A method for performing chemical analyses, the method comprising the steps of: a) fractionating a complex reference sample comprising two polypeptides into a first sample portion and a second sample portion each including portions of the two polypeptides though in different concentration ratios; b) digesting, according to a pre-selected digestion method, the first sample portion to obtain a plurality of precursors associated with the two polypeptides; c) separating, according to a pre-selected chromatographic method, the plurality of precursors of the digested first sample portion, and determining values associated with retention times of the separated plurality of precursors of the first sample portion; d) ionizing, according to a pre-selected ionization method, at least some of said separated plurality of precursors to form a plurality of precursor ions of the first sample portion; e) mass analyzing said plurality of precursor ions to determine values associated with mass and values associated with ion intensity of said plurality of precursor ions; f) digesting, according to a pre-selected digestion method, the second sample portion to obtain a plurality of precursors associated with the two polypeptides; g) separating, according to a pre-selected chromatographic method, the plurality of precursors of the digested second sample portion, and determining values associated with retention times of the separated plurality of precursors of the second sample portion; h) ionizing, according to a pre-selected ionization method, at least some of said separated plurality of precursors to form a plurality of precursor ions of the second sample portion; i) mass analyzing said plurality of precursor ions to determine values associated with mass and values associated with ion intensity of said plurality of precursor ions; j) associating the observed precursor ions with their corresponding ones of the two polypeptides in response to ratios of the observed intensities of the precursor ions in the first and second sample portions; k) storing in a polypeptide catalog a profile of said polypeptides, the profile being defined by an identity of said polypeptides, the values associated with mass and ion intensity of said plurality of precursor ions, and the values associated with retention times of the separated plurality of precursors corresponding to said plurality of precursors ions; l) repeating steps (b) through (j) on a subject sample in place of said complex reference sample to obtain subject-sample values associated with mass, ion intensity, and retention time; and m) identifying said polypeptides in the subject sample in response to a match between the subject-sample values and the values of the stored profile of said polypeptides. a) fractionating a complex reference sample comprising two polypeptides into a first sample portion and a second sample portion each including portions of the two polypeptides though in different concentration ratios; b) digesting, according to a pre-selected digestion method, the first sample portion to obtain a plurality of precursors associated with the two polypeptides; c) separating, according to a pre-selected chromatographic method, the plurality of precursors of the digested first sample portion, and determining values associated with retention times of the separated plurality of precursors of the first sample portion; d) ionizing, according to a pre-selected ionization method, at least some of said separated plurality of precursors to form a plurality of precursor ions of the first sample portion; e) mass analyzing said plurality of precursor ions to determine values associated with mass and values associated with ion intensity of said plurality of precursor ions; f) digesting, according to a pre-selected digestion method, the second sample portion to obtain a plurality of precursors associated with the two polypeptides; g) separating, according to a pre-selected chromatographic method, the plurality of precursors of the digested second sample portion, and determining values associated with retention times of the separated plurality of precursors of the second sample portion; h) ionizing, according to a pre-selected ionization method, at least some of said separated plurality of precursors to form a plurality of precursor ions of the second sample portion; i) mass analyzing said plurality of precursor ions to determine values associated with mass and values associated with ion intensity of said plurality of precursor ions; j) associating the observed precursor ions with their corresponding ones of the two polypeptides in response to ratios of the observed intensities of the precursor ions in the first and second sample portions; k) storing in a polypeptide catalog a profile of said polypeptides, the profile being defined by an identity of said polypeptides, the values associated with mass and ion intensity of said plurality of precursor ions, and the values associated with retention times of the separated plurality of precursors corresponding to said plurality of precursors ions; l) repeating steps (b) through (j) on a subject sample in place of said complex reference sample to obtain subject-sample values associated with mass, ion intensity, and retention time; and m) identifying said polypeptides in the subject sample in response to a match between the subject-sample values and the values of the stored profile of said polypeptides.