US 12,140,577 B2
Method and apparatus for analysing samples of biomolecules using mass spectrometry with data-independent acquisition
Roman Zubarev, Stockholm (SE); and Christian Beusch, Solna (SE)
Assigned to Thermo Fisher Scientific (Bremen ) GmbH, Bremen (DE)
Filed by Thermo Fisher Scientific (Bremen) GmbH, Bremen (DE)
Filed on Feb. 16, 2022, as Appl. No. 17/673,409.
Claims priority of application No. 21157833 (EP), filed on Feb. 18, 2021.
Prior Publication US 2022/0260534 A1, Aug. 18, 2022
Int. Cl. G01N 30/72 (2006.01); G01N 30/14 (2006.01); G01N 33/68 (2006.01); G01N 30/02 (2006.01)
CPC G01N 30/7233 (2013.01) [G01N 30/14 (2013.01); G01N 33/6851 (2013.01); G01N 2030/027 (2013.01); G01N 2570/00 (2013.01)] 23 Claims
OG exemplary drawing
 
1. A method of mass spectrometry for analysing samples of biomolecules, comprising:
providing a multiplexed sample comprising a mixture of biomolecule-containing samples, wherein the biomolecule-containing samples are respectively tagged with mass tags having respective reporter ions;
acquiring MS2 spectra by data-dependent acquisition (DDA) of the multiplexed sample or another mass tagged mixture of the biomolecule-containing samples as it elutes from a liquid chromatographic device;
acquiring MS2 spectra by data-independent acquisition (DIA) of the multiplexed sample as it elutes from the liquid chromatographic device;
forming a spectral library from the MS2 spectra acquired by DDA comprising a plurality of MS2 spectra representing a plurality of mass-tagged molecular ions of biomolecules and their fragment ions and the retention times of the biomolecules;
matching peaks of fragment ions in the MS2 spectra acquired by DIA to peaks of fragment ions in the MS2 spectra of the spectral library to find matched biomolecules;
determining a total abundance for all mass tags for each matched biomolecule from the MS2 spectra acquired by DIA at each of a plurality of retention times;
determining abundances of respective reporter ions derived from the mass tags from the MS2 spectra acquired by DIA at the plurality of retention times; and
deconvoluting relative abundances of the biomolecules in each respectively tagged biomolecule-containing sample based on the determined abundances of the respective reporter ions and the determined total abundances of the matched biomolecules at corresponding retention times over the plurality of retention times,
wherein the deconvoluting comprises using a set of linear equations, wherein each linear equation relates to a different one of the plurality of retention times.