Here we describe a method for stable isotope labeling and solid-phase capture of cysteinyl peptides from complex protein mixtures. Site-specific, quantitative labeling of cysteine residues with tags that differ in isotopic content enables quantification of relative peptide abundance between samples. Labeling on a solid phase provides for simultaneous simplification of a complex peptide mixture by isolating cysteinyl, and subsequently tagged, peptides. Peptides from proteolytic digests of protein samples are labeled in preparation for analysis by microcapillary liquid chromatography and tandem mass spectrometry (microLC-MS/MS) to determine their sequences and relative abundance between samples. This approach enables rapid identification and accurate quantification of relative abundance of individual proteins from different biological contexts.