Lecture
Plasma proteomics – learnings from the Munich area and Germany-wide ring trials
- at -
- ICM Saal 2
- Type: Lecture
Lecture description
In depth proteome coverage is one of the key challenges in the current biomarker field and comprehensive robust quantifications are key to any (multi-) omics approach. Plasma is the most easily accessible clinical specimen and it´s protein composition
reports on a person’s well-being at the time point of collection. Results from the Munich and Germany-wide ring trials will be presented, which were performed as overarching standardization and quality assurance in the ClinspectM consortium and the
MSCoreSys initiative aiming to successfully establish mass spectrometry for systems medicine and develop start-to-finish and fit-for purpose workflows. In brief, it is now possible to assess ~70% of the FDA approved biomarkers accessible by mass spec
robustly with very low variations even between different labs [1, 2].
As a complementary and alternative approach, proximity extension assays (PEA) can capture also low abundant proteins in a targeted fashion. PEA achieves very high correlation with DDA and DIA methods in overlapping proteins [3]. Most interestingly,
when comparing high performing PEA with latest bead-based enrichments coupled to LC-MSMS the overlap of detected proteins is restricted to ~20% while the overall coverage expands to more than 4000 proteins robustly detected above LOD. Recent
results from a cohort study comprising 422 participants analysed with Olink Explore3k and Preomics Enrich-iST coupled to timsTOF HT will be discussed [4].
While routine clinical diagnostics most often rely on serum or Li-heparin plasma, research in the proteomics field primarily focuses on maximizing analytical depth in EDTA plasma. This disconnect between clinical practice and research poses a risk of
further divergence, and bridging this gap is essential to ensure that methodological advances remain relevant to clinical laboratories. When systematically comparing five commonly used sample preparation strategies across five blood matrices, we revealed
significant differences in protein group identifications, even in widely used diagnostic markers, such as CRP [5]. EDTA and heparinized plasma consistently yielded the highest number of protein identifications, whereas citrated plasma proved the least
effective across all preparation methods. Notably, numerous proteins were detected only in specific matrix-method combinations, highlighting the importance of deliberate and informed matrix selection in proteomic workflows.
Literature:
[1] Kardell O et al., J Proteome Res, 2024, Jan 5;23(1):117-129
[2] Kardell O et al., J Proteome Res 2025 Mar 7;24(3):1017-1029.
reports on a person’s well-being at the time point of collection. Results from the Munich and Germany-wide ring trials will be presented, which were performed as overarching standardization and quality assurance in the ClinspectM consortium and the
MSCoreSys initiative aiming to successfully establish mass spectrometry for systems medicine and develop start-to-finish and fit-for purpose workflows. In brief, it is now possible to assess ~70% of the FDA approved biomarkers accessible by mass spec
robustly with very low variations even between different labs [1, 2].
As a complementary and alternative approach, proximity extension assays (PEA) can capture also low abundant proteins in a targeted fashion. PEA achieves very high correlation with DDA and DIA methods in overlapping proteins [3]. Most interestingly,
when comparing high performing PEA with latest bead-based enrichments coupled to LC-MSMS the overlap of detected proteins is restricted to ~20% while the overall coverage expands to more than 4000 proteins robustly detected above LOD. Recent
results from a cohort study comprising 422 participants analysed with Olink Explore3k and Preomics Enrich-iST coupled to timsTOF HT will be discussed [4].
While routine clinical diagnostics most often rely on serum or Li-heparin plasma, research in the proteomics field primarily focuses on maximizing analytical depth in EDTA plasma. This disconnect between clinical practice and research poses a risk of
further divergence, and bridging this gap is essential to ensure that methodological advances remain relevant to clinical laboratories. When systematically comparing five commonly used sample preparation strategies across five blood matrices, we revealed
significant differences in protein group identifications, even in widely used diagnostic markers, such as CRP [5]. EDTA and heparinized plasma consistently yielded the highest number of protein identifications, whereas citrated plasma proved the least
effective across all preparation methods. Notably, numerous proteins were detected only in specific matrix-method combinations, highlighting the importance of deliberate and informed matrix selection in proteomic workflows.
Literature:
[1] Kardell O et al., J Proteome Res, 2024, Jan 5;23(1):117-129
[2] Kardell O et al., J Proteome Res 2025 Mar 7;24(3):1017-1029.
[3] Petrera A et al., J Proteome Res 2021, Jan 1;20(1):751-762.
[4] König A et al., PreOmics Application Note, 2025 [5] Gronauer TF et al., J Proteome Res 2025,
