Systems and Methods for Calculating Protein Confidence Values

A method for calculating protein confidence values in proteomic analysis, comprising:

• a. performing a plurality of scans of a sample producing a plurality of spectra using one or more mass spectrometers;
• b. obtaining the plurality of spectra from the mass spectrometer using a processor;
• c. identifying a plurality of peptides from the plurality of spectra using the processor;
• d. searching a protein database for proteins matching peptides from the plurality of peptides producing a set of proteins and a corresponding set of peptides using the processor;
• e. determining peptide confidence values for the set of peptides using the processor;
• f. calculating a protein confidence value for each protein in the set of proteins based on one or more peptide confidence values of one or more corresponding peptides from the set of peptides using the processor;
• g. selecting a protein from the set of proteins with a largest protein confidence value, saving the largest protein confidence value for the protein, removing the protein from the set of proteins, and removing one or more peptides corresponding to the protein from the set of peptides using the processor;
• and
• h. recalculating the protein confidence value for each protein in the set of proteins based on one or more peptide confidence values of one or more corresponding peptides from the set of peptides and an effect of removing the one or more peptides corresponding to the removed protein from the set of peptides using the processor.

A computer program product, comprising a tangible computer-readable storage medium whose contents include a program with instructions being executed on a processor so as to perform a method for calculating protein confidence values in proteomic analysis, the method comprising:

• a. providing a system, wherein the system comprises distinct software modules, and wherein the distinct software modules comprise a measurement module and an analysis module;
• b. obtaining a plurality of spectra from one or more mass spectrometers that perform a plurality of scans of a sample using the measurement module;
• c. identifying a plurality of peptides from the plurality of spectra using the analysis module;
• d. searching a protein database for proteins matching peptides from the plurality of peptides producing a set of proteins and a corresponding set of peptides using the analysis module;
• e. determining peptide confidence values for the set of peptides using the analysis module;
• f. calculating a protein confidence value for each protein in the set of proteins based on one or more peptide confidence values of one or more corresponding peptides from the set of peptides using the analysis module;
• g. selecting a protein from the set of proteins with a largest protein confidence value, saving the largest protein confidence value for the protein, removing the protein from the set of proteins, and removing one or more peptides corresponding to the protein from the set of peptides using the analysis module;
• and
• h. recalculating the protein confidence value for each protein in the set of proteins based on one or more peptide confidence values of one or more corresponding peptides from the set of peptides and an effect of removing the one or more peptides corresponding to the removed protein from the set of peptides using the analysis module.