< No: 19 >

Targeted proteomics

The recombinant protein fragments generated within the HPA program were used to develop a new concept for targeted proteomics based on stable isotope–labeled standards to allow for multiplex quantification of proteins in tissues and blood. This work was done in collaboration with Matthias Mann and coworkers at the Max Planck Institute of Biochemistry in Martinsried, Germany. This concept was later used by the HPA group to analyze the correlation of RNA and proteins in cells and tissues; and recently, multiplex assays for blood analysis have been developed to explore protein profiles in healthy and diseased individuals.

Key publication

  • Zeiler M et al., A Protein Epitope Signature Tag (PrEST) library allows SILAC-based absolute quantification and multiplexed determination of protein copy numbers in cell lines. Mol Cell Proteomics. (2012)
    PubMed: 21964433 DOI: 10.1074/mcp.O111.009613

Other selected publications

  • Lamond AI et al., Advancing cell biology through proteomics in space and time (PROSPECTS). Mol Cell Proteomics. (2012)
    PubMed: 22311636 DOI: 10.1074/mcp.O112.017731

  • Geiger T et al., Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse. Mol Cell Proteomics. (2013)
    PubMed: 23436904 DOI: 10.1074/mcp.M112.024919

  • Edfors F et al., Immunoproteomics using polyclonal antibodies and stable isotope-labeled affinity-purified recombinant proteins. Mol Cell Proteomics. (2014)
    PubMed: 24722731 DOI: 10.1074/mcp.M113.034140

  • Edfors F et al., Screening a Resource of Recombinant Protein Fragments for Targeted Proteomics. J Proteome Res. (2019)
    PubMed: 31094526 DOI: 10.1021/acs.jproteome.8b00924

  • Hober A et al., Absolute Quantification of Apolipoproteins Following Treatment with Omega-3 Carboxylic Acids and Fenofibrate Using a High Precision Stable Isotope-labeled Recombinant Protein Fragments Based SRM Assay. Mol Cell Proteomics. (2019)
    PubMed: 31591263 DOI: 10.1074/mcp.RA119.001765

Figure legend: The principle of targeted proteomics using stable isotope-labeled recombinant protein fragments (QPRESTs).

Key facts

  • A resource of 26,840 individually purified recombinant protein fragments corresponding to more than 16,000 human protein– coding genes has been analyzed using targeted proteomics
  • More than 500 stable isotope–labeled recombinant protein fragments have been used for plasma analysis
  • The absolute concentration of endogenous target proteins can be determined using this method