Methods and systems for discovering protein modifications and mutations
View Patent ↗Accordingly, systems and methods for protein identification are provided. The present teaching provide for a system with one protein identification methodology based on one method and a second protein identification methodology based on a second protein identification methodology to interact and increase confidence in protein identification. Various embodiments employ protein identification methodologies that identify portions of a peptide. Various embodiments provide for a hypothesis generation module that can suggest modifications for the peptide based on differences between experimental and theoretical values. Various embodiments provide for an identifier module that can select one or more hypotheses from the hypothesis module as most probable. In this way, the present teachings can provide for systems and methods to combine protein identification results from multiple protein identification methodologies with the possibility of identifying modifications.
1. A system for identifying proteins and modifications from two or more identification methods, comprising:
a mass spectrometer that measures a plurality of spectra from a sample; and
a processor in communication with the mass spectrometer that
receives the plurality of spectra from the mass spectrometer and produces a plurality of peak lists from the plurality of spectra,
performs a first identification method that compares a first peak list from the plurality of peak lists with a peak list generated by computationally digesting a first protein database producing a first list of proteins from the comparison,
performs a second identification method that applies a de novo peptide sequencing technique to a second peak list from the plurality of peak lists producing one or more putative sequences and matches the one or more putative sequences to a second protein database using an alignment tool producing a second list of proteins from the matching,
if a protein of the second list of proteins matches a protein of the first list of proteins, performs a first comparison of the precursor peptide of the second peak list to a full peptide sequence found in the protein,
if the precursor peptide does not match the full peptide sequence in the first comparison, performs a second comparison of a difference between the precursor peptide and the full peptide sequence to a modification database, and
if a modification from the modification database that matches the difference is found from the second comparison, identifies the protein in the sample from the precursor peptide and the modification.
2. The system of claim 1 , wherein the processor performs the second identification method on the second peak list if the processor performs the first identification method on the second peak list and no matched proteins are produced.
3. The system of claim 1 , wherein the processor performs the second identification method on the second peak list if the processor performs the first identification method on the second peak list and only weakly matched proteins are produced.
4. The system of claim 1 , wherein the first list of proteins includes a protein confidence value that indicates the degree of confidence in the protein identification.
5. The system of claim 1 , wherein the difference between the precursor peptide and the full peptide sequence comprises a mass difference.
6. The system of claim 5 , wherein the processor ranks the modification based on a score that reflects the ability of the modification to explain the mass difference.
7. The system of claim 1 , wherein the processor ranks the modification based on a frequency of such a modification occurring.
8. A method for identifying proteins and modifications from two or more identification methods, comprising:
measuring a plurality of spectra from a sample using a mass spectrometer;
receiving the plurality of spectra from the mass spectrometer and producing a plurality of peak lists from the plurality of spectra using a processor;
performing a first identification method that compares a first peak list from the plurality of peak lists with a peak list generated by computationally digesting a first protein database producing a first list of proteins from the comparison using the processor;
performing a second identification method that applies a de novo peptide sequencing technique to a second peak list from the plurality of peak lists producing one or more putative sequences and matching the one or more putative sequences to a second protein database using an alignment tool producing a second list of proteins from the matching using the processor;
if a protein of the second list of proteins matches a protein of the first list of proteins, performing a first comparison of the precursor peptide of the second peak list to a full peptide sequence found in the protein using the processor,
if the precursor peptide does not match the full peptide sequence in the first comparison, performing a second comparison of a difference between the precursor peptide and the full peptide sequence to a modification database using the processor, and
if a modification from the modification database that matches the difference is found from the second comparison, identifying the protein in the sample from the precursor peptide and the modification using the processor.
9. The method of claim 8 , further comprising performing the first identification method on the second peak list, and if no matched proteins are produced, performing the second identification method on the second peak list.
10. The method of claim 8 , further comprising performing the first identification method on the second peak list, and if only weakly matched proteins are produced, performing the second identification method on the second peak list.
11. The method of claim 8 , wherein the first list of proteins includes a protein confidence value that indicates the degree of confidence in the protein identification.
12. The method of claim 8 , wherein the difference between the precursor peptide and the full peptide sequence comprises a mass difference.
13. The method of claim 12 , further comprising ranking the modification based on a score that reflects the ability of the modification to explain the mass difference using the processor.
14. The method of claim 8 , further comprising ranking the modification based on a frequency of such a modification occurring.
15. A computer program product, comprising a computer-readable storage medium whose contents include a program with instructions being executed on a processor so as to perform a method for identifying proteins and modifications from two or more identification methods, the method comprising:
providing a system, wherein the system comprises distinct software modules, and wherein the distinct software modules comprise a measurement module, a first identification modules, a second identification module, a comparison module, a hypothesis module, and an identifier module;
receiving a plurality of spectra from a mass spectrometer that measured the plurality of spectra from a sample using the measurement module;
producing a plurality of peak lists from the plurality of spectra using the measurement module;
performing a first identification method that compares a first peak list from the plurality of peak lists with a peak list generated by computationally digesting a first protein database producing a first list of proteins from the comparison using the first identification module;
performing a second identification method that applies a de novo peptide sequencing technique to a second peak list from the plurality of peak lists producing one or more putative sequences and matching the one or more putative sequences to a second protein database using an alignment tool producing a second list of proteins from the matching using the second identification module;
if a protein of the second list of proteins matches a protein of the first list of proteins, performing a first comparison of the precursor peptide of the second peak list to a full peptide sequence found in the protein using the processor using the comparison module,
if the precursor peptide does not match the full peptide sequence in the first comparison, performing a second comparison of a difference between the precursor peptide and the full peptide sequence to a modification database using the hypothesis module, and
if a modification from the modification database that matches the difference is found from the second comparison, identifying the protein in the sample from the precursor peptide and the modification using the identifier module.
16. The computer program product of claim 15 , further comprising performing the first identification method on the second peak list, and if no matched proteins are produced, performing the second identification method on the second peak list.
17. The computer program product of claim 15 , further comprising performing the first identification method on the second peak list, and if only weakly matched proteins are produced, performing the second identification method on the second peak list.
18. The computer program product of claim 15 , wherein the first list of proteins includes a protein confidence value that indicates the degree of confidence in the protein identification.
19. The computer program product of claim 15 , wherein the difference between the precursor peptide and the full peptide sequence comprises a mass difference.
20. The computer program product of claim 19 , further comprising ranking the modification based on a score that reflects the ability of the modification to explain the mass difference using the identifier module processor.