Cryo-slicing Blue Native-Mass Spectrometry (csBN-MS), a Novel Technology for High Resolution Complexome Profiling

Mol Cell Proteomics. 2016 Feb;15(2):669-81. doi: 10.1074/mcp.M115.054080. Epub 2015 Nov 23.


Blue native (BN) gel electrophoresis is a powerful method for protein separation. Combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS), it enables large scale identification of protein complexes and their subunits. Current BN-MS approaches, however, are limited in size resolution, comprehensiveness, and quantification. Here, we present a new methodology combining defined sub-millimeter slicing of BN gels by a cryo-microtome with high performance LC-MS/MS and label-free quantification of protein amounts. Application of this cryo-slicing BN-MS approach to mitochondria from rat brain demonstrated a high degree of comprehensiveness, accuracy, and size resolution. The technique provided abundance-mass profiles for 774 mitochondrial proteins, including all canonical subunits of the oxidative respiratory chain assembled into 13 distinct (super-)complexes. Moreover, the data revealed COX7R as a constitutive subunit of distinct super-complexes and identified novel assemblies of voltage-dependent anion channels/porins and TOM proteins. Together, cryo-slicing BN-MS enables quantitative profiling of complexomes with resolution close to the limits of native gel electrophoresis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Brain / metabolism
  • Chromatography, Liquid / methods*
  • Electron Transport / genetics
  • Electrophoresis, Gel, Two-Dimensional
  • Mass Spectrometry / methods*
  • Mitochondria / metabolism
  • Mitochondrial Proteins / biosynthesis*
  • Mitochondrial Proteins / genetics
  • Protein Biosynthesis / genetics*
  • Rats
  • Tandem Mass Spectrometry / methods


  • Mitochondrial Proteins