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US 10,541,119 B2Granted
Method for identifying microorganisms by mass spectrometry
AssigneeBiomerieux
InventorsGrégory Strubel, Maud Arsac, Denis Desseree, Pierre-Jean Cotte-Pattat
Life of this patent
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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.
Claims14
A method of providing an identification decision for a microorganism by mass spectrometry using a mass spectrometer connected to a processor-based calculation unit, comprising:
- (i) acquiring at least one mass spectrum of a sample of the microorganism over a predetermined range of mass-to-charge ratios, said mass spectrum being generated by the 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
- max
- +
- 1
- )
- ln
-
-
- m
- min
- -
- ln
-
-
- m
- max
- β
- =
- (
- b
- max
- +
- 1
- )
- ×
- ln
-
-
- m
- min
- -
- b
- min
- ×
- ln
-
-
- m
- max
- ln
-
-
- m
- min
- -
- ln
-
-
- m
- max
- 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, which is stored in a memory of the calculation unit,
- wherein the matrix is stored 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;
- and
- (iii) providing an identification decision for the microorganism to be identified by comparing the representative matrix stored in the memory of the calculation unit with a knowledge base of binarized matrices representative of previously-identified microorganisms and/or types of microorganisms, said knowledge base being also stored in the memory of the calculation unit.
92 more elements
A device for providing an identification decision for a microorganism by mass spectrometry, comprising:
- a mass spectrometer that generates mass spectrums of microorganisms to be identified;
- a processor-based calculation unit that implements the following instructions:
- (i) acquiring by 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 generated by the 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
- max
- +
- 1
- )
- ln
-
-
- m
- min
- -
- ln
-
-
- m
- max
- β
- =
- (
- b
- max
- +
- 1
- )
- ×
- ln
-
-
- m
- min
- -
- b
- min
- ×
- ln
-
-
- m
- max
- ln
-
-
- m
- min
- -
- ln
-
-
- m
- max
- 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, said matrix being stored in a memory of the calculation unit,
- wherein the matrix is stored 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;
- and
- (iii) providing an identification decision for the microorganism to be identified by comparing the representative matrix stored in the memory of the calculation unit with a knowledge base of binarized matrices representative of previously-identified microorganisms and/or types of microorganisms, said knowledge base being also stored in the memory of the calculation unit.
94 more elements
Dependencies are inferred from the claim text.