Methods and apparatus for identification of polymeric species from mass spectrometry output
Methods and apparatus are provided for the identification of one or more candidate chemical formulas from mass spectrometry data corresponding to an unidentified chemical compound. By restricting the generation of candidate formulas to those having repeating units and/or end units with specified limitations, the methods and apparatus may more efficiently iteratively search for a chemical formula having matching mass spectrometry output within a threshold tolerance. In another aspect, methods and apparatus are provided for the identification of one or more candidate chemical formulas from mass spectrometry data based at least in part upon neutral loss.
1. A method for identifying a species of an unidentified chemical compound, the method comprising:
accessing, by a processor of a computing device, mass spectrometry data for a sample comprising the unidentified chemical compound;
identifying, by the processor, at least a first candidate chemical formula for the unidentified chemical compound based at least in part on the mass spectrometry data;
determining, by the processor, the first candidate chemical formula is a neutral loss match to the unidentified chemical compound, said determining of the neutral loss match comprising, for each of a plurality of spectral peaks of the mass spectrometry data:
calculating a respective mass difference between a theoretical mass of the first candidate chemical formula and a respective experimental mass corresponding to the spectral peak, and
comparing the respective mass difference with a mass of each of one or more corresponding neutral molecular compositions to identify one or more candidate neutral molecular compositions corresponding to the spectral peak.
2. The method of claim 1 , wherein the mass spectrometry data comprises a collision-induced dissociation (CID) mass spectrum.
3. The method of claim 1 , comprising:
identifying, by the processor, a second candidate chemical formula;
determining, by the processor, the second candidate chemical formula is a neutral loss match to the unidentified chemical compound; and
ranking, by the processor, the first candidate chemical formula and the second candidate chemical formula as matches to the unknown chemical compound based in part upon similarity in neutral loss match.
4. The method of claim 1 , wherein identifying the one or more candidate neutral molecular compositions comprises identifying that each candidate neutral molecular composition of the one or more candidate neutral molecular compositions having a respective mass within range of a mass measurement accuracy of the respective experimental mass of the spectral peak.
5. The method of claim 1 , wherein determining the first candidate chemical formula is a neutral loss match to the unidentified chemical compound comprises identifying that a stoichiometry of the first candidate chemical formula allows for at least a first candidate neutral molecular composition of the one or more candidate neutral molecular compositions.
6. The method of claim 5 , wherein identifying that the stoichiometry of the first candidate chemical formula allows for the first candidate neutral molecular composition comprises determining, for the first candidate neutral molecular composition, a number of atoms of each type in the first candidate chemical formula is greater than a number of atoms of each corresponding type in the candidate neutral loss composition.
7. The method of claim 1 , wherein the unidentified chemical compound comprises a repeating structural unit, and optionally one or more end units and identifying the first candidate chemical formula comprises:
determining at least one of (a) a chemical formula of the repeating structural unit, and (b) an estimated mass of a portion of the unidentified chemical compound made up of the repeating structural unit; and
identifying the first candidate chemical formula for the unidentified chemical compound based at least in part upon the mass spectrometry data, and based further in part on at least one of (a) the chemical formula of the repeating structural unit, and (b) the estimated mass of the portion of the unidentified chemical compound made up of the repeating structural unit.
8. A system comprising:
a processor; and
a memory having instructions stored thereon, wherein the instructions, when executed by the processor, cause the processor to:
access mass spectrometry data for a sample comprising an unidentified chemical compound;
identify at least a first candidate chemical formula for the unidentified chemical compound based at least in part on the mass spectrometry data; and
determine the first candidate chemical formula is a neutral loss match to the unidentified chemical compound, said determining of the neutral loss match comprising, for each of a plurality of spectral peaks of the mass spectrometry data:
calculating a respective mass difference between a theoretical mass of the first candidate chemical formula and a respective experimental mass corresponding to the spectral peak, and
comparing the respective mass difference with a mass of each of one or more corresponding neutral molecular compositions to identify one or more candidate neutral molecular compositions corresponding to the spectral peak.
9. A non-transitory computer readable medium having instructions stored thereon, wherein the instructions, when executed by a processor, cause the processor to:
access mass spectrometry data for a sample comprising an unidentified chemical compound;
identify at least a first candidate chemical formula for the unidentified chemical compound based at least in part on the mass spectrometry data; and
determine the first candidate chemical formula is a neutral loss match to the unidentified chemical compound, said determining of the neutral loss match comprising, for each of a plurality of spectral peaks of the mass spectrometry data:
calculating a respective mass difference between a theoretical mass of the first candidate chemical formula and a respective experimental mass corresponding to the spectral peak, and
comparing the respective mass difference with a mass of each of one or more corresponding neutral molecular compositions to identify one or more candidate neutral molecular compositions corresponding to the spectral peak.
10. The method of claim 1 , comprising generating the mass spectrometry data for the sample comprising the unidentified chemical compound.
11. The method of claim 1 , wherein identifying at least a first candidate chemical formula for the unidentified chemical compound comprises comparing a monoisotopic mass determined from the mass spectrometry data to a monoisotopic mass of each of one or more candidate parent ions.
12. The method of claim 11 wherein the first candidate chemical formula corresponds to a chemical formula of a parent ion having a monoisotopic mass within a predefined tolerance of the monoisotopic mass determined from the mass spectrometry data.
13. The method of claim 2 , wherein each of the plurality of spectral peaks of the mass spectrometry data is a peak in the CID mass spectrum.
14. The method of claim 1 , wherein the theoretical mass of the first candidate chemical formula is a mass of a monoisotopic peak.
15. The method of claim 7 , wherein identifying the first candidate chemical formula comprises:
determining a calculated mass of the first candidate chemical formula based on at least one of (a) the chemical formula of the repeating structural unit, and (b) the estimated mass of the portion of the unidentified chemical compound made up of the repeating structural unit; and
determining the calculated mass of the first candidate chemical formula is within a predefined threshold of the estimated mass of the unidentified chemical compound.
16. The method of claim 15 , wherein the calculated mass of the first candidate chemical formula corresponds to a mass of a monoisotopic peak of the first candidate chemical formula, and the estimated mass of the unidentified chemical compound corresponds to a mass of the monoisotopic peak of the unidentified chemical compound.
17. The system of claim 8 , comprising a mass spectrometer for generating the mass spectrometry data for the sample comprising the unidentified chemical compound.
18. The system of claim 17 , wherein the mass spectrometer is a tandem mass spectrometer.
19. The system of claim 8 , wherein the instructions cause the processor to:
identify a second candidate chemical formula;
determine the second candidate chemical formula is a neutral loss match to the unidentified chemical compound; and
rank the first candidate chemical formula and the second candidate chemical formula as matches to the unknown chemical compound based in part upon similarity in neutral loss match.
20. The non-transitory computer readable medium of claim 9 , wherein the instructions cause the processor to:
identify a second candidate chemical formula;
determine the second candidate chemical formula is a neutral loss match to the unidentified chemical compound; and
rank the first candidate chemical formula and the second candidate chemical formula as matches to the unknown chemical compound based in part upon similarity in neutral loss match.