Clinical Proteomics

Clinical Proteomics

Title of the document

We support translational research and the development of:

  1. Mass spectrometry-assisted diagnostics (identification and validation of disease-specific biomarkers)
  2. Therapeutic drugs (drug target identification, mode-of-action analyses, drug response monitoring, etc.)

Further reading:

Quantitative protein biomarker panels: a path to improved clinical practice through proteomics

Hartl J et al., EMBO Mol Med. 2023 Mar 20:e16061.

Previous product developments:

We have produced mass spectrometry kits for detection and quantification of:

  • SARS-CoV-2, SARS-CoV, Coronaviridae and the lowest common ancestor (Cov-MS)
  • SARS-CoV-2, Influenza A, Influenza B and RSVA (Cov-MS2)
  • Biomarkers associated with the development and staging of cardiovascular diseases (CVDQuant)
References for Cov-MS
  • Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients
    Bart Van Puyvelde, Katleen Van Uytfanghe, Olivier Tytgat, Laurence Van Oudenhove, Ralf Gabriels, Robbin Bouwmeester, Simon Daled, Tim Van Den Bossche, Pathmanaban Ramasamy, Sigrid Verhelst, Laura De Clerck, Laura Corveleyn, Sander Willems, Nathan Debunne, Evelien Wynendaele, Bart De Spiegeleer, Peter Judak, Kris Roels, Laurie De Wilde, Peter Van Eenoo, Tim Reyns, Marc Cherlet, Emmie Dumont, Griet Debyser, Ruben t’Kindt, Koen Sandra, Surya Gupta, Nicolas Drouin, Amy Harms, Thomas Hankemeier, Donald J. L. Jones, Pankaj Gupta, Dan Lane, Catherine S. Lane, Said El Ouadi, Jean-Baptiste Vincendet, Nick Morrice, Stuart Oehrle, Nikunj Tanna, Steve Silvester, Sally Hannam, Florian C. Sigloch, Andrea Bhangu-Uhlmann, Jan Claereboudt, N. Leigh Anderson, Morteza Razavi, Sven Degroeve, Lize Cuypers, Christophe Stove, Katrien Lagrou, Geert A. Martens, Dieter Deforce, Lennart Martens, Johannes P. C. Vissers, and Maarten Dhaenens.
    JACS Au 2021, 1, 6, 750–765.[Pubmed]
    The authors established a consortium consisting of 15 academic laboratories and several industrial partners to identify peptides for MS-based detection of SARS-CoV-2 infection. They describe the full pipeline for developing a fast and sensitive MS-based assay for detection of viral presence directly in clinical samples using conventional instrumentation.
  • Cov2MS: An Automated and Quantitative Matrix-Independent Assay for Mass Spectrometric Measurement of SARS-CoV-2 Nucleocapsid Protein.
    Van Puyvelde B, Van Uytfanghe K, Van Oudenhove L, Gabriels R, Van Royen T, Matthys A, Razavi M, Yip R, Pearson T, Drouin N, Claereboudt J, Foley D, Wardle R, Wyndham K, Hankemeier T, Jones D, Saelens X, Martens G, Stove CP, Deforce D, Martens L, Vissers JPC, Anderson NL, Dhaenens M.
    Anal Chem. 2022 Dec 20;94(50):17379-17387. [Pubmed]
    Van Puyvelde et al improved Cov-MS by adding SISCAPA technology to enrich proteotypic peptides of the SARS-CoV-2 nucleocapsid (N) protein from trypsin-digested patient samples. The Cov2MS assay is compatible with most matrices including nasopharyngeal swabs, saliva, and plasma, has increased sensitivity and a strong positive correlation with qPCR detection beyond a quantification cycle of 30-31.
  • A fast and sensitive absolute quantification assay for the detection of SARS-CoV-2 peptides using parallel reaction monitoring mass spectrometry
    Gajbhiye A, Nalbanta A, Heunisa T, Sidgwick F, Porter A, Tahab Y, Trost M
    Journal of Proteomics. Vol. 265, 15 August 2022. [Pubmed]
    Gajbhiyea et al. developed a high-throughput PRM-MS assay to directly detect viral peptides in nasopharyngeal swab samples. The assay enables sensitive detection and absolute quantification of SARS-CoV-2 nucleocapsid peptides with short turn-around times by using the Cov-MS isotopically labelled synthetic polypeptide as reference standard.
References for CVDQuant
  • Targeted LC-MS/MS for the evaluation of proteomics biomarkers in the blood of neonates with necrotizing enterocolitis and late-onset sepsis.
    Chatziioannou AC, Wolters JC, Sarafidis K, Thomaidou A, Agakidis C, Govorukhina N, Kuivenhoven JA, Bischoff R, Theodoridis G.
    Anal Bioanal Chem. 2018 Nov;410(27):7163-7175. [Pubmed]
    Chatziioannou et al. used QconCATs and synthetic peptides belonging to 47 protein markers for a prospective case-control study evaluating serum proteomics profiles. They were able to define two panels of three proteins each that allow highly sensitive diagnosis of late-onset sepsis (LOS) and differential diagnosis between LOS and necrotizing enterocolitis.
  • Targeting Ligand Independent Tropism of siRNA-LNP by Small Molecules for Directed Therapy of Liver or Myeloid Immune Cells.
    Lin C, Mostafa A, Jans A, Wolters JC, Mohamed MR, Van der Vorst EPC, Trautwein C, Bartneck M.
    Adv Healthc Mater. 2023 Jan 8:e2202670. [Pubmed]
    mRNA-based vaccine research made huge progress during the SARS-CoV-2 pandemic. These vaccines require lipid nanoparticles (LNPs) for stability and to ensure intracellular delivery. To study the mechanism of LNP distribution in the body, Lin et al analyzed the proteome of liver tissue and serum in wild type and (Ldlr)-/- mice. They performed untargeted proteomics to detect alterations of protein abundance in serum upon siRNA-LNP administration and targeted proteomics for more in-depth analysis of selected proteins using QconCATs (CVDQuant).


Identification of therapeutic targets

Drug response prediction and monitoring

Precision medicine:

  • Biomarker identification and validation for diagnostics
  • High throughput analyses for clinical routine
  • Companion diagnostics

Translational research

Our offer

PolyQuant offers support at every step of the project: from protocol development to target protein and biomarker identification and validation. Consulting and support for external projects.

Receive high quality data and detailed reporting.


For more information, assistance and support in planning and execution of your clinical proteomics project you can contact us:

E-Mail: info[at]

Phone: +49 (0)9405 96999 10

Fax: +49 (0)9405 96999 28

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