System and methods for qualitatively and quantitatively comparing

Abstract

System for analyzing a protein sample, comprising a reactor vessel, a chromatographic column, a mass spectrometer, and a computer system. The reactor vessel comprises an enzyme activity capable of digesting the protein sample in order to provide a plurality of peptide digests, an inlet port for receiving the protein to be digested, and an exit port for discharging the peptide digests. The chromatographic column comprises a chromatographic medium capable of chromatographically fractionating the peptide digests as the peptide digests are eluted through the column, wherein the chromatographic column comprises an inlet port for receiving the peptide digests, said inlet port being in flow communication with the exit port of the reactor vessel, and wherein the chromatographic column comprises an exit port for discharging an effluent comprising the chromatographically fractionated peptide digests. The mass spectrometer is capable of generating a mass spectroscopic data set comprising data from which a first plurality of selective ion chromatograms for the fractionated peptide digests can be generated. The mass spectrometer has an inlet port for receiving the chromatographically fractionated peptide digests. The inlet port is in flow communication with the exit port of the chromatographic column. The computer system is operationally coupled to the mass spectrometer such that the computer system is capable of analyzing the mass spectroscopic data set. The computer system comprises programming enabling the computer system to analyze protein samples using selective ion chromatograms derived from the mass spectroscopic data set.