Methods and apparatuses for determining the intact mass of large molecules from mass spectrographic data

• US 10,319,573 B2
• Filed: 01/26/2018
• Issued: 06/11/2019
• Est. Priority Date: 01/26/2017
• Status: Active Grant

• Current Assignee: Protein Metrics LLC
• Original Assignee: Protein Metrics Inc. (Insightful Science LLC)
• Inventors: Bern, Marshall
• Primary Examiner(s): Osenbaugh-Stewar, Eliza W
• Application Number:
  US15/881,698
• Publication Number:
  US 20180301326A1
• Time in Patent Office: 501 Days
• CPC Class Codes: G06N 3/126 Evolutionary algorithms, e.g. genetic algorithms or genetic programming
• CPC Class Codes: H01J 49/0036 Step by step routines describing the handling of the data generated during a measurement
• CPC Class Codes: H01J 49/165 Electrospray ionisation

Abstract

Methods and apparatuses for the identification and/or characterization of properties of a sample using mass spectrometry. The method involves using a measured spectrum of data from a sample taken with a mass spectrometer, deconvoluting the measured spectrum of data by applying parsimony weighting to minimize the number of charge states based on one or more of: the number of intense peaks in the mass spectrum; the number of harmonic relationships (e.g., masses in small integer ratios); and the number of off-by-one relationships (e.g., m/z bins with high probability for two adjacent charges). Thus, the underlying m/z spectrum may be inferred from the family of plausible deconvoluted spectra determined by applying parsimony and the inferred m/z spectrum may be used to identify and/or characterize the sample.

Claims

1. A method of identifying or characterizing at least one property of a sample, the method comprising the steps of:

receiving a measured mass over charge (m/z) spectrum for the sample;

setting charge assignments for a number of bins of the measured m/z spectrum based on a deconvolution of the measured m/z spectrum;

applying parsimony weighting to adjust the charge assignments to a reduced number of charges;

generating an intermediate neutral mass spectrum using the adjusted charge assignments;

iterating the steps of applying parsimony weighting and generating the intermediate neutral mass spectrum to determine a parsimonious neutral mass spectrum after the intermediate neutral mass spectrum either converges or after a predetermined number of iterations; and

using the parsimonious neutral mass spectrum to identify or characterize at least one property of the sample.

2. The method of claim 1, wherein applying parsimony weighting comprises re-weighting the charge assignments to reduce how many different charges are included.

3. The method of claim 1, wherein applying parsimony weighting further comprising estimating a minimum expected number of molecules.

4. The method of claim 1, wherein the parsimony weighting is based on one or more of:

a number of intense peaks from the deconvolution of the measured m/z spectrum, a smoothness of the deconvolution of the measured m/z spectrum, a number of harmonic relationships in the deconvolution of the measured m/z spectrum, and a number of off-by-one relationships in the deconvolution of the m/z spectrum.

5. The method of claim 1, wherein applying parsimony weighting comprises identifying a number of harmonic relationships in the deconvolution of the measured m/z spectrum and assigning a minimum number of molecules to achieve the identified number of harmonic relationships.

6. The method of claim 1, wherein applying parsimony weighting comprises identifying a number of off-by-one relationships in the deconvolution of the m/z spectrum and selecting charge assignments to adjust based on the identified off-by-one relationships.

7. The method of claim 1, wherein generating the intermediate neutral mass spectrum comprises multiplying m/z values from the spectrum by the charges and subtracting masses of charge carriers to determine a neutral mass.

8. The method of claim 1, wherein generating the intermediate neutral mass spectrum comprises deconvoluting the measured m/z spectrum using the reduced number of charges.

9. The method of claim 1, wherein the measured m/z spectrum comprises electrospray mass spectral data.

10. The method of claim 1, wherein using the parsimonious neutral mass spectrum to identify or characterize at least one property of the sample comprises determining the intact mass of large molecules in the sample.

11. A method of identifying or characterizing at least one property of a sample, the method comprising the steps of:

receiving a measured mass over charge (m/z) spectrum for a sample;

setting charge assignments for a number of bins of the measured m/z spectrum based on a deconvolution of the measured m/z spectrum;

applying parsimony weighting to adjust the charge assignments to a reduced number of charges and to reduce an expected number of molecules from the measured m/z spectrum, wherein the parsimony weighting is based on one or more of;

a number of intense peaks from the deconvolution of the measured m/z spectrum, a smoothness of the deconvolution of the measured m/z spectrum, a number of harmonic relationships in the deconvolution of the measured m/z spectrum, and a number of off-by-one relationships in the deconvolution of the m/z spectrum;

generating an intermediate neutral mass spectrum using the adjusted charge assignments;

iterating the steps of applying parsimony weighting and generating the intermediate neutral mass spectrum to determine a parsimonious neutral mass spectrum after the intermediate neutral mass spectrum either converges or after a predetermined number of iterations; and

using the parsimonious neutral mass spectrum to identify or characterize at least one property of the sample.

12. The method of claim 11, wherein applying parsimony weighting comprises re-weighting the charge assignments to reduce how many different charges are included.

13. The method of claim 11, wherein applying parsimony weighting comprises identifying a number of harmonic relationships in the deconvolution of the measured m/z spectrum and assigning a minimum number of molecules to achieve the identified number of harmonic relationships.

14. The method of claim 11, wherein applying parsimony weighting comprises identifying a number of off-by-one relationships in the deconvolution of the m/z spectrum and selecting charge assignments to adjust based on the identified off-by-one relationships.

15. The method of claim 11, wherein generating the intermediate neutral mass spectrum comprises multiplying m/z values from the spectrum by the charges and subtracting masses of charge carriers to determine a neutral mass.

16. The method of claim 11, wherein generating the intermediate neutral mass spectrum comprises deconvoluting the measured m/z spectrum using the reduced number of charges and the expected number of molecules.

17. The method of claim 11, wherein the measured m/z spectrum comprises electrospray mass spectral data.

18. The method of claim 11, wherein using the parsimonious neutral mass spectrum to identify or characterize at least one property of the sample comprises determining the intact mass of large molecules in the sample.

19. A non-transitory computer-readable storage medium storing a set of instructions capable of being executed by a processor, that when executed by the processor causes the processor to:

receive a measured mass over charge (m/z) spectrum for the sample;

set charge assignments for a number of bins of the measured m/z spectrum based on a deconvolution of the measured m/z spectrum;

apply parsimony weighting to adjust the charge assignments to a reduced number of charges;

generate an intermediate neutral mass spectrum using the adjusted charge assignments;

iterate the application of parsimony weighting and generation of the intermediate neutral mass spectrum to determine a parsimonious neutral mass spectrum after the intermediate neutral mass spectrum either converges or after a predetermined number of iterations; and

use the parsimonious neutral mass spectrum to identify or characterize at least one property of the sample.

20. The non-transitory computer-readable storage medium of claim 19, wherein the set of instructions cause the processor to re-weight the estimated charge states to reduce the estimated number of different charges when applying parsimony weighting.

21. The non-transitory computer-readable storage medium of claim 19, wherein the set of instructions cause the processor to estimate a minimum expected number of molecules when applying parsimony weighting.

22. The non-transitory computer-readable storage medium of claim 19, wherein the set of instructions cause the processor to apply parsimony weighting based on identifying one or more of:

a number of intense peaks from the deconvolution of the measured m/z spectrum, a smoothness of the deconvolution of the measured m/z spectrum, a number of harmonic relationships in the deconvolution of the measured m/z spectrum, and a number of off-by-one relationships in the deconvolution of the m/z spectrum.

23. The non-transitory computer-readable storage medium of claim 19, wherein the set of instructions cause the processor to identify a number of harmonic relationships in the deconvolution of the measured m/z spectrum and assign a minimum number of molecules to achieve the identified number of harmonic relationships when applying parsimony weighting.

24. The non-transitory computer-readable storage medium of claim 19, wherein the set of instructions cause the processor to identify a number of off-by-one relationships in the deconvolution of the m/z spectrum and select estimated charge states based on the identified off-by-one relationships when applying parsimony weighting.

25. The non-transitory computer-readable storage medium of claim 19, wherein the set of instructions cause the processor to multiply m/z values from the spectrum by the estimated charges and subtract masses of the charge carriers to determine a neutral mass when generating the intermediate neutral mass spectrum.

26. The non-transitory computer-readable storage medium of claim 19, wherein the set of instructions cause the processor to deconvolute the measured mass over charge (m/z) spectrum using the reduced number of estimated charge states when generating the intermediate neutral mass spectrum.

27. The non-transitory computer-readable storage medium of claim 19, wherein the set of instructions cause the processor to determine the intact mass of large molecules in the sample when using the parsimonious neutral mass spectrum to identify or characterize at least one property of the sample.