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Bioinformatics 2008 24(13):i416-i423; doi:10.1093/bioinformatics/btn184
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Multi-spectra peptide sequencing and its applications to multistage mass spectrometry

Nuno Bandeira 1,*, Jesper V. Olsen 2, Matthias Mann 2 and Pavel A. Pevzner 2

1Department of Computer Science and Engineering, University of California, San Diego, USA and 2Max-Planck Institute for Biochemistry, Germany

*To whom correspondence should be addressed.


  Abstract

Despite a recent surge of interest in database-independent peptide identifications, accurate de novo peptide sequencing remains an elusive goal. While the recently introduced spectral network approach resulted in accurate peptide sequencing in low-complexity samples, its success depends on the chance of presence of spectra from overlapping peptides. On the other hand, while multistage mass spectrometry (collecting multiple MS 3 spectra from each MS 2 spectrum) can be applied to all spectra in a complex sample, there are currently no software tools for de novo peptide sequencing by multistage mass spectrometry. We describe a rigorous probabilistic framework for analyzing spectra of overlapping peptides and show how to apply it for multistage mass spectrometry. Our software results in both accurate de novo peptide sequencing from multistage mass spectra (despite the inferior quality of MS 3 spectra) and improved interpretation of spectral networks. We further study the problem of de novo peptide sequencing with accurate parent mass (but inaccurate fragment masses), the protocol that may soon become the dominant mode of spectral acquisition. Most existing peptide sequencing algorithms (based on the spectrum graph approach) do not track the accurate parent mass and are thus not equipped for solving this problem. We describe a de novo peptide sequencing algorithm aimed at this experimental protocol and show that it improves the sequencing accuracy on both tandem and multistage mass spectrometry.

Availability: The open-source implementation of our software is available at http://proteomics.bioprojects.org.

Contact: bandeira{at}ucsd.edu

Supplementary information:: Supplementary data are available at Bioinformatics online.


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This article has been cited by other articles:


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 Mol. Cell. ProteomicsHome page
S. Kim, N. Bandeira, and P. A. Pevzner
Spectral Profiles, a Novel Representation of Tandem Mass Spectra and Their Applications for de Novo Peptide Sequencing and Identification
Mol. Cell. Proteomics, June 1, 2009; 8(6): 1391 - 1400.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
S. Kim, N. Gupta, N. Bandeira, and P. A. Pevzner
Spectral Dictionaries: Integrating de novo Peptide Sequencing with Database Search of Tandem Mass Spectra
Mol. Cell. Proteomics, January 1, 2009; 8(1): 53 - 69.
[Abstract] [Full Text] [PDF]


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