Serum proteomics system and associated methods

A method for comparing multiple mass spectra from different biological samples, locating mass ions that are quantitatively different after using approaches to compensate for non-biological variability, and isolating and sequencing at least one peptide of interest thus allowing for identification of the peptide from a biological sample, comprising:

• fractionating each of a plurality of biological samples to form a plurality of elutions;
• obtaining a plurality of mass spectra from each of the plurality of elutions at a plurality of elution times;
• finding a molecular ion peak of interest that appears to be quantitatively different between biological samples;
• identifying a mass spectrum reference peak corresponding to an endogenous reference molecule that is substantially consistent between biological samples, the endogenous reference molecule having an elution time and a mass to charge ratio that are substantially similar to the peak of interest;
• compensating for non-biological variation for each biological sample across the plurality of elutions by normalizing the peak of interest to a mass spectrum peak of the endogenous reference molecule;
• and
• conducting collision-induced fragmentation studies that use each of a plurality of collision energies one run at a time and summing resulting pluralities of fragment ion mass spectra without averaging to form a single cumulative daughter fragment mass spectrum;
• and
• using the daughter fragment mass spectrum to establish amino acid sequence data which is then used in identifying a peptide corresponding to a peak of interest in the single aligned mass spectrum.