Immunoproteomics technologies in the discovery of autoantigens in autoimmune diseases

Vinitha Ganesan, Dana P. Ascherman, Jonathan S. Minden

Research output: Contribution to journalReview articlepeer-review

17 Scopus citations


Proteomics technologies are often used for the identification of protein targets of the immune system. Here, we discuss the immunoproteomics technologies used for the discovery of autoantigens in autoimmune diseases where immune system dysregulation plays a central role in disease onset and progression. These autoantigens and associated autoantibodies can be used as potential biomarkers for disease diagnostics, prognostics and predicting/monitoring drug responsiveness (theranostics). Here, we compare a variety of methods such as mass spectrometry (MS)-based [serological proteome analysis (SERPA), antibody mediated identification of antigens (AMIDA), circulating immune complexome (CIC) analysis, surface enhanced laser desorption/ionization-time of flight (SELDI-TOF)], nucleic acid based serological analysis of antigens by recombinant cDNA expression cloning (SEREX), phage immunoprecipitation sequencing (PhIP-seq) and array-based immunoscreening (proteomic microarrays), luciferase immunoprecipitation systems (LIPS), nucleic acid programmable protein array (NAPPA) methods. We also review the relevance of immunoproteomic data generated in the last 10 years, with a focus on the aforementioned MS based methods.

Original languageEnglish (US)
Pages (from-to)133-143
Number of pages11
JournalBiomolecular Concepts
Issue number2
StatePublished - May 1 2016


  • autoantibodies
  • autoantigens
  • autoimmune diseases
  • biomarkers
  • immunoproteomics

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Cellular and Molecular Neuroscience


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