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Plasma Profiling

National facility

Biobank profiling

The Plasma Profiling facility offers high-throughput immunoassay analysis of proteins from body fluids. With access to the unique resource of validated polyclonal antibodies from the Human Protein Atlas project, it performs multiplexed protein profiling by using the suspension bead technology. With protein targets proposed by the user, up to 384 antibodies can be combined in one array to analyze 384 or more samples in one experiment. For exploratory analyses, the facility employs an assay based on single antibody capture combined with direct labeling of target proteins. In serum or plasma samples, the screening assay consumes only µl of sample. The Plasma Profiling facility also conducts technical verification of the identified candidates, using multiple binders or dual binder assays or other types of immunoassay systems.

SERVICES

  • Protein profiling of body fluids; mainly plasma, serum and cerebrospinal fluid.
  • General consulting on methods for protein analysis using immunoassays.
  • Support and guidance for
    • Antibody selection
  • Study design
  • Data analyses
  • Develop customized assays and methods for protein analysis

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

1) Initial screen of project by facility:

  • Technical feasibility and suitability
  • Capacity and resources requested 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)

EQUIPMENT

  • Affinity reagents: 47,000  protein array validated antibodies from the Human Protein Atlas project.
  • Instrumentation:  2x FLEXMAP 3D, LX200 and MAGPIX, all from Luminex®.
  • Liquid-handling : 2x Tecan EVO150, CyBio® SELMA.
  • Magnetic bead handler: KingFisher.
  • Plate washer: Biotek EL406.

APPLICATIONS

The platform is involved in

  • Screening for potential protein biomarkers with high sample throughput.
  • Building customized antibody bead arrays.
  • Analysis of human body fluids or fluid samples (e.g. lysates)
  • Studies across different disease areas and clinical applications.
  • Assay development for antibody-based protein analysis.

RECENT PROJECTS

  • We profiled more then 3,000 plasma samples using a customized bead array with 384 HPA antibodies for the discovery of disease-associated proteins. The aims are to identify and validate potential biomarkers; (1) to stratify populations by risk of disease progression, and (2) to monitor organ function in response to treatment.
  • We designed a new immunoassay to study up to 300 proteins for their involvement in protein-protein interactions. We analyzed samples from immunoprecipitations derived from transfected human cells.
  • We developed a new immunoassay to validate proposed biomarker candidates by analyzing lysates of cells collected from 200 cancer patients.

Publications using the facility:

Circulating Carnosine Dipeptidase 1 Associates with Weight Loss and Poor Prognosis in Gastrointestinal Cancer. P Arner et al, PLoS ONE, 2015. 

Heat differentiated complement factor profiling. Hamsten et al, J of Proteomics, 2015.

Affinity proteomics within rare diseases: a BIO-NMD study for blood biomarkers of muscular dystrophies. B Ayoglu et al, EMBO Mol Med, 2014.

Identification of Candidate Serum Proteins for Classifying Well-Differentiated Small Intestinal Neuroendocrine Tumors. S Darmanis et al, PLoS ONE, 2013.