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D-score: a search engine independent MD-score

(2013) PROTEOMICS. 13(6). p.1036-1041
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
While peptides carrying PTMs are routinely identified in gel-free MS, the localization of the PTMs onto the peptide sequences remains challenging. Search engine scores of secondary peptide matches have been used in different approaches in order to infer the quality of site inference, by penalizing the localization whenever the search engine similarly scored two candidate peptides with different site assignments. In the present work, we show how the estimation of posterior error probabilities for peptide candidates allows the estimation of a PTM score called the D-score, for multiple search engine studies. We demonstrate the applicability of this score to three popular search engines: Mascot, OMSSA, and X!Tandem, and evaluate its performance using an already published high resolution data set of synthetic phosphopeptides. For those peptides with phosphorylation site inference uncertainty, the number of spectrum matches with correctly localized phosphorylation increased by up to 25.7% when compared to using Mascot alone, although the actual increase depended on the fragmentation method used. Since this method relies only on search engine scores, it can be readily applied to the scoring of the localization of virtually any modification at no additional experimental or in silico cost.
Keywords
DATABASE, SITE LOCALIZATION, MS/MS, SPECTROMETRY, PEPTIDE, PARSE, STRATEGIES, PROTEIN IDENTIFICATION, TANDEM MASS-SPECTRA, OPEN-SOURCE LIBRARY, PTM localization scores, PTM, Peptide identification, Bioinformatics

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Citation

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Chicago
Vaudel, Marc, Daniela Breiter, Florian Beck, Jörg Rahnenführer, Lennart Martens, and René P Zahedi. 2013. “D-score: a Search Engine Independent MD-score.” Proteomics 13 (6): 1036–1041.
APA
Vaudel, M., Breiter, D., Beck, F., Rahnenführer, J., Martens, L., & Zahedi, R. P. (2013). D-score: a search engine independent MD-score. PROTEOMICS, 13(6), 1036–1041.
Vancouver
1.
Vaudel M, Breiter D, Beck F, Rahnenführer J, Martens L, Zahedi RP. D-score: a search engine independent MD-score. PROTEOMICS. 2013;13(6):1036–41.
MLA
Vaudel, Marc, Daniela Breiter, Florian Beck, et al. “D-score: a Search Engine Independent MD-score.” PROTEOMICS 13.6 (2013): 1036–1041. Print.
@article{4248893,
  abstract     = {While peptides carrying PTMs are routinely identified in gel-free MS, the localization of the PTMs onto the peptide sequences remains challenging. Search engine scores of secondary peptide matches have been used in different approaches in order to infer the quality of site inference, by penalizing the localization whenever the search engine similarly scored two candidate peptides with different site assignments. In the present work, we show how the estimation of posterior error probabilities for peptide candidates allows the estimation of a PTM score called the D-score, for multiple search engine studies. We demonstrate the applicability of this score to three popular search engines: Mascot, OMSSA, and X!Tandem, and evaluate its performance using an already published high resolution data set of synthetic phosphopeptides. For those peptides with phosphorylation site inference uncertainty, the number of spectrum matches with correctly localized phosphorylation increased by up to 25.7\% when compared to using Mascot alone, although the actual increase depended on the fragmentation method used. Since this method relies only on search engine scores, it can be readily applied to the scoring of the localization of virtually any modification at no additional experimental or in silico cost.},
  author       = {Vaudel, Marc and Breiter, Daniela and Beck, Florian and Rahnenf{\"u}hrer, J{\"o}rg and Martens, Lennart and Zahedi, Ren{\'e} P},
  issn         = {1615-9853},
  journal      = {PROTEOMICS},
  keyword      = {DATABASE,SITE LOCALIZATION,MS/MS,SPECTROMETRY,PEPTIDE,PARSE,STRATEGIES,PROTEIN IDENTIFICATION,TANDEM MASS-SPECTRA,OPEN-SOURCE LIBRARY,PTM localization scores,PTM,Peptide identification,Bioinformatics},
  language     = {eng},
  number       = {6},
  pages        = {1036--1041},
  title        = {D-score: a search engine independent MD-score},
  url          = {http://dx.doi.org/10.1002/pmic.201200408},
  volume       = {13},
  year         = {2013},
}

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