Generation and use of a catalog of polypeptide-related information for chemical analyses

A method for chemical analysis, the method comprising:

• providing a catalog of protein profiles generated in response to a pre-selected LC/MS method, each protein profile defined by an identity of a protein, and values associated with chromatographic retention time, mass and intensity of precursor ions associated with the protein;
• obtaining, through use of the pre-selected LC/MS method, values associated with retention time, mass, and intensity of precursor ions of a sample comprising one or more unidentified proteins;
• and
• identifying the one or more unidentified proteins in response to one or more matches between the obtained values and values of one or more protein profiles in the protein catalog.

An apparatus for performing chemical analyses, comprising:

• a chromatography module;
• a mass-spectrometry module in fluid communication with the chromatography module to receive an eluent from the chromatography module;
• and
• a computer unit, in communication with the chromatography module and the mass-spectrometry module, comprising at least one processor and at least one memory for storing a plurality of instructions, which, when executed by the at least one processor, causes implementation of the steps of
• a) digesting, according to a pre-selected digestion method, a reference sample comprising a polypeptide to obtain a plurality of precursors associated with the polypeptide,
• b) separating, according to a pre-selected chromatographic method, the plurality of precursors, and determining values associated with retention times of the separated plurality of precursors,
• c) ionizing, according to a pre-selected ionization method, some of the separated plurality of precursors to form a plurality of precursor ions and forming a plurality of product ions from at least some of the remaining separated plurality of precursors,
• d) mass analyzing the plurality of precursor ions and plurality of product ions to determine values associated with mass and values associated with ion intensity, thereby validating identities of the plurality of precursor ions in response to corresponding identified product ions, and
• e) storing in a polypeptide catalog a profile of the polypeptide, the profile defined by the polypeptide, the values associated with mass and intensity, and the values associated with retention times.