Method of isotope labeling and determining protein synthesis, quantitation and protein expression

A method comprising:

• using a processor, determining a protein turnover ratio in a cell associated with cancer based on a newly synthesized and a pre-existing fraction of a protein from a mass spectra of a peptide produced by enzyme digestion of the protein before and after isotope labeling, wherein the resultant spectra are presented as integrated peak heights of a corresponding mass to charge ratio in a centroid mode;
• and
• predicting an outcome of a therapeutic intervention associated with cancer based on changes in the protein turnover ratio,
• wherein non-essential amino acids of the-newly synthesized protein arc labeled with an isotope with low abundance through metabolism of the amino acids, an average enrichment of which is determined from the peptide containing such isotopically labeled amino acids and isotope labeling comprises introducing one of 13C, 15N in the form of 15N or 13C amino acids, 13C in the form of [U13C]-glucose,[13C]-lactate or [13C]-acetate into the non-essential amino acids.