WO2003006951A3 - System and method of determining proteomic differences - Google Patents

System and method of determining proteomic differences Download PDF

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Publication number
WO2003006951A3
WO2003006951A3 PCT/US2002/022320 US0222320W WO03006951A3 WO 2003006951 A3 WO2003006951 A3 WO 2003006951A3 US 0222320 W US0222320 W US 0222320W WO 03006951 A3 WO03006951 A3 WO 03006951A3
Authority
WO
WIPO (PCT)
Prior art keywords
peptide
expression
populations
spectra
proteomic differences
Prior art date
Application number
PCT/US2002/022320
Other languages
French (fr)
Other versions
WO2003006951A9 (en
WO2003006951A2 (en
Inventor
Michael Washburn
Cosmin Deciu
Ryan Ulasek
Original Assignee
Syngenta Participations Ag
Michael Washburn
Cosmin Deciu
Ryan Ulasek
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 Syngenta Participations Ag, Michael Washburn, Cosmin Deciu, Ryan Ulasek filed Critical Syngenta Participations Ag
Priority to EP02759149A priority Critical patent/EP1428019A4/en
Priority to CA002453725A priority patent/CA2453725A1/en
Publication of WO2003006951A2 publication Critical patent/WO2003006951A2/en
Publication of WO2003006951A3 publication Critical patent/WO2003006951A3/en
Publication of WO2003006951A9 publication Critical patent/WO2003006951A9/en

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Classifications

    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6803General methods of protein analysis not limited to specific proteins or families of proteins
    • G01N33/6848Methods of protein analysis involving mass spectrometry
    • G01N33/6851Methods of protein analysis involving laser desorption ionisation mass spectrometry
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/58Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving labelled substances
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6803General methods of protein analysis not limited to specific proteins or families of proteins
    • G01N33/6818Sequencing of polypeptides
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/30Detection of binding sites or motifs
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/50Mutagenesis
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N30/00Investigating or analysing materials by separation into components using adsorption, absorption or similar phenomena or using ion-exchange, e.g. chromatography or field flow fractionation
    • G01N30/02Column chromatography
    • G01N2030/022Column chromatography characterised by the kind of separation mechanism
    • G01N2030/027Liquid chromatography
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2458/00Labels used in chemical analysis of biological material
    • G01N2458/15Non-radioactive isotope labels, e.g. for detection by mass spectrometry
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N30/00Investigating or analysing materials by separation into components using adsorption, absorption or similar phenomena or using ion-exchange, e.g. chromatography or field flow fractionation
    • G01N30/02Column chromatography
    • G01N30/62Detectors specially adapted therefor
    • G01N30/72Mass spectrometers
    • G01N30/7233Mass spectrometers interfaced to liquid or supercritical fluid chromatograph
    • G01N30/724Nebulising, aerosol formation or ionisation
    • G01N30/7266Nebulising, aerosol formation or ionisation by electric field, e.g. electrospray
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • YGENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10TTECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00Chemistry: analytical and immunological testing
    • Y10T436/13Tracers or tags
    • YGENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10TTECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00Chemistry: analytical and immunological testing
    • Y10T436/24Nuclear magnetic resonance, electron spin resonance or other spin effects or mass spectrometry

Abstract

The present invention relates to a system and methods for identifying differential peptide expression in one or more peptide populations. Each population 109 is labeled with a discernable label and provides a mechanism to resolve mixed peptide populations 130 using mass spectroscopy-based techniques. Spectra 146 produced by the peptide sample are used to interrogate a spectral database in which peptide sequences of known spectra are stored. In addition to providing sequence information, the methods presented herein may be used to determine qualitative and quantitative measurements of peptide expression. These measurements may further be used to determine proteomic differences and novel peptide expression.
PCT/US2002/022320 2001-07-13 2002-07-12 System and method of determining proteomic differences WO2003006951A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
EP02759149A EP1428019A4 (en) 2001-07-13 2002-07-12 System and method of determining proteomic differences
CA002453725A CA2453725A1 (en) 2001-07-13 2002-07-12 System and method of determining proteomic differences

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US30516901P 2001-07-13 2001-07-13
US60/305,169 2001-07-13
US35952402P 2002-02-21 2002-02-21
US60/359,524 2002-02-21

Publications (3)

Publication Number Publication Date
WO2003006951A2 WO2003006951A2 (en) 2003-01-23
WO2003006951A3 true WO2003006951A3 (en) 2003-05-22
WO2003006951A9 WO2003006951A9 (en) 2004-05-13

Family

ID=26974441

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2002/022320 WO2003006951A2 (en) 2001-07-13 2002-07-12 System and method of determining proteomic differences

Country Status (4)

Country Link
US (2) US20030068825A1 (en)
EP (1) EP1428019A4 (en)
CA (1) CA2453725A1 (en)
WO (1) WO2003006951A2 (en)

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CA2349265A1 (en) * 2001-05-30 2002-11-30 Andrew Emili Protein expression profile database
CA2393726A1 (en) * 2002-07-16 2004-01-16 Steven J. Locke Quantitative proteomics via isotopically differentiated derivatization
JP3917625B2 (en) * 2003-02-14 2007-05-23 富士通株式会社 Data analysis device
US8507285B2 (en) * 2003-03-13 2013-08-13 Agilent Technologies, Inc. Methods and devices for identifying biopolymers using mass spectroscopy
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JP4393206B2 (en) * 2004-01-19 2010-01-06 株式会社日立ハイテクノロジーズ Data processor for mass spectrometer
US20050251774A1 (en) * 2004-05-07 2005-11-10 Shah Gaurav R Circuit design property storage and manipulation
US20080044857A1 (en) * 2004-05-25 2008-02-21 The Gov Of Usa As Represented By The Secretary Of Methods For Making And Using Mass Tag Standards For Quantitative Proteomics
US7736905B2 (en) * 2006-03-31 2010-06-15 Biodesix, Inc. Method and system for determining whether a drug will be effective on a patient with a disease
WO2007149498A2 (en) * 2006-06-21 2007-12-27 Northeastern University Narrow bore porous layer open tube capillary column and uses thereof
EP2087433A4 (en) * 2006-11-14 2017-11-29 ABB, Inc. System for storing and presenting sensor and spectral data for batch processes
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US7897405B2 (en) * 2008-02-11 2011-03-01 Thermo Finnigan Llc Method for identifying the elution time of an analyte
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EP3660504A1 (en) * 2018-11-30 2020-06-03 Thermo Fisher Scientific (Bremen) GmbH Systems and methods for determining mass of an ion species
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Also Published As

Publication number Publication date
EP1428019A4 (en) 2006-04-26
WO2003006951A9 (en) 2004-05-13
US20060004525A1 (en) 2006-01-05
WO2003006951A2 (en) 2003-01-23
US20030068825A1 (en) 2003-04-10
CA2453725A1 (en) 2003-01-23
EP1428019A2 (en) 2004-06-16

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