WO2001079523A3 - Method and system for microorganism identification by mass spectrometry-based proteome database searching - Google Patents

Method and system for microorganism identification by mass spectrometry-based proteome database searching Download PDF

Info

Publication number
WO2001079523A3
WO2001079523A3 PCT/US2001/011649 US0111649W WO0179523A3 WO 2001079523 A3 WO2001079523 A3 WO 2001079523A3 US 0111649 W US0111649 W US 0111649W WO 0179523 A3 WO0179523 A3 WO 0179523A3
Authority
WO
WIPO (PCT)
Prior art keywords
microorganism identification
mass spectrometry
proteins
data
robust
Prior art date
Application number
PCT/US2001/011649
Other languages
French (fr)
Other versions
WO2001079523A2 (en
Inventor
Fernando J Pineda
Jeffrey S Lin
Original Assignee
Univ Johns Hopkins
Fernando J Pineda
Jeffrey S Lin
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 Univ Johns Hopkins, Fernando J Pineda, Jeffrey S Lin filed Critical Univ Johns Hopkins
Priority to JP2001577506A priority Critical patent/JP2003530858A/en
Priority to EP01928435A priority patent/EP1272657A2/en
Priority to AU55293/01A priority patent/AU764402B2/en
Publication of WO2001079523A2 publication Critical patent/WO2001079523A2/en
Publication of WO2001079523A3 publication Critical patent/WO2001079523A3/en

Links

Classifications

    • H—ELECTRICITY
    • H01—ELECTRIC ELEMENTS
    • H01J—ELECTRIC DISCHARGE TUBES OR DISCHARGE LAMPS
    • H01J49/00—Particle spectrometers or separator tubes
    • H01J49/0027—Methods for using particle spectrometers
    • H01J49/0036—Step by step routines describing the handling of the data generated during a measurement
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • G16B50/30—Data warehousing; Computing architectures
    • 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
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/569—Immunoassay; Biospecific binding assay; Materials therefor for microorganisms, e.g. protozoa, bacteria, viruses
    • 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
    • G01N33/6851—Methods of protein analysis involving laser desorption ionisation mass spectrometry
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2570/00—Omics, e.g. proteomics, glycomics or lipidomics; Methods of analysis focusing on the entire complement of classes of biological molecules or subsets thereof, i.e. focusing on proteomes, glycomes or lipidomes
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Molecular Biology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Immunology (AREA)
  • Chemical & Material Sciences (AREA)
  • Urology & Nephrology (AREA)
  • Biomedical Technology (AREA)
  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Hematology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Medicinal Chemistry (AREA)
  • Bioethics (AREA)
  • Pathology (AREA)
  • Cell Biology (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Biology (AREA)
  • Microbiology (AREA)
  • Databases & Information Systems (AREA)
  • Food Science & Technology (AREA)
  • General Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Optics & Photonics (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Virology (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Information Retrieval, Db Structures And Fs Structures Therefor (AREA)
  • Other Investigation Or Analysis Of Materials By Electrical Means (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

A simple statistical model that predicts the distribution of false matches between peaks in matrix-assisted laser desorption/ionization mass spectrometry data and proteins in proteome databases is derived and validated. Given the cluttered and incomplete nature of the data, it is likely that neither simple ranking, nor simple hypothesis testing will be sufficient for truly robust microorganism identification over a large number of candidate microorganisms. In an effort to increase robust microorganism identification, the proteome databases are restricted to include data related to a given set of proteins, and not all proteins. By removing data from the proteome databases, the model is made more robust, i.e., there is a decrease in the number of false matches.
PCT/US2001/011649 2000-04-12 2001-04-11 Method and system for microorganism identification by mass spectrometry-based proteome database searching WO2001079523A2 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
JP2001577506A JP2003530858A (en) 2000-04-12 2001-04-11 Method and system for microbial identification by mass spectrometry based proteome database survey
EP01928435A EP1272657A2 (en) 2000-04-12 2001-04-11 Method and system for microorganism identification by mass spectrometry-based proteome database searching
AU55293/01A AU764402B2 (en) 2000-04-12 2001-04-11 Method and system for microorganism identification by mass spectrometry-based proteome database searching

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US19636800P 2000-04-12 2000-04-12
US60/196,368 2000-04-12

Publications (2)

Publication Number Publication Date
WO2001079523A2 WO2001079523A2 (en) 2001-10-25
WO2001079523A3 true WO2001079523A3 (en) 2002-03-21

Family

ID=22725109

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2001/011649 WO2001079523A2 (en) 2000-04-12 2001-04-11 Method and system for microorganism identification by mass spectrometry-based proteome database searching

Country Status (4)

Country Link
EP (1) EP1272657A2 (en)
JP (1) JP2003530858A (en)
AU (1) AU764402B2 (en)
WO (1) WO2001079523A2 (en)

Families Citing this family (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
DE10155707B4 (en) * 2001-11-13 2006-11-16 Bruker Daltonik Gmbh Mass determination for biopolymers
EP2157599A1 (en) * 2008-08-21 2010-02-24 Nederlandse Organisatie voor toegepast- natuurwetenschappelijk onderzoek TNO Method and apparatus for identification of biological material
EP2439536A1 (en) 2010-10-01 2012-04-11 Nederlandse Organisatie voor toegepast- natuurwetenschappelijk onderzoek TNO New classification method for spectral data
US20150186754A1 (en) 2012-07-18 2015-07-02 Nederlandse Organisatie Voor Toegepast- Natuurwetenschappelijk Onderzoek Tno Classification method for spectral data
JP7151556B2 (en) * 2019-03-05 2022-10-12 株式会社島津製作所 Microorganism identification system and program for identification of microorganisms
CN112614542B (en) * 2020-12-29 2024-02-20 北京携云启源科技有限公司 Microorganism identification method, device, equipment and storage medium

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1998035609A1 (en) * 1997-02-14 1998-08-20 Biomar International, Inc. A system for predicting future health
US5910655A (en) * 1996-01-05 1999-06-08 Maxent Solutions Ltd. Reducing interferences in elemental mass spectrometers

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5910655A (en) * 1996-01-05 1999-06-08 Maxent Solutions Ltd. Reducing interferences in elemental mass spectrometers
WO1998035609A1 (en) * 1997-02-14 1998-08-20 Biomar International, Inc. A system for predicting future health

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
BIN ZHENG ET AL: "Application of a Bayesian belief network in a computer-assisted diagnosis scheme for mass detection", MEDICAL IMAGING 1999: IMAGE PROCESSING, SAN DIEGO, CA, USA, 22-25 FEB. 1999, vol. 3661, pt.1-2, Proceedings of the SPIE - The International Society for Optical Engineering, 1999, SPIE-Int. Soc. Opt. Eng, USA, pages 1553 - 1561, XP001039884, ISSN: 0277-786X *
DEMIREV P A ET AL: "MICROORGANISM IDENTIFICATION BY MASS SPECTROMETRY AND PROTEIN DATABASE SEARCHES", ANALYTICAL CHEMISTRY, AMERICAN CHEMICAL SOCIETY. COLUMBUS, US, vol. 71, no. 14, 15 July 1999 (1999-07-15), pages 2732 - 2738, XP001031956, ISSN: 0003-2700 *
HAYEK C S ET AL: "Computer-assisted interpretation of mass spectra", JOHNS HOPKINS APL TECHNICAL DIGEST, JULY-SEPT. 1999, JOHNS HOPKINS UNIV. APPL. PHYS. LAB, USA, vol. 20, no. 3, pages 363 - 371, XP001039877, ISSN: 0270-5214 *

Also Published As

Publication number Publication date
AU764402B2 (en) 2003-08-21
EP1272657A2 (en) 2003-01-08
AU5529301A (en) 2001-10-30
WO2001079523A2 (en) 2001-10-25
JP2003530858A (en) 2003-10-21

Similar Documents

Publication Publication Date Title
WO2001057518A3 (en) Method of non-targeted complex sample analysis
US8975577B2 (en) System and method for grouping precursor and fragment ions using selected ion chromatograms
Xu et al. MassMatrix: a database search program for rapid characterization of proteins and peptides from tandem mass spectrometry data
WO2004114611A3 (en) Architecture for network search engines with fixed latency, high capacity, and high throughput
US20090300486A1 (en) Multiple-document summarization using document clustering
WO2000067194A3 (en) Method and apparatus for scalable probabilistic clustering using decision trees
WO2002050662A3 (en) Apparatus and method of video program classification based on syntax of transcript information
WO2007002729A3 (en) Method and system for predicting consumer behavior
WO2005050367A3 (en) Systems and methods for search query processing using trend analysis
WO2004070574A3 (en) System and method for semantic software analysis
CA2373568A1 (en) Method of searching similar document, system for performing the same and program for processing the same
TW200511048A (en) Patent family analysis system and method
WO2001079523A3 (en) Method and system for microorganism identification by mass spectrometry-based proteome database searching
EP2163616A3 (en) Jp170 subtilase variants
WO2002011121A8 (en) Method of and system for improving accuracy in a speech recognition system
JP2008281411A (en) Protein database retrieval method and recording medium
WO2003098190A3 (en) Protein identification from protein product ion spectra
WO2004079505A3 (en) Matching queries to partitioned document path segments
WO2006133025A3 (en) Method for fragmenting macromolecules using metastable-activated dissociation mass spectrometry
WO2004112084A3 (en) Space charge adjustment of activation frequency
CN107563148B (en) Ion index-based integral protein identification method and system
CN112182019B (en) Semantic parsing search method for power grid statistics professional index feature extraction
WO2003006678A3 (en) System and method for storing mass spectrometry data
SE0004875L (en) Satellite capture procedure
US20130144585A1 (en) Apparatus and method for idendificaton of protein modification

Legal Events

Date Code Title Description
AK Designated states

Kind code of ref document: A2

Designated state(s): AE AG AL AM AT AU AZ BA BB BG BR BY BZ CA CH CN CO CR CU CZ DE DK DM DZ EE ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX MZ NO NZ PL PT RO RU SD SE SG SI SK SL TJ TM TR TT TZ UA UG US UZ VN YU ZA ZW

AL Designated countries for regional patents

Kind code of ref document: A2

Designated state(s): GH GM KE LS MW MZ SD SL SZ TZ UG ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE TR BF BJ CF CG CI CM GA GN GW ML MR NE SN TD TG

121 Ep: the epo has been informed by wipo that ep was designated in this application
DFPE Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed before 20040101)
AK Designated states

Kind code of ref document: A3

Designated state(s): AE AG AL AM AT AU AZ BA BB BG BR BY BZ CA CH CN CO CR CU CZ DE DK DM DZ EE ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX MZ NO NZ PL PT RO RU SD SE SG SI SK SL TJ TM TR TT TZ UA UG US UZ VN YU ZA ZW

AL Designated countries for regional patents

Kind code of ref document: A3

Designated state(s): GH GM KE LS MW MZ SD SL SZ TZ UG ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE TR BF BJ CF CG CI CM GA GN GW ML MR NE SN TD TG

WWE Wipo information: entry into national phase

Ref document number: 55293/01

Country of ref document: AU

ENP Entry into the national phase

Ref country code: JP

Ref document number: 2001 577506

Kind code of ref document: A

Format of ref document f/p: F

WWE Wipo information: entry into national phase

Ref document number: 10204720

Country of ref document: US

WWE Wipo information: entry into national phase

Ref document number: 2001928435

Country of ref document: EP

WWP Wipo information: published in national office

Ref document number: 2001928435

Country of ref document: EP

WWG Wipo information: grant in national office

Ref document number: 55293/01

Country of ref document: AU

WWW Wipo information: withdrawn in national office

Ref document number: 2001928435

Country of ref document: EP