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: M800512-MCP200v1 8/9/2051    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 Google Scholar Articles by Sherman, J. Articles by Molloy, M. P. PubMed PubMed Citation Articles by Sherman, J. Articles by Molloy, M. P. Social Bookmarking                      What's this?

Molecular & Cellular Proteomics 8:2051-2062, 2009.
© 2009 by The American Society for Biochemistry and Molecular Biology, Inc.

---

Research

Unique Ion Signature Mass Spectrometry, a Deterministic Method to Assign Peptide Identity

Jamie Sherman, Matthew J. McKay, Keith Ashman and Mark P. Molloy^¶

From the Australian Proteome Analysis Facility, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney 2109, Australia

The growing use of selected reaction monitoring (SRM) mass spectrometry in proteomic analyses led us to investigate how to identify peptides by SRM using only a minimal number of fragment ions. By using a computational model of the SRM work flow we computed the potential interferences from other peptides in a given proteome. From these results, we selected the deterministic SRM addresses that contained sufficient information to confer peptide and protein identity that we termed unique ion signatures (UIS). We computationally showed that UIS comprised of only two transitions are diagnostic for >99% of Escherichia coli proteins and >96% of human proteins that possess a sequence-unique peptide. We demonstrated an example of experimental use of UIS using a modified SRM methodology to profile the E. coli tricarboxylic acid cycle from a single injection of cell lysate. In addition, we showed the potential of UIS to form the first functionally orthogonal approach to validate peptide assignments obtained from conventional analyses of MS/MS spectra. The UIS methodology is a novel deterministic peptide identification method for MS/MS spectra based on information content. These robust theoretical assays will have widespread use when integrated with previously collected MS/MS data and conventional proteomics technologies.

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

This article has been cited by other articles:

				S. E. Abbatiello, D. R. Mani, H. Keshishian, and S. A. Carr Automated Detection of Inaccurate and Imprecise Transitions in Peptide Quantification by Multiple Reaction Monitoring Mass Spectrometry Clin. Chem., February 1, 2010; 56(2): 291 - 305. [Abstract] [Full Text] [PDF]