Patent ID: 7476546

Claim:
A method for the comparison of a protein under different biological conditions using mass spectrometry comprising the steps of: a. digesting said protein of a first biological condition into peptides with either a peptidyl-Lys metalloendopeptidase or a peptidyl-Asp metalloendopeptidase in a buffer using 18 O enriched water to incorporate a single 18 O atom into at least 90% of the digested peptides; b. digesting said protein of a second biological condition into peptides with said peptidyl-Lys metalloendopeptidase or peptidyl-Asp metalloendopeptidase in the buffer using 16 O water to incorporate a single 16 O atom into the digested peptides; c. mixing digested peptides containing enriched 18 O of the first biological condition and digested peptides containing 16 O of the second biological condition; d. performing mass spectrometry analysis of the relative ratio of 18 O and 16 O in said mixed digested peptides; and e. determining a ratio of labeled peptides to unlabeled peptides, wherein the ratio determined indicates a change in an amount of said protein of a second biological condition relative to an amount of said protein of a first biological condition.