D‐score: A search engine independent MD‐score. Issue 6 (15th February 2013)
- Record Type:
- Journal Article
- Title:
- D‐score: A search engine independent MD‐score. Issue 6 (15th February 2013)
- Main Title:
- D‐score: A search engine independent MD‐score
- Authors:
- Vaudel, Marc
Breiter, Daniela
Beck, Florian
Rahnenführer, Jörg
Martens, Lennart
Zahedi, René P.
Zahedi, René
Sickmann, Albert - Abstract:
- <abstract abstract-type="main"> <title> <x xml:space="preserve">Abstract</x> </title> <p>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.</p> </abstract>
- Is Part Of:
- Proteomics. Volume 13:Issue 6(2013:Mar.)
- Journal:
- Proteomics
- Issue:
- Volume 13:Issue 6(2013:Mar.)
- Issue Display:
- Volume 13, Issue 6 (2013)
- Year:
- 2013
- Volume:
- 13
- Issue:
- 6
- Issue Sort Value:
- 2013-0013-0006-0000
- Page Start:
- 1036
- Page End:
- 1041
- Publication Date:
- 2013-02-15
- Subjects:
- Proteins -- Separation -- Periodicals
Bioinformatics -- Periodicals
Proteomics -- Periodicals
Genomes -- Periodicals
Molecular genetics -- Periodicals
572.605 - Journal URLs:
- http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1615-9861 ↗
http://onlinelibrary.wiley.com/ ↗ - DOI:
- 10.1002/pmic.201200408 ↗
- Languages:
- English
- ISSNs:
- 1615-9853
- Deposit Type:
- Legaldeposit
- View Content:
- Available online (eLD content is only available in our Reading Rooms) ↗
- Physical Locations:
- British Library DSC - 6936.178000
British Library DSC - BLDSS-3PM
British Library HMNTS - ELD Digital store - Ingest File:
- 3117.xml