HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) Supplemental Data All Versions of this Article: M700293-MCP200v1 7/5/962    most recent Submit a response Alert me when this article is cited Alert me when eLetters are posted Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Request Permissions Glossary Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Brosch, M. Articles by Choudhary, J. Search for Related Content PubMed PubMed Citation Articles by Brosch, M. Articles by Choudhary, J. Social Bookmarking                      What's this?

Molecular & Cellular Proteomics 7:962-970, 2008.
© 2008 by The American Society for Biochemistry and Molecular Biology, Inc.

---

Research

Comparison of Mascot and X!Tandem Performance for Low and High Accuracy Mass Spectrometry and the Development of an Adjusted Mascot Threshold^*,S

Markus Brosch, Sajani Swamy, Tim Hubbard and Jyoti Choudhary

From The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom

It is a major challenge to develop effective sequence database search algorithms to translate molecular weight and fragment mass information obtained from tandem mass spectrometry into high quality peptide and protein assignments. We investigated the peptide identification performance of Mascot and X!Tandem for mass tolerance settings common for low and high accuracy mass spectrometry. We demonstrated that sensitivity and specificity of peptide identification can vary substantially for different mass tolerance settings, but this effect was more significant for Mascot. We present an adjusted Mascot threshold, which allows the user to freely select the best trade-off between sensitivity and specificity. The adjusted Mascot threshold was compared with the default Mascot and X!Tandem scoring thresholds and shown to be more sensitive at the same false discovery rates for both low and high accuracy mass spectrometry data.

CiteULike    Complore    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				J. Zhang, J. Ma, L. Dou, S. Wu, X. Qian, H. Xie, Y. Zhu, and F. He Bayesian Nonparametric Model for the Validation of Peptide Identification in Shotgun Proteomics Mol. Cell. Proteomics, March 1, 2009; 8(3): 547 - 557. [Abstract] [Full Text] [PDF]

				K. Helsens, E. Timmerman, J. Vandekerckhove, K. Gevaert, and L. Martens Peptizer, a Tool for Assessing False Positive Peptide Identifications and Manually Validating Selected Results Mol. Cell. Proteomics, December 1, 2008; 7(12): 2364 - 2372. [Abstract] [Full Text] [PDF]