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Permanent URL to this publication: http://dx.doi.org/10.5167/uzh-24599

Nesvizhskii, A I; Roos, F F; Grossmann, J; Vogelzang, M; Eddes, J S; Gruissem, W; Baginsky, S; Aebersold, R (2006). Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. Molecular and Cellular Proteomics, 5(4):652-670.

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Abstract

In mass spectrometry-based proteomics, frequently hundreds of thousands of MS/MS spectra are collected in a single experiment. Of these, a relatively small fraction is confidently assigned to peptide sequences, whereas the majority of the spectra are not further analyzed. Spectra are not assigned to peptides for diverse reasons. These include deficiencies of the scoring schemes implemented in the database search tools, sequence variations (e.g. single nucleotide polymorphisms) or omissions in the database searched, post-translational or chemical modifications of the peptide analyzed, or the observation of sequences that are not anticipated from the genomic sequence (e.g. splice forms, somatic rearrangement, and processed proteins). To increase the amount of information that can be extracted from proteomic MS/MS datasets we developed a robust method that detects high quality spectra within the fraction of spectra unassigned by conventional sequence database searching and computes a quality score for each spectrum. We also demonstrate that iterative search strategies applied to such detected unassigned high quality spectra significantly increase the number of spectra that can be assigned from datasets and that biologically interesting new insights can be gained from existing data.

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Functional Genomics Center Zurich
08 University Research Priority Programs > Systems Biology / Functional Genomics
DDC:570 Life sciences; biology
610 Medicine & health
Language:English
Date:2006
Deposited On:17 Dec 2009 17:06
Last Modified:28 Nov 2013 01:57
Publisher:American Society for Biochemistry and Molecular Biology
ISSN:1535-9476
Additional Information:This research was originally published in Nesvizhskii, A I; Roos, F F; Grossmann, J; Vogelzang, M; Eddes, J S; Gruissem, W; Baginsky, S; Aebersold, R (2006). Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. Molecular & Cellular Proteomics, 5(4):652-670. © the American Society for Biochemistry and Molecular Biology.
Publisher DOI:10.1074/mcp.M500319-MCP200
PubMed ID:16352522
Citations:Web of Science®. Times Cited: 96
Google Scholar™
Scopus®. Citation Count: 103

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