Title:
A COMPUTER SYSTEM AND METHOD USING MASS SPECTROMETRY DATA AND A PROTEIN DATABASE FOR IDENTIFYING UNKNOWN PROTEINS
Document Type and Number:
WIPO Patent Application WO2003038728
Kind Code:
A3
Abstract:
The present invention relates to a computer system and a method for selecting one or more candidate proteins from a plurality of proteins stored in a database. The invention relates in particular to a method for providing a measure applicable in selecting proteins in a database storing a numerical representation of theoretical mass spectrum for a plurality of proteins. The method comprises the steps of: extracting noise-free mono-isotopic peptide peaks from the numerical representation of the mass spectrum to be identified based on a numerical representation of a mass spectrum of a protein to be identified in the form of corresponding values of entity mass/electric charge and intensity, thereby providing, if possible, a list of selected peaks; selecting at least one candidate protein from the database, said candidate(s) being selected based on a closeness-of-fit algorithm providing a set of peak matches between the list of selected peaks and peaks of the candidate protein(s), determining the probability for the set of peak matches to occur, thereby providing a measure applicable in selecting protein candidates. The present invention also relates to a graphical user interface rendering utilisation of the method easy.
Inventors:
HAEKKINEN JARI (SE)
ROEGNVALDSSON THORSTEINN (SE)
SAMUELSSON JIM (SE)
ROEGNVALDSSON THORSTEINN (SE)
SAMUELSSON JIM (SE)
Application Number:
PCT/IB2002/004839
Publication Date:
November 06, 2003
Filing Date:
November 01, 2002
Export Citation:
Assignee:
BIOBRIDGE COMPUTING AB (SE)
HAEKKINEN JARI (SE)
ROEGNVALDSSON THORSTEINN (SE)
SAMUELSSON JIM (SE)
HAEKKINEN JARI (SE)
ROEGNVALDSSON THORSTEINN (SE)
SAMUELSSON JIM (SE)
International Classes:
G01N33/68; (IPC1-7): G01N33/68; G06F19/00
Domestic Patent References:
| WO2000073787A1 | 2000-12-07 | |||
| WO2001057519A2 | 2001-08-09 | |||
| WO2002021139A2 | 2002-03-14 |
Foreign References:
| US5538897A | 1996-07-23 |
Other References:
BERNDT P ET AL: "Reliable automatic protein identification from matrix-assisted laser desorption/ionization mass spectrometric peptide fingerprints", ELECTROPHORESIS, WEINHEIM, DE, vol. 20, 18 December 1999 (1999-12-18), pages 3521 - 3526, XP002223132, ISSN: 0173-0835
OLE N JENSEN ET AL: "Delayed extraction improves specificity in database searches by matrix-assisted laser desorption / ionization peptide maps", RAPID COMMUNICATIONS IN MASS SPECTROMETRY, vol. 10, 23 July 1996 (1996-07-23), 1996 John Wiley & Sons ltd, pages 1371 - 1378, XP002902844, ISSN: 0951-4198
ROBIN GRAS ET AL: "Improving protein identification from peptide mass fingerprinting through a parameterized multi-level scoring algorithm and an optimized peak detection", ELECTROPHORESIS, vol. 20, 1999, Wiley-VCH Verlag GMBH 1999, pages 3535 - 3550, XP002902845, ISSN: 0173-0835
MARCO WEHOFSKY ET AL: "Automated deconvolution and deisotoping of electrospray mass spectra.", JOURNAL OF MASS SPECTROMETRY, vol. 37, 2002, John Wiley & Sons ltd 2002, pages 223 - 229, XP002902843
BREEN E J ET AL: "AUTOMATIC POISSON PEAK HARVESTING FOR HIGH THROUGHPUT PROTEIN IDENTIFICATION", ELECTROPHORESIS, VOL. 21, PAGE(S) 2243-2251, WILEY-VCH VERLAG GMBH, WEINHEIM DE,, ISSN: 0173-0835, XP001040008
MARTIN ETHIER ET AL: "Automated structural assignment of derivatized complex N-linked oligosaccharides from tandem mass spectra.", RAPID COMMUNICATIONS IN MASS SPECTROMETRY, vol. 16, 2002, 2002 John Wiley & sons ltd, pages 1743 - 1754, XP002902846
WENZHU ZHANG ET AL: "Profound: An expert system for protein identification using mass spectrometric peptide mapping information.", ANALYTICAL CHEMISTRY, vol. 72, no. 11, 1 June 2000 (2000-06-01), pages 2482 - 2489, XP002902847
PERKINS D N ET AL: "PROBABILITY-BASED PROTEIN IDENTIFICATION BY SEARCHING SEQUENCE DATABASES USING MASS SPECTROMETRY DATA.", ELECTROPHORESIS, VOL. 20, PAGE(S) 3551-3567, WILEY-VCH VERRLAG GMBH , WEINHEIM (DE), ISSN: 0173-0835, XP001051561
PAPPIN D J C ET AL: "RAPID IDENTIFICATION OF PROTEINS BY PEPTIDE-MASS FINGERPRINTING.", 1993, CURRENT BIOLOGY, CURRENT SCIENCE,, GB, VOL. 3, NR. 6, PAGE(S) 327-332, ISSN: 0960-9822, XP000856937
OLE N JENSEN ET AL: "Delayed extraction improves specificity in database searches by matrix-assisted laser desorption / ionization peptide maps", RAPID COMMUNICATIONS IN MASS SPECTROMETRY, vol. 10, 23 July 1996 (1996-07-23), 1996 John Wiley & Sons ltd, pages 1371 - 1378, XP002902844, ISSN: 0951-4198
ROBIN GRAS ET AL: "Improving protein identification from peptide mass fingerprinting through a parameterized multi-level scoring algorithm and an optimized peak detection", ELECTROPHORESIS, vol. 20, 1999, Wiley-VCH Verlag GMBH 1999, pages 3535 - 3550, XP002902845, ISSN: 0173-0835
MARCO WEHOFSKY ET AL: "Automated deconvolution and deisotoping of electrospray mass spectra.", JOURNAL OF MASS SPECTROMETRY, vol. 37, 2002, John Wiley & Sons ltd 2002, pages 223 - 229, XP002902843
BREEN E J ET AL: "AUTOMATIC POISSON PEAK HARVESTING FOR HIGH THROUGHPUT PROTEIN IDENTIFICATION", ELECTROPHORESIS, VOL. 21, PAGE(S) 2243-2251, WILEY-VCH VERLAG GMBH, WEINHEIM DE,, ISSN: 0173-0835, XP001040008
MARTIN ETHIER ET AL: "Automated structural assignment of derivatized complex N-linked oligosaccharides from tandem mass spectra.", RAPID COMMUNICATIONS IN MASS SPECTROMETRY, vol. 16, 2002, 2002 John Wiley & sons ltd, pages 1743 - 1754, XP002902846
WENZHU ZHANG ET AL: "Profound: An expert system for protein identification using mass spectrometric peptide mapping information.", ANALYTICAL CHEMISTRY, vol. 72, no. 11, 1 June 2000 (2000-06-01), pages 2482 - 2489, XP002902847
PERKINS D N ET AL: "PROBABILITY-BASED PROTEIN IDENTIFICATION BY SEARCHING SEQUENCE DATABASES USING MASS SPECTROMETRY DATA.", ELECTROPHORESIS, VOL. 20, PAGE(S) 3551-3567, WILEY-VCH VERRLAG GMBH , WEINHEIM (DE), ISSN: 0173-0835, XP001051561
PAPPIN D J C ET AL: "RAPID IDENTIFICATION OF PROTEINS BY PEPTIDE-MASS FINGERPRINTING.", 1993, CURRENT BIOLOGY, CURRENT SCIENCE,, GB, VOL. 3, NR. 6, PAGE(S) 327-332, ISSN: 0960-9822, XP000856937
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