Patent ID: 8030089

Claim:
A method for analyzing differential expression of proteins in proteomes, comprising: a) providing a control sample comprising a complex mixture of proteins; b1) adding a protein standard to the complex mixture of proteins of the control sample; b2) digesting the complex mixture of proteins of the control sample, and the added protein standard, to form polypeptides fragmented from the proteins and the protein standard; b3) measuring a liquid chromatographic elution profile and a retention time for each polypeptide of the digest; b4) measuring a mass spectrometric signal intensity and an accurate mass and for each eluting polypeptide; b5) determining, from the measured elution profile and signal intensity, an abundance, summed over all isotopes and all charge states, for each polypeptide; b6) determining a relative abundance of each polypeptide, relative to the abundance of the internal standard, thereby correcting for variability of digestion efficiency; c) repeating steps (b1) through (b6) for an experimental sample in place of the control sample, the experimental sample having a similar biological origin to that of the control sample; d) matching polypeptides of the experimental sample with polypeptides of the control sample in response to accurate mass and chromatographic retention time meeting threshold criteria; e) comparing the relative abundance in the experimental sample to the relative abundance in the control sample of each matched polypeptide to determine one or more differentially expressed polypeptides that are above or below expression-level threshold criteria; and f) identifying proteins that correspond to the differentially expressed polypeptides in association with the measured retention times and accurate masses of the differentially expressed polypeptides.