The invention provides a method for determining the presence of one or mo re polypeptide biomarkers in a sample, comprising the steps of: (a) subjecti ng the sample to a mass spectrometric (MS) analysis and recording retention time index and corresponding mass for each signal detected; (b) con-elating the mass corresponding to each signal to a reference database of biomarker m asses to form a con-elation between each signal and a reference biomarker, a nd discarding those signals whose masses do not correlate to a reference boi marker mass; (c) storing those signals whose masses correlate with a referen ce biomarker; (d) confirming the con-elation between each stored signal and a reference biomarker by matching the MS spectrum of each signal with the MS spectrum of the reference biomarker in the database using a similarity meas ure, to define a set of positively correlating signals; (d) measuring the in tensity of each positivley coreelating signal and scoring its absolute signa l intensity or its relative signal intensity using a discrimination function ; (e) applying a threshold to the score values obtained from the discriminat ion function to detemiine the presence or absence of the biomarker.
