Amine-reactive neutron-encoded labels for highly plexed proteomic quantitation

Mol Cell Proteomics. 2013 Nov;12(11):3360-9. doi: 10.1074/mcp.M113.032011. Epub 2013 Jul 23.


We describe a novel amine-reactive chemical label that exploits differential neutron-binding energy between (13)C and (15)N isotopes. These neutron-encoded (NeuCode) chemical labels enable up to 12-plex MS1-based protein quantification. Each structurally identical, but isotopically unique, tag is encoded with a 12.6-mDa mass difference-relative to its nearest neighbor-so that peptides bearing these NeuCode signatures do not increase spectral complexity and are detected only upon analysis with very high mass-resolving powers. We demonstrate that the method provides quantitative performance that is comparable to both metabolic labeling and isobaric tagging while combining the benefits of both strategies. Finally, we employ the tags to characterize the proteome of Saccharomyces cerevisiae during the diauxic shift, a metabolic transition from fermentation to aerobic respiration.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aerobiosis
  • Amines / chemistry
  • Carbon Isotopes
  • Chromatography, High Pressure Liquid / methods
  • Fermentation
  • Isotope Labeling / methods*
  • Neutrons
  • Nitrogen Isotopes
  • Proteomics / methods*
  • Saccharomyces cerevisiae / growth & development
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / analysis
  • Saccharomyces cerevisiae Proteins / metabolism
  • Tandem Mass Spectrometry / methods


  • Amines
  • Carbon Isotopes
  • Nitrogen Isotopes
  • Saccharomyces cerevisiae Proteins