Mass spectrometry detection and characterization of noncovalent protein complexes

Methods Mol Biol. 2009;492:273-82. doi: 10.1007/978-1-59745-493-3_16.


Protein noncovalent complexes compose most of the essential biological machines in the cell. The characterization of protein complexes and assemblies using mass spectrometry (MS) has significant advantages over many other biophysical methods because of the inherent sensitivity and resolution of MS. The applicability of MS coupled with electrospray ionization (ESI) for the measurement of large proteins and protein complexes has been furthered by the development of sensitive analyzers, such as the time-of-flight (TOF) analyzer. Moreover, sample preparation has a very important role for such studies, as it could significantly affect the results of mass spectrometry experiments. We discuss the experimental variables for the ESI-MS detection of noncovalent protein complexes by featuring two different protein systems: yeast enolase is a 93-kDa homodimeric complex, and alpha-synuclein is a small, 14-kDa protein implicated in the pathogenesis of Parkinson's disease and binds noncovalently to endogenous polyamines, such as spermine.

Publication types

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

MeSH terms

  • Analytic Sample Preparation Methods
  • Animals
  • Fungal Proteins / analysis
  • Fungal Proteins / chemistry
  • Fungal Proteins / metabolism
  • Humans
  • Hydrogen-Ion Concentration
  • Ligands
  • Myoglobin / analysis
  • Myoglobin / chemistry
  • Myoglobin / metabolism
  • Phosphopyruvate Hydratase / analysis
  • Phosphopyruvate Hydratase / chemistry
  • Phosphopyruvate Hydratase / metabolism
  • Protein Denaturation
  • Proteins / analysis*
  • Proteins / chemistry
  • Proteins / metabolism*
  • Spectrometry, Mass, Electrospray Ionization / methods*
  • Spermine / metabolism
  • alpha-Synuclein / analysis
  • alpha-Synuclein / chemistry
  • alpha-Synuclein / metabolism


  • Fungal Proteins
  • Ligands
  • Myoglobin
  • Proteins
  • alpha-Synuclein
  • Spermine
  • Phosphopyruvate Hydratase