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Autoimmunity Profiling

National facility

The Autoimmunity profiling facility provides infrastructure and technologies for analysis of the autoantibody repertoire in body fluids and antibody validation using custom designed protein and peptide arrays.

Supported by the resource of more than 42 000 unique human protein fragments generated within the Human Protein Atlas, representing more than 18 000 human protein coding genes, we offer proteome wide screening for autoantibody reactivity on large microarrays in individual or pooled samples, as well as downstream solutions for investigation of autoantibody repertoires in hundreds of patient samples in parallel. Instrumentation and know-how is available for generating customized spotted protein microarrays as well as measurement and analysis of commercially available protein microarrays.



  • A new microarrayer, Arrayjet Super Marathon with JetMosphere Max™, was installed in July 2019 to allow more efficient and accurate printing under highly controlled environmental conditions.
  • The procurement process for the purchase of a new microarray scanner has been initiated.


  • Autoantibody profiling
  • Epitope mapping
  • Antibody validation
  • Infrastructure for commercial protein arrays


Proposed projects are assessed and prioritized according to the following model.

1) Initial assessment by facility:

  • Technical feasibility and suitability
  • Required capacity and resources for the project


2) Project prioritization by committee:

  • Scientific potential
  • Supporting preliminary data
  • Significance of facility specific technique for project
  • Supports facility development (competence and techniques)


  • Profiling the autoantibody repertoire in plasma, serum or CSF by screening on microarrays of randomly selected antigens. Usually done in the range of the lower hundreds of samples and lower thousands of antigens.
  • Verification of autoantibody profiles on suspension bead arrays with selected antigens. Usually in the range of lower hundreds of antigens and higher hundreds of samples.
  • Epitope mapping and off-target analysis of affinity reagents as well as identified autoantibodies on antigen or peptide microarrays.
  • Infrastructure and know-how to analyze commercial protein arrays such as ProtoArray (ThermoFisher), HuProt (Cambridge Protein Arrays), Immunome (Sengenics), and peptide arrays from Nimblegen Roche, Pepperprint and JPT.



  • Access to affinity reagents and high density arrays.
    • 42 100 mass spectrometry validated antigens (protein fragments) from the Human Protein Atlas project.
    • High density antigen array containing 42 100 protein fragments from the Human Protein Atlas
    • Ultra-high-density peptide microarrays from Roche NimbleGen, specifically designed and containing 2.9M peptides in one array or 173 000 peptides in 12 replicate subarrays.
  • Liquid-handling: Tecan FLUENT, 2x Tecan EVO150, CyBio® SELMA.
  • Microarray printer: Arrayjet Super Marathon with JetMosphere Max™ controlled environment.
  • Microarray scanners: CapitalBio LuxScan HT24 and Roche NimbleGen Inc. MS200.
  • Bead array instruments: 2x FLEXMAP 3D and 1x MAGPIX, all from Luminex®.
  • Plate washer: Biotek EL406.


  • The facility printed the world's largest protein array, which is available for autoantibody screenings.
  • Autoantibody screening using planar protein arrays based on Human Protein Atlas protein fragments, with subsequent verification using suspension bead arrays in a larger patient sample material.
  • Epitope mapping of a selection of antibodies using peptide arrays containing 175 000 peptides covering hundreds of proteins.
  • Using assay infrastructure for autoantibody profiling with commercially available protein arrays
  • Verification of monoclonal antibody target interaction using protein arrays containing Human Protein Atlas protein fragments

Publications associated to the facility: