WO2002061661A3 - Methods for determining protein and peptide terminal sequences - Google Patents

Methods for determining protein and peptide terminal sequences Download PDF

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Publication number
WO2002061661A3
WO2002061661A3 PCT/US2001/049491 US0149491W WO02061661A3 WO 2002061661 A3 WO2002061661 A3 WO 2002061661A3 US 0149491 W US0149491 W US 0149491W WO 02061661 A3 WO02061661 A3 WO 02061661A3
Authority
WO
WIPO (PCT)
Prior art keywords
sequence
ranking
methods
acid sequences
amino acid
Prior art date
Application number
PCT/US2001/049491
Other languages
French (fr)
Other versions
WO2002061661A2 (en
Inventor
Luke V Schneider
Robert Petesch
Michael P Hall
Original Assignee
Target Discovery Inc
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 Target Discovery Inc filed Critical Target Discovery Inc
Priority to EP01994337A priority Critical patent/EP1430436A2/en
Priority to IL15528101A priority patent/IL155281A0/en
Priority to AU2002246744A priority patent/AU2002246744B2/en
Priority to JP2002561757A priority patent/JP4259869B2/en
Priority to CA000000001A priority patent/CA2425798A1/en
Publication of WO2002061661A2 publication Critical patent/WO2002061661A2/en
Priority to IL155281A priority patent/IL155281A/en
Priority to IS6781A priority patent/IS6781A/en
Priority to NO20033632A priority patent/NO20033632D0/en
Publication of WO2002061661A3 publication Critical patent/WO2002061661A3/en

Links

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
    • G01N33/6848—Methods of protein analysis involving mass spectrometry
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869—Methods for sequencing
    • C12Q1/6872—Methods for sequencing involving mass spectrometry
    • H—ELECTRICITY
    • H01—ELECTRIC ELEMENTS
    • H01J—ELECTRIC DISCHARGE TUBES OR DISCHARGE LAMPS
    • H01J49/00—Particle spectrometers or separator tubes
    • H01J49/004—Combinations of spectrometers, tandem spectrometers, e.g. MS/MS, MSn
    • H01J49/0045—Combinations of spectrometers, tandem spectrometers, e.g. MS/MS, MSn characterised by the fragmentation or other specific reaction
    • Y—GENERAL 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
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10T—TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00—Chemistry: analytical and immunological testing
    • Y10T436/10—Composition for standardization, calibration, simulation, stabilization, preparation or preservation; processes of use in preparation for chemical testing
    • Y10T436/105831—Protein or peptide standard or control [e.g., hemoglobin, etc.]
    • Y—GENERAL 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
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10T—TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00—Chemistry: analytical and immunological testing
    • Y10T436/14—Heterocyclic carbon compound [i.e., O, S, N, Se, Te, as only ring hetero atom]
    • Y10T436/142222—Hetero-O [e.g., ascorbic acid, etc.]
    • Y10T436/143333—Saccharide [e.g., DNA, etc.]
    • Y—GENERAL 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
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10T—TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00—Chemistry: analytical and immunological testing
    • Y10T436/24—Nuclear magnetic resonance, electron spin resonance or other spin effects or mass spectrometry
    • Y—GENERAL 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
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10T—TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00—Chemistry: analytical and immunological testing
    • Y10T436/25—Chemistry: analytical and immunological testing including sample preparation
    • Y10T436/25125—Digestion or removing interfering materials

Abstract

Methods and apparatuses for deriving the sequence of an oligomer. In one exemplary method for deriving the sequence of a polypeptide, a predetermined set of mass/charge values for amino acid sequences is stored. An abundance value from mass spectrum data for each mass/charge value in the predetermined set is determined to produce a plurality of abundance values. A first ranking, based on the plurality of abundance values, is calculated for each sequence of a set of amino acid sequences having a first number of amino acids. A second ranking, based on the plurality of abundance values, for each sequence of a set of amino acid sequences having a second number of amino acids is calculated. A cumulative ranking, based on the first ranking and the second ranking, is calculated for each sequence of a set of amino acid sequences having at least the second number of amino acids.
PCT/US2001/049491 2000-10-19 2001-10-19 Methods for determining protein and peptide terminal sequences WO2002061661A2 (en)

Priority Applications (8)

Application Number Priority Date Filing Date Title
EP01994337A EP1430436A2 (en) 2000-10-19 2001-10-19 Methods for determining protein and peptide terminal sequences
IL15528101A IL155281A0 (en) 2000-10-19 2001-10-19 Methods for determining protein and peptide terminal sequences
AU2002246744A AU2002246744B2 (en) 2000-10-19 2001-10-19 Methods for determining protein and peptide terminal sequences
JP2002561757A JP4259869B2 (en) 2000-10-19 2001-10-19 Method for determining protein and peptide terminal sequences
CA000000001A CA2425798A1 (en) 2000-10-19 2001-10-19 Methods for determining protein and peptide terminal sequences
IL155281A IL155281A (en) 2000-10-19 2003-04-08 Methods for determining protein and peptide terminal sequences
IS6781A IS6781A (en) 2000-10-19 2003-04-11 Procedures for the determination of terminal sequences of proteins and peptides
NO20033632A NO20033632D0 (en) 2000-10-19 2003-08-15 Methods for determining protein and peptide terminal sequences

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US24239800P 2000-10-19 2000-10-19
US24216500P 2000-10-19 2000-10-19
US60/242,165 2000-10-19
US60/242,398 2000-10-19

Publications (2)

Publication Number Publication Date
WO2002061661A2 WO2002061661A2 (en) 2002-08-08
WO2002061661A3 true WO2002061661A3 (en) 2004-04-08

Family

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Family Applications (2)

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PCT/US2001/049951 WO2002066952A2 (en) 2000-10-19 2001-10-19 Mass defect labeling for the determination of oligomer sequences
PCT/US2001/049491 WO2002061661A2 (en) 2000-10-19 2001-10-19 Methods for determining protein and peptide terminal sequences

Family Applications Before (1)

Application Number Title Priority Date Filing Date
PCT/US2001/049951 WO2002066952A2 (en) 2000-10-19 2001-10-19 Mass defect labeling for the determination of oligomer sequences

Country Status (13)

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US (4) US20040209251A1 (en)
EP (3) EP1430436A2 (en)
JP (3) JP4259869B2 (en)
AT (1) ATE552348T1 (en)
AU (2) AU2002253825B8 (en)
CA (2) CA2426580C (en)
DK (1) DK1358458T3 (en)
ES (1) ES2385335T3 (en)
IL (5) IL155518A0 (en)
IS (1) IS6781A (en)
NO (1) NO20033632D0 (en)
PT (1) PT1358458E (en)
WO (2) WO2002066952A2 (en)

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