MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics

A triple-stage mass spectrometry (MS3)-based method is used to remove ratio interference, resulting in accurate, large-scale, multiplexed quantitative proteomics measurements using isobaric labeling. Also in this issue, Wenger et al . provide a different solution to the same problem. Quantitative mass spectrometry–based proteomics is highly versatile but not easily multiplexed. Isobaric labeling strategies allow mass spectrometry–based multiplexed proteome quantification; however, ratio distortion owing to protein quantification interference is a common effect. We present a two-proteome model (mixture of human and yeast proteins) in a sixplex isobaric labeling system to fully document the interference effect, and we report that applying triple-stage mass spectrometry (MS3) almost completely eliminates interference.