csbi.ltdk.helsinki.fi/phomsval
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