uu.seUppsala University Publications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Alternative methods for verifying the results of the mass spectrometric identification of peptides in shotgun proteomics
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
Show others and affiliations
2010 (English)In: Journal of Analytical Chemistry, ISSN 1061-9348, E-ISSN 1608-3199, Vol. 65, no 14, 1462-1468 p.Article in journal (Refereed) Published
Abstract [en]

Database search is the most popular approach used for the identification of peptides in contemporary shotgun proteomics; it utilizes only mass spectrometric data. In this work, we introduce three criteria for the verification of peptide identification; these are based on the analysis of data orthogonal to tandem mass spectra. The first one utilizes chromatographic retention times of peptides. The development of such approaches has been hindered by the relatively low accuracy of retention time prediction algorithms. In this work, we suggest the use of two independent models of the liquid chromatography of peptides, which increase the reliability of the results. The second criterion utilizes the mean number of missed tryptic cleavages per peptide. The third one results from the analysis of the difference between theoretical and experimentally measured peptide masses. The proposed criteria were applied to the tandem mass spectra of tryptic peptides from rat kidney tissue, which were processed by the Mascot search engine. All the criteria showed that Mascot significantly overestimated the reliability of an identification. This conclusion was supported by the PeptideProphet algorithm.

Place, publisher, year, edition, pages
2010. Vol. 65, no 14, 1462-1468 p.
Keyword [en]
proteomics, Mascot, mass spectrometry, liquid chromatography, retention time prediction
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-148612DOI: 10.1134/S1061934810140042ISI: 000287150000004OAI: oai:DiVA.org:uu-148612DiVA: diva2:402475
Available from: 2011-03-08 Created: 2011-03-08 Last updated: 2017-12-11Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full text
By organisation
Department of Cell and Molecular Biology
In the same journal
Journal of Analytical Chemistry
Biological Sciences

Search outside of DiVA

GoogleGoogle Scholar

doi
urn-nbn

Altmetric score

doi
urn-nbn
Total: 321 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf