Title:
SYSTEM AND METHOD FOR SCORING PEPTIDE MATCHES
Document Type and Number:
WIPO Patent Application WO2004013635
Kind Code:
A3
Abstract:
The present invention relates to a system and method for scoring peptide matches. Embodiments of the present invention improves identification of peptides and proteins by introducing an appropriate signal detection based scoring system and what is believed to be the new concept of an extended match. To score a match between a first peptide and a second peptide, a stochastic model may be generated based on one or more match characteristics associated with the first peptide, the second peptide and their fragments. A first probability that the first peptide matches the second peptide, and a second probability that the first peptide does not match the second peptide, may be calculated based on the stochastic model. And a match between the first peptide and the second peptide may be scored based at least in part on a ratio between the first probability and the second probability.
Inventors:
COLINGE JACQUES (CH)
MASSELOT ALEXANDRE (CH)
MASSELOT ALEXANDRE (CH)
Application Number:
PCT/IB2003/003409
Publication Date:
December 16, 2004
Filing Date:
July 25, 2003
Export Citation:
Assignee:
GENEVA BIOINFORMATICS S A (CH)
COLINGE JACQUES (CH)
MASSELOT ALEXANDRE (CH)
COLINGE JACQUES (CH)
MASSELOT ALEXANDRE (CH)
International Classes:
G01N33/68; G16B20/00; (IPC1-7): G06F19/00; G01N33/68
Foreign References:
| US6017693A | 2000-01-25 | |||
| US6393367B1 | 2002-05-21 |
Other References:
BAFNA V ET AL: "SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database", BIOINFORMATICS, OXFORD UNIVERSITY PRESS, SURREY, GB, vol. 17 Suppl 1, 2001, pages S13 - S21, XP002247078, ISSN: 1367-4803
ZHANG W ET AL: "Profound: An expert system for protein identification using mass spectrometric peptide mapping information", ANALYTICAL CHEMISTRY, AMERICAN CHEMICAL SOCIETY. COLUMBUS, US, vol. 72, no. 11, 1 June 2000 (2000-06-01), pages 2482 - 2489, XP002902847, ISSN: 0003-2700
YATES J R: "Database searching using mass spectrometry data", ELECTROPHORESIS, WEINHEIM, DE, vol. 19, 1998, pages 893 - 900, XP002964174, ISSN: 0173-0835
ZHANG W ET AL: "Profound: An expert system for protein identification using mass spectrometric peptide mapping information", ANALYTICAL CHEMISTRY, AMERICAN CHEMICAL SOCIETY. COLUMBUS, US, vol. 72, no. 11, 1 June 2000 (2000-06-01), pages 2482 - 2489, XP002902847, ISSN: 0003-2700
YATES J R: "Database searching using mass spectrometry data", ELECTROPHORESIS, WEINHEIM, DE, vol. 19, 1998, pages 893 - 900, XP002964174, ISSN: 0173-0835
Download PDF: