MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics

Nat Methods. 2011 Oct 2;8(11):937-40. doi: 10.1038/nmeth.1714.


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • HeLa Cells
  • Humans
  • Mass Spectrometry
  • Proteomics*
  • Saccharomyces cerevisiae / chemistry