Our hosting provider will be performing UPS maintenance on Tuesday, Oct 25, 2016 between 8 AM and 5 PM PDT. SciCrunch searching services will be down during this time.

Preparing your results

Our searching services are busy right now. Your search will reload in five seconds.

Forgot Password

If you have forgotten your password you can enter your email here and get a temporary password sent to your email.

Streamlined analysis schema for high-throughput identification of endogenous protein complexes.


Immunoprecipitation followed by mass spectrometry (IP/MS) has recently emerged as a preferred method in the analysis of protein complex components and cellular protein networks. Targeting endogenous protein complexes of higher eukaryotes, particularly in large-scale efforts, has been challenging due to cellular heterogeneity, high proteome complexity, and, compared to lower organisms, lack of efficient in-locus epitope-tagging techniques. It is further complicated by variability in nonspecific identifications and cross-reactivity of primary antibodies. Still, the study of endogenous human protein networks is highly desired despite its challenges. Here we describe a streamlined IP/MS protocol for the purification and identification of extended endogenous protein complexes. We investigate the sources of nonspecific protein binding and develop semiquantitative specificity filters that are based on peptide spectral count measurements. We also outline logical constraints for the derivation of accurate complex composition from IP/MS data and demonstrate the effectiveness of this approach by presenting our analyses of different transcriptional coregulator complexes. We show consistent purification of novel components for the Integrator complex, analyze the composition of the Mediator complex solely from our data to demonstrate the wide usability of spectral counts, and deconvolute heterogeneous HDAC1/2 networks into core complex modules and several novel subcomplex interactions.

Pubmed ID: 20133760


  • Malovannaya A
  • Li Y
  • Bulynko Y
  • Jung SY
  • Wang Y
  • Lanz RB
  • O'Malley BW
  • Qin J


Proceedings of the National Academy of Sciences of the United States of America

Publication Data

February 9, 2010

Associated Grants

  • Agency: NCI NIH HHS, Id: CA84199
  • Agency: NIDDK NIH HHS, Id: U19-DK62434

Mesh Terms

  • HeLa Cells
  • Histone Deacetylase 1
  • Histone Deacetylase 2
  • Humans
  • Immunoprecipitation
  • Mass Spectrometry
  • Models, Biological
  • Multiprotein Complexes
  • Protein Binding
  • Protein Interaction Mapping
  • Proteins