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WO2003038728A3 - A computer system and method using mass spectrometry data and a protein database for identifying unknown proteins - Google Patents

A computer system and method using mass spectrometry data and a protein database for identifying unknown proteins Download PDF

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Publication number
WO2003038728A3
WO2003038728A3 PCT/IB2002/004839 IB0204839W WO03038728A3 WO 2003038728 A3 WO2003038728 A3 WO 2003038728A3 IB 0204839 W IB0204839 W IB 0204839W WO 03038728 A3 WO03038728 A3 WO 03038728A3
Authority
WO
WIPO (PCT)
Prior art keywords
proteins
selecting
providing
protein
candidate
Prior art date
Application number
PCT/IB2002/004839
Other languages
French (fr)
Other versions
WO2003038728A2 (en
Inventor
Jari Haekkinen
Thorsteinn Roegnvaldsson
Jim Samuelsson
Original Assignee
Biobridge Computing Ab
Jari Haekkinen
Thorsteinn Roegnvaldsson
Jim Samuelsson
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Biobridge Computing Ab, Jari Haekkinen, Thorsteinn Roegnvaldsson, Jim Samuelsson filed Critical Biobridge Computing Ab
Priority to AU2002347462A priority Critical patent/AU2002347462A1/en
Publication of WO2003038728A2 publication Critical patent/WO2003038728A2/en
Publication of WO2003038728A3 publication Critical patent/WO2003038728A3/en

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Classifications

    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins

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  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Molecular Biology (AREA)
  • Hematology (AREA)
  • Chemical & Material Sciences (AREA)
  • Urology & Nephrology (AREA)
  • Physics & Mathematics (AREA)
  • Immunology (AREA)
  • Biomedical Technology (AREA)
  • Biophysics (AREA)
  • Food Science & Technology (AREA)
  • Biotechnology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Microbiology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Cell Biology (AREA)
  • Medicinal Chemistry (AREA)
  • Analytical Chemistry (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • General Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Other Investigation Or Analysis Of Materials By Electrical Means (AREA)

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.
PCT/IB2002/004839 2001-11-01 2002-11-01 A computer system and method using mass spectrometry data and a protein database for identifying unknown proteins WO2003038728A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2002347462A AU2002347462A1 (en) 2001-11-01 2002-11-01 A computer system and method using mass spectrometry data and a protein database for identifying unknown proteins

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
DKPA200101616 2001-11-01
DKPA200101616 2001-11-01

Publications (2)

Publication Number Publication Date
WO2003038728A2 WO2003038728A2 (en) 2003-05-08
WO2003038728A3 true WO2003038728A3 (en) 2003-11-06

Family

ID=8160803

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/IB2002/004839 WO2003038728A2 (en) 2001-11-01 2002-11-01 A computer system and method using mass spectrometry data and a protein database for identifying unknown proteins

Country Status (2)

Country Link
AU (1) AU2002347462A1 (en)
WO (1) WO2003038728A2 (en)

Families Citing this family (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6936813B2 (en) * 2004-02-02 2005-08-30 Agilent Technologies, Inc. Dynamic library searching
WO2006133568A1 (en) * 2005-06-16 2006-12-21 Caprion Pharmaceuticals Inc. Virtual mass spectrometry
US7894650B2 (en) * 2005-11-10 2011-02-22 Microsoft Corporation Discover biological features using composite images
KR100853786B1 (en) * 2006-07-12 2008-08-22 한국기초과학지원연구원 Protein database reconstruction method for protein identification and protein identification method using the same
CN103389335A (en) * 2012-05-11 2013-11-13 中国科学院大连化学物理研究所 Analysis device and method for identifying biomacromolecules
CN115129836B (en) * 2022-06-08 2025-05-09 阿里巴巴（中国）有限公司 Dialogue data processing method, device, equipment and storage medium

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5538897A (en) * 1994-03-14 1996-07-23 University Of Washington Use of mass spectrometry fragmentation patterns of peptides to identify amino acid sequences in databases
WO2000073787A1 (en) * 1999-05-27 2000-12-07 Rockefeller University An expert system for protein identification using mass spectrometric information combined with database searching
WO2001057519A2 (en) * 2000-02-07 2001-08-09 MAX-PLANCK-Gesellschaft zur Förderung der Wissenschaften e.V. Method for identifying and/or characterizing a (poly)peptide
WO2002021139A2 (en) * 2000-09-08 2002-03-14 Oxford Glycosciences (Uk) Ltd. Automated identification of peptides

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5538897A (en) * 1994-03-14 1996-07-23 University Of Washington Use of mass spectrometry fragmentation patterns of peptides to identify amino acid sequences in databases
WO2000073787A1 (en) * 1999-05-27 2000-12-07 Rockefeller University An expert system for protein identification using mass spectrometric information combined with database searching
WO2001057519A2 (en) * 2000-02-07 2001-08-09 MAX-PLANCK-Gesellschaft zur Förderung der Wissenschaften e.V. Method for identifying and/or characterizing a (poly)peptide
WO2002021139A2 (en) * 2000-09-08 2002-03-14 Oxford Glycosciences (Uk) Ltd. Automated identification of peptides

Non-Patent Citations (9)

* Cited by examiner, † Cited by third party
Title
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 *
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 *
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 *
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 *
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 *
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 *
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 *
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 *
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 *

Also Published As

Publication number Publication date
AU2002347462A1 (en) 2003-05-12
WO2003038728A2 (en) 2003-05-08

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