US 12,322,583 B2
Extracting mass spectrometry data using mass and retention time windows
Mohit Jain, San Diego, CA (US); Saumya Tiwari, San Diego, CA (US); and Jeramie Watrous, San Diego, CA (US)
Assigned to Sapient Bioanalytics, LLC, San Diego, CA (US)
Filed by Sapient Bioanalytics, LLC, San Diego, CA (US)
Filed on May 20, 2022, as Appl. No. 17/750,252.
Prior Publication US 2023/0377862 A1, Nov. 23, 2023
Int. Cl. G06F 11/30 (2006.01); H01J 49/00 (2006.01)
CPC H01J 49/0036 (2013.01) [G06F 2218/08 (2023.01)] 18 Claims
OG exemplary drawing
 
1. A computer-implemented method, comprising:
obtaining raw mass spectrometry data from samples, the raw mass spectrometry data comprising mass-to-charge ratio data corresponding to a mass-to-charge ratio axis and retention time data corresponding to a retention time axis;
transforming the raw mass spectrometry data into a frequency representation of the raw mass spectrometry data, wherein the transforming the raw mass spectrometry data into the frequency representation comprises:
binning the raw mass spectrometry data with respect to the retention time axis and the mass-to-charge ratio axis;
determining any local maxima in each bin of the raw mass spectrometry data for each of the samples; and
generating the frequency representation indicating frequencies of occurrence of the any local maxima across the samples;
obtaining a portion of the raw mass spectrometry data based on the frequencies;
determining, using a machine learning model, veracities of signals within the portion of the raw mass spectrometry data;
extracting a subset of the portion of the raw mass spectrometry data, the subset corresponding to true signal;
extracting mass-to-charge ratios and extracting retention times corresponding to the subset;
based on the extracted mass-to-charge ratios and the extracted retention times, inferring composition data within the samples to diagnose any one or more particular disease conditions, the composition data comprising an elemental or isotopic signature, or chemical identities or structures of molecules or compounds within the samples; and implementing a treatment based on the diagnosis of the one or more particular disease conditions.