Method and apparatus for identifying proteins in mixtures

A method for identifying proteins in a mixture comprising:

• performing an LC/MS experiment using the mixture and acquiring first mass information and first retention time information associated with precursors and second mass information and second retention time information associated with fragments of the precursors;
• selecting a target peptide, wherein said target peptide is a theoretical peptide having a target precursor and corresponding Y and B fragment ions of the target precursor, wherein the target precursor and said corresponding Y and B fragment ions of the target precursor have associated masses;
• comparing the associated masses of the target precursor and the corresponding Y and B fragment ions of the target precursor to the first mass information and the second mass information;
• detecting mass matches based on said comparing;
• determining retention times of the mass matches;
• and
• identifying, in accordance with said mass matches and the retention times of the mass matches, whether the target peptide is present in the mixture.

A system comprising:

• a liquid chromatograph to which a mixture is applied to separate the mixture producing a separated mixture;
• a mass spectrometer that measures masses in the separated mixture;
• a database from which a target peptide is selected;
• a computer coupled to the database and an output of the mass spectrometer, said computer having code executing thereon which, when executed, causes the computer to perform a method, the method comprising:
• acquiring first mass information and first retention time information associated with precursors and second mass information and second retention time information associated with fragments of the precursors;
• selecting said target peptide, wherein said target peptide is a theoretical peptide having a target precursor and corresponding Y and B fragment ions of the target precursor, wherein the target precursor and said corresponding Y and B fragment ions of the target precursor have associated masses;
• comparing the associated masses of the target precursor and the corresponding Y and B fragment ions of the target precursor to the first mass information and the second mass information;
• detecting mass matches based on said comparing;
• determining retention times of the mass matches;
• and
• identifying, in accordance with said mass matches and the retention times of the mass matches, whether the target peptide is present in the mixture.

A non-transitory computer readable medium comprising code stored thereon for identifying proteins in a mixture, the non-transitory computer readable medium comprising code stored thereon for:

• performing an LC/MS experiment using the mixture and acquiring first mass information and first retention time information associated with precursors and second mass information and second retention time information associated with fragments of the precursors;
• selecting a target peptide, wherein said target peptide is a theoretical peptide having a target precursor and corresponding Y and B fragment ions of the target precursor, wherein the target precursor and said corresponding Y and B fragment ions of the target precursor have associated masses;
• comparing the associated masses of the target precursor and the corresponding Y and B fragment ions of the target precursor to the first mass information and the second mass information;
• detecting mass matches based on said comparing;
• determining retention times of the mass matches;
• and
• identifying, in accordance with said mass matches and the retention times of the mass matches, whether the target peptide is present in the mixture.

A non-transitory computer readable medium comprising code stored thereon for identifying proteins in a mixture, the non-transitory computer readable medium comprising code stored thereon for:

• receiving a first set of mass and retention time information associated with precursors and a second set of mass and retention time information associated with fragments of the precursors, wherein said first set of mass and retention time information and said second set of mass and retention time information are obtained from an LC/MS experiment using the mixture;
• selecting a target peptide;
• determining, for the target peptide, a target precursor and corresponding Y and B fragment ions of the target precursor, wherein the target precursor and said corresponding Y and B fragment ions of the target precursor have associated masses;
• determining mass matches for a substantially same retention time in said first set of mass and retention time information and said second set of mass and retention time information in accordance with the masses of said target precursor and said corresponding Y and B fragment ions of the target precursor;
• and
• identifying, in accordance with said mass matches for a substantially same retention time, whether the target peptide is present in the mixture.