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Submitted on March 23, 2007
Revised on September 12, 2007
Accepted on September 13, 2007

Investigating MS2-MS3 matching statistics: A model for coupling consecutive stage mass spectrometry data for increased peptide identification confidence

Peter J. Ulintz, Bernd Bodenmiller, Philip C. Andrews, Ruedi Aebersold, and Alexey I. Nesvizhskii

Pathology, University of Michigan Medical School, Ann Arbor, MI 48109

Corresponding Author: nesvi{at}med.umich.edu

Improvements in ion trap instrumentation have made n-dimensional mass spectrometry more practical. The overall goal of the study is to describe a model for making use of MS2 and MS3 information in mass spectrometry experiments. We present a statistical model for adjusting peptide identification probabilities based on the combined information obtained by coupling peptide assignments of consecutive MS2 and MS3 spectra. Using two data sets, a mixture of known proteins and a complex phosphopeptide-enriched sample, we demonstrate an increase in discriminating power of the adjusted probabilities, compared to models using MS2 or MS3 data only. This work also addresses the overall value of generating MS3 data as compared to an MS2-only approach, with a focus on the analysis of phosphopeptide data.


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N. Bandeira, J. V. Olsen, M. Mann, and P. A. Pevzner
Multi-spectra peptide sequencing and its applications to multistage mass spectrometry
Bioinformatics, July 1, 2008; 24(13): i416 - i423.
[Abstract] [Full Text] [PDF]


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