Extracting, enriching, and identifying nuclear body sub-complexes using label-based quantitative mass spectrometry

Methods Mol Biol. 2015;1262:215-38. doi: 10.1007/978-1-4939-2253-6_13.


Determining the proteome of a nuclear body is a crucial step toward understanding its function; however, it is extremely challenging to obtain pure nuclear body preparations. Moreover, many nuclear proteins dynamically associate with multiple bodies and subnuclear compartments, confounding analysis. We have found that a more practical approach is to carry out affinity purification of nuclear body sub-complexes via the use of tagged nuclear-body-specific marker proteins. Here we describe in detail the method to identify new nuclear body protein sub-complexes through SILAC (stable isotope labeling by amino acids in culture)-based affinity purification followed by quantitative mass spectrometry.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line
  • HeLa Cells
  • Humans
  • Intranuclear Inclusion Bodies / metabolism
  • Isotope Labeling / methods
  • Mass Spectrometry / methods*
  • Nuclear Proteins / isolation & purification*
  • Proteomics / methods*


  • Nuclear Proteins