Updated project metadata. The ability of the TMTPro isobaric labeling reagents to form complementary ions for accurate multiplexed proteomics at the MS2 level was investigated. Human and yeast peptides were labeled in distinct ratios to analyze the effect of interference on the quantification accuracy. A method, TMTProC, was developed and optimized for accurate, sensitive MS2-level quantification of up to 8 conditions in one MS-run.