1. A method of comparing protein compositions of interest between at least two different samples which comprises: (a) preparing an extract of proteins from each of said at least two different samples; (b) providing a set of substantially chemically identical and differentially isotopically labeled protein reagents, one for each sample wherein said reagent has a formula selected from the group consisting of: A-L-PRG and L-PRG wherein A is an affinity label that selectively binds to a captive reagent, L is a linker group in which one or more atoms are differentially labeled with one or more stable isotopes and PRG is a protein reactive group that selectively reacts with a given protein functional group or is a substrate for an enzyme; (c) reacting each protein sample of step (a) with a different reagent from said set of step (b) to provide isotopically labeled proteins; (d) mixing each of said isotopically labeled proteins to form a single mixture of different isotopically labeled proteins; (e) electrophoresing the mixture of step (d) by an electrophoresing method capable of separating proteins within said mixture; and (f) detecting the difference in the expression levels of the proteins in the two samples by mass spectrometry based on individual peptides derived from chemical or enzymatic digestion.