1. A method for determining the expression level oI target proteins in a subject, comprising: generating a plurality of respective peptide transitions from a plurality of proteins obtained from a biological sample from the subject, wherein the plurality of proteins comprises both target and normalizing proteins; measuring a mass spectroscopy (MS) signal intensity from the respective plurality of peptide transitions and a plurality of corresponding stable isotope-labeled internal standard (SIS) peptide transitions; for each of the plurality of proteins, calculating a response ratio between the MS signal intensity of the peptide transition and the corresponding SIS peptide transition; normalizing the response ratio for each target protein by a sample-dependent normalization factor calculated from the response ratio for each normalizing protein, wherein the normalized response ratios provide a determination of the expression level of the target proteins.