US 12,191,129 B2Granted

Method for identifying microorganisms by mass spectrometry

AssigneeBiomerieux

InventorsGrégory Strubel, Maud Arsac, Denis Desseree, Pierre-Jean Cotte-Pattat

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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.

Claims20

Dependent claims

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.

106 more elements

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.

106 more elements

Dependencies are inferred from the claim text.

Facts

Application: 16/708,419Filed 9 Dec 2019 · continuation
Priority: EP 113066102 Dec 2011
Published: US 2020/0111653 A19 Apr 2020
Granted: 7 Jan 2025
Term ends: Not estimatedThe source records don’t support an estimate.

Classification7 codes

H01J 49/0036
Methods for using particle spectrometers: step by step routines describing the handling of the data generated during a measurement
G01N 33/6848
General methods of protein analysis not limited to specific proteins or families of proteins: methods of protein analysis involving mass spectrometry
G16B 40/10
ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge…: signal…
G16B 99/00
Subject matter not provided for in other groups of this subclass

Family

Application61/566,025Us provisional application · filed 2 Dec 2011
PCT/IB2012/056860Parent of this continuation · filed 30 Nov 2012
US 2020/0111653 A1Pre-grant publication · published 9 Apr 2020
Application14/361,794Parent of this continuation
US 10,541,119 B2Parent of this continuation
US 2014/0358449 A1Published application
US 12,191,129 B2This patent

From the US filing history. Foreign family members aren’t listed.

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