Skip Navigation



Bioinformatics Advance Access published online on December 13, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti829
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
22/4/400    most recent
bti829v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Salmi, J.
Right arrow Articles by Aittokallio, T.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Salmi, J.
Right arrow Articles by Aittokallio, T.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received July 21, 2005
Revised December 7, 2005
Accepted December 8, 2005

Article

Quality classification of tandem mass spectrometry data

Jussi Salmi 1 *, Robert Moulder 2, Jan-Jonas Filén 3, Olli S. Nevalainen 1, Tuula A. Nyman 4, Riitta Lahesmaa 2, and Tero Aittokallio 5

1 Department of Information Technology and Turku Centre for Computer Science, University of Turku, Finland
2 Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Finland
3 Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Finland; The National Graduate School in Informational and Structural Biology, Finland
4 Finnish Institute of Occupational Health, Helsinki, Finland
5 Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Finland; Department of Mathematics, University of Turku, Finland

* To whom correspondence should be addressed.
Jussi Salmi, E-mail: jussi.salmi{at}it.utu.fi


  Abstract

Motivation: Peptide identification by tandem mass spectrometry is an important tool in proteomic research. Powerful identification programs exist, such as SEQUEST, ProICAT and Mascot, which can relate experimental spectra to the theoretical ones derived from protein databases, thus removing much of the manual input needed in the identification process. However, the time-consuming validation of the peptide identifications is still the bottleneck of many proteomic studies. One way to further streamline this process is to remove those spectra that are unlikely to provide a confident or valid peptide identification, and in this way to reduce the labour from the validation phase.

Results: We propose a prefiltering scheme for evaluating the quality of spectra before the database search. The spectra are classified into two classes: spectra which contain valuable information for peptide identification and spectra that are not derived from peptides or contain insufficient information for interpretation. The different spectral features developed for the classification are tested on a real-life material originating from human lymphoblast samples and on a standard mixture of 9 proteins, both labelled with the ICAT reagent. The results show that the prefiltering scheme efficiently separates the two spectra classes.

Availability: The software tools are available on request from the authors.

Supplementary information: The Mascot ion score distributions and the C4.5 classification rules can be found at address http://staff.cs.utu.fi/staff/jussi.salmi/Supplementary_material.pdf.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.