WO2003038728A3 - Systeme informatique et procede utilisant des donnees de spectrometrie de masse et une base de donnees proteine pour l'identification de proteines inconnues - Google Patents

Systeme informatique et procede utilisant des donnees de spectrometrie de masse et une base de donnees proteine pour l'identification de proteines inconnues 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
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WO
WIPO (PCT)
Prior art keywords
proteins
selecting
providing
protein
candidate
Prior art date
Application number
PCT/IB2002/004839
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English (en)
Other versions
WO2003038728A2 (fr
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/fr
Publication of WO2003038728A3 publication Critical patent/WO2003038728A3/fr

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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

L'invention concerne un système informatique et un procédé permettant de sélectionner une ou plusieurs protéines candidates à partir d'une pluralité de protéines mémorisées dans une base de données. L'invention concerne en particulier un procédé fournissant une mesure applicable à la sélection des protéines dans une base de données mémorisant une représentation numérique de spectre de masse théorique pour une pluralité de protéines. Le procédé selon l'invention comprend les étapes suivantes : extraction, sans bruit de fond, de pics de peptides mono-isotopes à partir de la représentation numérique du spectre de masse à identifier, sur la base d'une représentation numérique d'un spectre de masse d'une protéine à identifier sous la forme de valeurs correspondantes de masse d'entité/charge électrique et intensité, fournissant, si possible, une liste de pics sélectionnés ; sélection d'au moins une protéine candidate à partir de la base de données, lesdites candidates étant sélectionnées sur la base d'un algorithme précision d'ajustement fournissant une série d'appariemments de pics entre la liste de pics sélectionnés et de pics des protéines candidates, avec détermination de la probabilité que ladite série d'appariements se présente, ce qui permet d'obtenir une mesure applicable dans la sélection des protéines candidates. L'invention concerne également une interface utilisateur graphique facilitant l'utilisation dudit procédé.
PCT/IB2002/004839 2001-11-01 2002-11-01 Systeme informatique et procede utilisant des donnees de spectrometrie de masse et une base de donnees proteine pour l'identification de proteines inconnues WO2003038728A2 (fr)

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 (fr) 2003-05-08
WO2003038728A3 true WO2003038728A3 (fr) 2003-11-06

Family

ID=8160803

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/IB2002/004839 WO2003038728A2 (fr) 2001-11-01 2002-11-01 Systeme informatique et procede utilisant des donnees de spectrometrie de masse et une base de donnees proteine pour l'identification de proteines inconnues

Country Status (2)

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

Families Citing this family (5)

* 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 (fr) * 2005-06-16 2006-12-21 Caprion Pharmaceuticals Inc. Spectrometrie de masse virtuelle
WO2007059117A2 (fr) 2005-11-10 2007-05-24 Rosetta Inpharmatics Llc Methode de recherche de caracteristiques biologiques faisant appel a des images composites
KR100853786B1 (ko) 2006-07-12 2008-08-22 한국기초과학지원연구원 단백질 동정을 위한 단백질 데이터베이스의 재구성방법 및이를 이용한 단백질 동정 방법
CN103389335A (zh) * 2012-05-11 2013-11-13 中国科学院大连化学物理研究所 一种鉴定生物大分子的分析装置和方法

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 (fr) * 1999-05-27 2000-12-07 Rockefeller University Systeme expert pour l'identification de proteines utilisant l'information en spectrometrie de masse combinee a la recherche de base de donnees
WO2001057519A2 (fr) * 2000-02-07 2001-08-09 MAX-PLANCK-Gesellschaft zur Förderung der Wissenschaften e.V. Procede d'identification et/ou de caracterisation d'un (poly)peptide
WO2002021139A2 (fr) * 2000-09-08 2002-03-14 Oxford Glycosciences (Uk) Ltd. Identification automatisee de 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 (fr) * 1999-05-27 2000-12-07 Rockefeller University Systeme expert pour l'identification de proteines utilisant l'information en spectrometrie de masse combinee a la recherche de base de donnees
WO2001057519A2 (fr) * 2000-02-07 2001-08-09 MAX-PLANCK-Gesellschaft zur Förderung der Wissenschaften e.V. Procede d'identification et/ou de caracterisation d'un (poly)peptide
WO2002021139A2 (fr) * 2000-09-08 2002-03-14 Oxford Glycosciences (Uk) Ltd. Identification automatisee de 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 *

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

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