A method for determining the abundances of an analyte in a plurality of samples, said method comprising the steps of: (a) providing a plurality of cell cultures including at least a first cell culture and a second cell culture; (b) providing a different isotopically labeled amino acid to each of said cell cultures, wherein said isotopically labeled amino acids of each of said cell cultures are isotopologues of the same amino acid; (c) growing cells of each of said cell cultures, thereby introducing a different isotopic label into proteins generated by each cell culture; (d) generating a sample for each of said cell cultures, wherein each sample is characterized by a different isotopically labeled analyte, said samples including at least a first sample for said first cell culture having a first isotopically labeled analyte and a second sample for said second cell culture having a second isotopically labeled analyte, wherein said isotopically labeled analytes of each sample are isotopologues; and wherein the difference of the molecular masses of said first isotopically labeled analyte and said second isotopically labeled analyte is less than or equal to 300 mDa; (e) analyzing said isotopically labeled analytes for each sample using a mass spectrometry analysis technique providing a resolving power equal to or greater than 100,000, thereby generating an independent and distinguishable mass spectrometry signal for the isotopically labeled analytes of each sample; and (f) comparing said mass spectrometry signals for the isotopically labeled analytes of each sample, thereby determining the abundances of the analyte in said plurality of samples, wherein said analyte is a protein, a peptide, a modified protein or a modified peptide. (a) providing a plurality of cell cultures including at least a first cell culture and a second cell culture; (b) providing a different isotopically labeled amino acid to each of said cell cultures, wherein said isotopically labeled amino acids of each of said cell cultures are isotopologues of the same amino acid; (c) growing cells of each of said cell cultures, thereby introducing a different isotopic label into proteins generated by each cell culture; (d) generating a sample for each of said cell cultures, wherein each sample is characterized by a different isotopically labeled analyte, said samples including at least a first sample for said first cell culture having a first isotopically labeled analyte and a second sample for said second cell culture having a second isotopically labeled analyte, wherein said isotopically labeled analytes of each sample are isotopologues; and wherein the difference of the molecular masses of said first isotopically labeled analyte and said second isotopically labeled analyte is less than or equal to 300 mDa; (e) analyzing said isotopically labeled analytes for each sample using a mass spectrometry analysis technique providing a resolving power equal to or greater than 100,000, thereby generating an independent and distinguishable mass spectrometry signal for the isotopically labeled analytes of each sample; and (f) comparing said mass spectrometry signals for the isotopically labeled analytes of each sample, thereby determining the abundances of the analyte in said plurality of samples, wherein said analyte is a protein, a peptide, a modified protein or a modified peptide.