# US 12,191,129 B2 · Method for identifying microorganisms by mass spectrometry > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 12,191,129 B2 - Document ID: US12191129B2 - Status: Granted - Kind: B2 - Application number: 16/708,419 - Filed: 2019-12-09 - Published: 2020-04-09 - Granted: 2025-01-07 - Earliest claimed: 2011-12-02 - Assignees: Biomerieux - Applicants: Biomerieux, Inc. - Inventors: Grégory Strubel; Maud Arsac; Denis Desseree; Pierre-Jean Cotte-Pattat - Web page: https://patentgrep.com/patent/US12191129B2 ## CPC - H01J 49/0036: {Step by step routines describing the handling of the data generated during a measurement} - G01N 33/6848: {Methods of protein analysis involving mass spectrometry} - G16B 40/10: Signal processing, e.g. from mass spectrometry [MS] or from PCR - G16B 99/00: Subject matter not provided for in other groups of this subclass - H01J: ELECTRIC DISCHARGE TUBES OR DISCHARGE LAMPS (spark-gaps H01T; electric arc lamps H05B31/00; particle accelerators H05H) - G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q) - G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY ## Abstract A method of identifying a microorganism by mass spectrometry, including acquiring at least one mass spectrum of said microorganism; for each acquired mass spectrum: detecting peaks of the spectrum in a predetermined mass range; generating a list of peaks identifying at most one peak in each interval of a predetermined subdivision of the range of mass-to-charge ratios, the width of the intervals of the subdivision logarithmically increasing along with the mass-to-charge ratio, and analyzing the list(s) of peaks obtained according to a knowledge base of previously-identified microorganisms and/or types of microorganisms. ## Claims ### Claim 1 A method of providing an identification decision for a microorganism using a processor-based calculation unit and a mass spectrum obtained by mass spectrometry from a mass spectrometer, comprising: (i) providing at least one mass spectrum of a sample of the microorganism over a predetermined range of mass-to-charge ratios, wherein said mass spectrum was generated by a mass spectrometer; (ii) for each of said acquired at least one mass spectrum: (a) detecting, using the processor of the calculation unit, peaks of the mass spectrum in the predetermined range of mass-to-charge ratios; (b) generating, using the processor of the calculation unit, a list of peaks in intervals of a predetermined subdivision of the predetermined range of mass-to-charge ratios, the width of the intervals of the subdivision increasing along with the mass-to-charge ratio according to relations: L ⁡ ( b ) = exp ⁡ ( b - β α ) × ( exp ⁡ ( 1 α ) - 1 ) α = b min - ( b ma ⁢ ⁢ x + 1 ) ln ⁢ ⁢ m min - ln ⁢ ⁢ m ma ⁢ ⁢ x β = ( b ma ⁢ ⁢ x + 1 ) × ln ⁢ ⁢ m min - b min × ln ⁢ ⁢ m ma ⁢ ⁢ x ln ⁢ ⁢ m min - ln ⁢ ⁢ m ma ⁢ ⁢ x where the subdivision intervals are referenced with integers greater than 1, from integer bmin, for the lowest mass-to-charge ratios in the predetermined range of mass-to-charge ratios, to integer bmax, for the higher mass-to-charge ratios in the predetermined range of mass-to-charge ratios, L(b) is the width of the interval referenced with integer b, mmin is a lower bound of the predetermined range of mass-to-charge ratios, and mmax is an upper bound of the predetermined range of mass-to-charge ratios, wherein, in the list of peaks, the processor of the calculation unit identifies at most one peak in each interval, so as to obtain a vector for each of said at least one mass spectrum, wherein the vector(s) for the at least one mass spectrum form a matrix representative of the microorganism; and (iii) providing an identification decision for the microorganism to be identified by comparing the representative matrix with a knowledge base of matrices representative of previously-identified microorganisms and/or types of microorganisms, wherein said knowledge base is stored in a memory. ### Claim 2 (depends on 1) The method of claim 1, wherein the predetermined range of mass-to-charge ratios is in the range from 3,000 Thomsons to 17,000 Thomsons. ### Claim 3 (depends on 1) The method of claim 1, wherein there are from 900 to 1,500 intervals. ### Claim 4 (depends on 3) The method of claim 3, wherein there are from 1,200 to 1,400 intervals. ### Claim 5 (depends on 1) The method of claim 1, wherein the peak kept in an interval of the subdivision is a maximum peak. ### Claim 6 (depends on 1) The method of claim 1, wherein the at least one mass spectrum of the sample of the microorganism was generated using MALDI-TOF spectrometry. ### Claim 7 (depends on 1) The method of claim 1, further comprising returning an identification decision to a user. ### Claim 8 (depends on 1) The method of claim 1, further comprising generating the at least one mass spectrum of the sample of the microorganism to be identified by the mass spectrometer. ### Claim 9 (depends on 1) The method of claim 1, further comprising storing the matrix representative of the microorganism to be identified in the memory of the calculation unit. ### Claim 10 (depends on 1) The method of claim 1, wherein the matrix representative of the microorganism to be identified is in the form of a binarized matrix that identifies for each of the at least one mass spectrum the presence or absence of a peak in the intervals. ### Claim 11 A device for providing an identification decision regarding a microorganism based on mass spectrum data, comprising a computer program stored in a non-transitory storage medium, wherein the computer program is adapted to implement the following instructions when the computer program is executed by a processor: (i) providing to the calculation unit at least one mass spectrum of a sample of a microorganism to be identified over a range of mass-to-charge ratios, wherein the mass spectrum was generated by a mass spectrometer; (ii) for each of said acquired at least one mass spectrum: (a) detecting peaks of said mass spectrum in the predetermined range of mass-to-charge ratios; (b) generating a list of peaks in intervals of a predetermined subdivision of the predetermined range of mass-to-charge ratios, the width of the intervals of the subdivision increasing along with the mass-to-charge ratio according to relations: L ⁡ ( b ) = exp ⁡ ( b - β α ) × ( exp ⁡ ( 1 α ) - 1 ) α = b min - ( b ma ⁢ ⁢ x + 1 ) ln ⁢ ⁢ m min - ln ⁢ ⁢ m ma ⁢ ⁢ x β = ( b ma ⁢ ⁢ x + 1 ) × ln ⁢ ⁢ m min - b min × ln ⁢ ⁢ m ma ⁢ ⁢ x ln ⁢ ⁢ m min - ln ⁢ ⁢ m ma ⁢ ⁢ x where the subdivision intervals are referenced with integers greater than 1, from integer bmin, for the lowest mass-to-charge ratios in the predetermined range of mass-to-charge ratios, to integer bmax, for the higher mass-to-charge ratios in the predetermined range of mass-to-charge ratios, L(b) is the width of the interval referenced with integer b, mmin is a lower bound of the predetermined range of mass-to-charge ratios, and mmax is an upper bound of the predetermined range of mass-to-charge ratios, wherein the list of peaks identifies at most one peak in each interval, so as to obtain a vector for each of said at least one mass spectrum, wherein the vector(s) for the at least one mass spectrum form a matrix representative of the microorganism; and (iii) providing an identification decision for the microorganism to be identified by comparing the representative matrix with a knowledge base of matrices representative of previously-identified microorganisms and/or types of microorganisms, wherein said knowledge base is stored in a memory. ### Claim 12 (depends on 11) The device of claim 11, wherein the predetermined range of mass-to-charge ratios is in the range from 3,000 Thomsons to 17,000 Thomsons. ### Claim 13 (depends on 11) The device of claim 11, wherein there are from 900 to 1,500 intervals. ### Claim 14 (depends on 13) The device of claim 13, wherein there are from 1,200 to 1,400 intervals. ### Claim 15 (depends on 11) The device of claim 11, wherein the peak kept in an interval of the subdivision is a maximum peak. ### Claim 16 (depends on 11) The device of claim 11, wherein the at least one mass spectrum of the sample of the microorganism was generated using MALDI-TOF spectrometry. ### Claim 17 (depends on 11) The device of claim 11, wherein the device further returns an identification decision to a user. ### Claim 18 (depends on 11) The device of claim 11, further comprising a mass spectrometer, wherein the at least one mass spectrum of the microorganism to be identified is generated by the mass spectrometer. ### Claim 19 (depends on 11) The device of claim 11, wherein the matrix representative of the microorganism to be identified is stored in the memory of the calculation unit. ### Claim 20 (depends on 11) The device of claim 11, wherein the matrix representative of the microorganism to be identified is in the form of a binarized matrix that identifies for each of the at least one mass spectrum the presence or absence of a peak in the intervals.