Cross-Platform Evaluation Reveals Sample Preparation-Driven Biological Biases despite Advances in Mass Spectrometry Performance in Serum Proteomics.
- 1Quantall B.V., L.J. Zielstraweg 1, 9713 GXGroningen, The Netherlands.
- 2Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, 9713 AVGroningen, The Netherlands.
- 3Department of Pediatrics, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AVGroningen, The Netherlands.
Abstract
Advances in mass spectrometry (MS) instrumentation and protein extraction technologies are reshaping proteomics; however, whether improved analytical performance alters the biological information accessible from different sample preparation strategies remains unclear. Here, we performed a cross-platform evaluation using identical benchmark serum samples previously analyzed on an Orbitrap Exploris 480 platform, including the newly introduced Seer Proteograph ONE workflow, to determine how MS advances and sample preparation influence analytical performance and biological interpretation. Across all preparation strategies, the timsTOF HT improved analytical performance by increasing protein and peptide identifications, reducing missing values, and improving linearity in spike-in experiments, particularly for low-abundance proteins. Despite these improvements, sample preparation remained the major determinant of the accessible serum proteome. Functional enrichment analysis revealed reproducible workflow-specific biases across MS platforms: nanoparticle-based enrichment expanded access to a broader range of serum proteins and improved detection of clinically relevant signaling-associated proteins, including cytokine- and chemokine-related marker classes, whereas the depletion-based strategy showed a distinct functional profile enriched for receptor-related activities. Together, these findings demonstrate that MS advances enhance analytical performance but do not eliminate sample preparation-driven differences in biological accessibility. This study provides a framework for selecting serum proteomics workflows according to specific biomarker and pathway objectives.
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BibTeX
@article{katsavelis2026crossplatform,
title = {{Cross-Platform Evaluation Reveals Sample Preparation-Driven Biological Biases despite Advances in Mass Spectrometry Performance in Serum Proteomics.}},
author = {Drosos Katsavelis and Marieke G C van der Hart and Justina C Wolters and Hjalmar P Permentier and Peter L Horvatovich and Thomas I F H Cremers},
journal = {Journal of proteome research},
year = {2026},
month = oct,
doi = {10.1021/acs.jproteome.6c00493},
url = {https://europepmc.org/article/MED/42918118},
note = {CC BY},
}
RIS
TY - JOUR
TI - Cross-Platform Evaluation Reveals Sample Preparation-Driven Biological Biases despite Advances in Mass Spectrometry Performance in Serum Proteomics.
AU - Drosos Katsavelis
AU - Marieke G C van der Hart
AU - Justina C Wolters
AU - Hjalmar P Permentier
AU - Peter L Horvatovich
AU - Thomas I F H Cremers
PY - 2026
DA - 2026/10/01
JO - Journal of proteome research
DO - 10.1021/acs.jproteome.6c00493
UR - https://europepmc.org/article/MED/42918118
AB - Advances in mass spectrometry (MS) instrumentation and protein extraction technologies are reshaping proteomics; however, whether improved analytical performance alters the biological information accessible from different sample preparation strategies remains unclear. Here, we performed a cross-platform evaluation using identical benchmark serum samples previously analyzed on an Orbitrap Exploris 480 platform, including the newly introduced Seer Proteograph ONE workflow, to determine how MS advances and sample preparation influence analytical performance and biological interpretation. Across all preparation strategies, the timsTOF HT improved analytical performance by increasing protein and peptide identifications, reducing missing values, and improving linearity in spike-in experiments, particularly for low-abundance proteins. Despite these improvements, sample preparation remained the major determinant of the accessible serum proteome. Functional enrichment analysis revealed reproducible workflow-specific biases across MS platforms: nanoparticle-based enrichment expanded access to a broader range of serum proteins and improved detection of clinically relevant signaling-associated proteins, including cytokine- and chemokine-related marker classes, whereas the depletion-based strategy showed a distinct functional profile enriched for receptor-related activities. Together, these findings demonstrate that MS advances enhance analytical performance but do not eliminate sample preparation-driven differences in biological accessibility. This study provides a framework for selecting serum proteomics workflows according to specific biomarker and pathway objectives.
SN - 1535-3893
SN - 1535-3907
ER -