A Systematic Statistical Analysis of Ion Trap Tandem Mass Spectra in View of Peptide Scoring
- Jacques ColingeAffiliated withGeneProt Inc.
- , Alexandre MasselotAffiliated withGeneProt Inc.
- , Jérôme MagninAffiliated withGeneProt Inc.
Tandem mass spectrometry has become central in proteomics projects. In particular, it is of prime importance to design sensitive and selective score functions to reliably identify peptides in databases. By using a huge collection of 140 000+ peptide MS/MS spectra, we systematically study the importance of many characteristics of a match (peptide sequence/spectrum) to include in a score function. Besides classical match characteristics, we investigate the value of new characteristics such as amino acid dependence and consecutive fragment matches. We finally select a combination of promising characteristics and show that the corresponding score function achieves very low false positive rates while being very sensitive, thereby enabling highly automated peptide identification in large proteomics projects. We compare our results to widely used protein identification systems and show a significant reduction in false positives.
- A Systematic Statistical Analysis of Ion Trap Tandem Mass Spectra in View of Peptide Scoring
- Book Title
- Algorithms in Bioinformatics
- Book Subtitle
- Third International Workshop, WABI 2003, Budapest, Hungary, September 15-20, 2003. Proceedings
- pp 25-38
- Print ISBN
- Online ISBN
- Series Title
- Lecture Notes in Computer Science
- Series Volume
- Series ISSN
- Springer Berlin Heidelberg
- Copyright Holder
- Springer-Verlag Berlin Heidelberg
- Additional Links
- Industry Sectors
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- Editor Affiliations
- 7. Department of Biomathematical Sciences, The Mount Sinai School of Medicine
- 8. Institute of Biomedical and Life Sciences, Division of Environmental and Evolutionary Biology, University of Glasgow
- Author Affiliations
- 9. GeneProt Inc., Pré de la Fontaine 2, CH-1219, Meyrin, Switzerland
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