US 12,033,839 B2
Data independent acquisition of product ion spectra and reference spectra library matching
Ronald F. Bonner, Newmarket (CA); Stephen A. Tate, Barrie (CA); Rudolf Aebersold, Zurich (CH); Pedro Jose Navarro Alvarez, Zurich (CH); Oliver Rinner, Zurich (CH); Lukas Reiter, Wil (CH); and Ludovic Gillet, Zurich (CH)
Assigned to DH Technologies Development Pte. Ltd., Singapore (SG); and ETH Zürich, Zürich (CH)
Filed by DH Technologies Development Pte. Ltd., Singapore (SG); and ETH Zürich, Zürich (CH)
Filed on Dec. 1, 2021, as Appl. No. 17/457,055.
Application 17/457,055 is a continuation of application No. 16/450,594, filed on Jun. 24, 2019, granted, now 11,222,775.
Application 16/450,594 is a continuation of application No. 15/293,517, filed on Oct. 14, 2016, abandoned.
Application 15/293,517 is a continuation of application No. 15/098,196, filed on Apr. 13, 2016, abandoned.
Application 15/098,196 is a continuation of application No. 14/741,948, filed on Jun. 17, 2015, granted, now 9,343,278, issued on May 17, 2016.
Application 14/741,948 is a continuation of application No. 14/329,645, filed on Jul. 11, 2014, granted, now 9,099,288, issued on Aug. 4, 2015.
Application 14/329,645 is a continuation of application No. 13/819,769, granted, now 8,809,770, issued on Aug. 19, 2014, previously published as PCT/IB2011/002139, filed on Sep. 14, 2011.
Claims priority of provisional application 61/383,137, filed on Sep. 15, 2010.
Claims priority of application No. 10009595 (EP), filed on Sep. 15, 2010.
Prior Publication US 2022/0181132 A1, Jun. 9, 2022
Int. Cl. H01J 49/00 (2006.01); G01N 30/72 (2006.01); G16C 20/20 (2019.01); G16C 20/90 (2019.01); H01J 49/42 (2006.01)
CPC H01J 49/0036 (2013.01) [G01N 30/7233 (2013.01); G16C 20/90 (2019.02); H01J 49/0031 (2013.01); H01J 49/004 (2013.01); H01J 49/0045 (2013.01); H01J 49/42 (2013.01); G16C 20/20 (2019.02)] 23 Claims
OG exemplary drawing
 
1. A system for quantitating detectable compounds of a sample, comprising:
a processor that
receives sample product ion spectra for each mass selection window of a plurality of precursor mass selection windows for each time step of a plurality of time steps; and
searches the received product ion spectra for the presence of one or more known compounds with known product ion spectra by:
a) receiving the known product ion spectra,
b) retrieving the sample product ion spectra corresponding to the precursor mass selection window expected to contain a precursor ion corresponding to the known product ion spectra,
c) generating product ion traces in time for the sample product ion spectra f or one or more of the known product ion spectra,
d) calculating a score for the product ion traces and product ion spectra that represents how well the known product ions and sample product ions match, and
e) calculating a quantitative value for a known compound from the product ion traces when the score exceeds a threshold value; and
wherein the processor receives the known product ion spectra from in-silico predictions.
 
10. A method for quantitating detectable compounds of a sample, comprising:
receiving sample product ion spectra for each mass selection window of a plurality of precursor mass selection windows for each time step of a plurality of time steps using a processor; and
searching the received sample product ion spectra f or the presence of one or more known compounds of interest with known product ion spectra using the processor by:
a) receiving the known product ion spectra,
b) retrieving the sample product ion spectra corresponding to the precursor mass selection window expected to contain a precursor ion corresponding to the known product ion spectra,
c) generating product ion traces in time for the sample product ion spectra for one or more of the known product ion spectra,
d) calculating a score for the product ion traces and product ion spectra that represents how well the known product ions and sample product ions match, and
e) calculating a quantitative value for the known compound from the product ion traces when the score exceeds a threshold value; and
wherein the processor receives the known product ion spectra from in-silico predictions.
 
19. A computer program product, comprising a tangible computer-readable storage medium whose contents include a program with instructions being executed on a processor so as to perform a method for quantitating detectable compounds of a sample, the method comprising:
providing a system, wherein the system comprises one or more distinct software modules, and wherein the distinct software modules comprise a measurement module; and
receiving sample product ion spectra for each mass selection window of a plurality of precursor mass selection windows for each time step of a plurality of time steps using the measurement module; and
searching the received product ion spectra for the presence of one or more known compounds with known product ion spectra using the measurement module by:
a) receiving the known product ion spectra,
b) retrieving the sample product ion spectra corresponding to the precursor mass selection window expected to contain a precursor ion corresponding to the known product ion spectra,
c) generating product ion traces in time for the sample product ion spectra f or one or more of the known product ion spectra,
d) calculating a score for the product ion traces and product ion spectra that represents how well the known product ions and sample product ions match, and
e) calculating a quantitative value for the known compound from the product ion traces when the score exceeds a threshold value; and
wherein the measurement module receives the known product ion spectra from in-silico predictions.