The authors describe a multiplexed protein quantitation strategy using isobaric reagents that label peptides at the N-terminus and lysine side chains. This method provides both relative and absolute measurements of proteins in complex mixtures. The reagents yield amine-derivatized peptides that are indistinguishable in MS but exhibit intense low-mass MS/MS signature ions, which support quantitation. The study examines global protein expression in wild-type yeast and two mutant strains, *upf1Δ* and *xrn1Δ*, defective in different mRNA decay pathways. The 4-fold multiplexing strategy enables simultaneous relative protein measurements and absolute quantification of target proteins using synthetic isobaric peptide standards. The results show that inactivation of Upf1p and Xrn1p causes both common and unique effects on protein expression, including up-regulation of amino acid biosynthesis and down-regulation of translation-related proteins. The multiplexed approach enhances peptide coverage and sensitivity compared to traditional methods, and it allows for the simultaneous comparison of multiple strains without increasing chromatographic or MS complexity.The authors describe a multiplexed protein quantitation strategy using isobaric reagents that label peptides at the N-terminus and lysine side chains. This method provides both relative and absolute measurements of proteins in complex mixtures. The reagents yield amine-derivatized peptides that are indistinguishable in MS but exhibit intense low-mass MS/MS signature ions, which support quantitation. The study examines global protein expression in wild-type yeast and two mutant strains, *upf1Δ* and *xrn1Δ*, defective in different mRNA decay pathways. The 4-fold multiplexing strategy enables simultaneous relative protein measurements and absolute quantification of target proteins using synthetic isobaric peptide standards. The results show that inactivation of Upf1p and Xrn1p causes both common and unique effects on protein expression, including up-regulation of amino acid biosynthesis and down-regulation of translation-related proteins. The multiplexed approach enhances peptide coverage and sensitivity compared to traditional methods, and it allows for the simultaneous comparison of multiple strains without increasing chromatographic or MS complexity.