Plasma Profiling

National facility

The Plasma Profiling facility offers high-throughput analysis of proteins in body fluids by immunoassay technologies. The services are based on affinity proteomics approaches and include (i) highly multiplexed antibody bead arrays, (ii) multiplexed immunoassays based on commercial kits and technologies, (iii) the development of novel sandwich immunoassays and (iv) the design of alternative multiplexed assays tailored for the user's projects.

The facility hosts a unique combination of technologies and an infrastructure of instrumentation and affinity reagents. We have expertise on processing highly dimensional data and have been working on projects spanning from exploratory discovery towards a possible implementation of customised immunoassays into validation and translation. Our expertise also covers study design, the important task of  antibody validation, biostatistical data analysis, and building parallelised assays for profiling of protein interaction. The facility also consults users to find the most suitable solution for their projects.

 

SERVICES

Exploratory protein profiling of body fluids (Luminex-based)

  • Utilising antibody bead arrays
  • Support with experimental study design and target selection
  • Perform single binder assays (96-384 antibodies; direct sample labelling)
  • Support with data analysis (optional)

Protein analysis by multiplexed immunoassays

  • Bead-based immunoassay (Luminex; Different kit providers)
  • Automated micro-fluidic immunoassays (ProteinSimple)
  • Proximity Extension Assays (Olink)

Development of novel sandwich immunoassays (Luminex-based)

  • Selection of antibodies and proteins
  • Multiplexed assessment of antibody pairs
  • Development of protocols for quantitative protein analysis

Development of alternative immunoassays concepts (Luminex-based)

Consulting on protein analysis using immunoassays


Each proposed projects is evaluated according to the following model:

A) Initial assessment by facility:

  • Technical feasibility and suitability
  • Capacity and resources requested for the project

B) Project prioritization by committee:

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

APPLICATIONS

  • Antibody-based protein profiling.
  • Biomarker discovery in larger sample sets.
  • Multiplexed antibody bead arrays assays (in-house development).
  • Multiplexed immunoassays (commercial kits and technologies).
  • Assay development for user defined proteins and projects.
  • Biostatistical processing and analysis of multiplexed data.
  • Expertise in analysis of human body fluids.

EQUIPMENT

Reagents

  • 50,000 antibodies from the Human Protein Atlas project, validated on protein arrays

Analytical equipment

  • 2x FLEXMAP 3D, Luminex®
  • LX200, Luminex®
  • MAGPIX, Luminex®
  • ELLA, ProteinSimple®,
  • Biomark HD, Fluidigm®

Liquid handling equipment

  • FLUENT, Tecan
  • 2x EVO150, Tecan
  • SELMA, CyBio®

Magnetic bead handling equipment

  • KingFisher Flex, Thermo
  • EL406 Washer Dispenser, Biotek

RECENT PROJECTS

  • Profiling 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.
  • Evaluation and translation of a novel immunoassay for a diabetes-related biomarker.
  • Design of 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.
  • Development of a new immunoassay to validate proposed biomarker candidates by analyzing lysates of cells collected from 200 cancer patients.

Examples of research projects using the facility:

Discovery of circulating proteins associated to knee radiographic osteoarthritis. Lourido et al., Scientific Reports, 2017

Elevated levels of circulating CDH5 and FABP1 in association with human drug‐induced liver injury. Mikus et al., Liver International, 2017

PDGFB, a new candidate plasma biomarker for venous thromboembolism: results from the VEREMA affinity proteomics study. Bruzelius et al., Blood, 2016

Elevated levels of FN1 and CCL2 in bronchoalveolar lavage fluid from sarcoidosis patients. Hamsten et al., Respiratory Research, 2016

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, Journal 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. 

 

Examples of technology development by the facility:

Multidimensional Normalization to Minimize Plate Effects of Suspension Bead Array Data. Hong et al. JPR, 2016

Multiplexed protein profiling by sequential affinity capture. Ayoglu et al., Proteomics, 2016