Optimized enzymatic conditions incorporate a single oxygen atom into digested peptides using a peptidase. The incorporation of a single oxygen atom is especially useful for proteolytic 18O labeling in comparative proteomics. The optimized proteolytic 18O labeling minimizes the generation of a mixture of isotopic isoforms of the peptides resulting from incorporation of either one or two 18O atoms. The outcome is accurate quantification of isotopically labeled peptides.