Proteomic analysis of blood plasma plays a crucial role in biomedical research for biomarker discovery, development of diagnostic systems, and monitoring of treatment efficacy. In this study, we combine mass spectrometric analysis with surface-assisted protein concentration using specially prepared atomic force microscopy chips (AFM/MS) for plasma proteomic profiling. The chip surface is modified with a photocrosslinker that forms covalent bonds with protein functional groups during incubation in the analyzed solution. Using AFM chips followed by MS identification, the protein composition of 102- and 104-fold diluted blood plasma from a small cohort of conditionally healthy volunteers (N = 4) was analyzed, demonstrating interindividual variability in the number of adsorbed proteins below 8%. Analysis of the core proteome, defined as proteins consistently detected across all volunteers within each experimental condition, revealed dilution-dependent and partially non-overlapping protein sets, as well as marked differences between samples analyzed with and without the on-chip concentration step. Identified proteins were further characterized using literature-derived annotations. The AFM chip surface enabled concentration and detection of proteins spanning a broad reported plasma concentration range, from approximately ∼10−10 M to ∼10−6 M, indicating that plasma dilution and surface-assisted enrichment substantially influence proteome coverage. This approach provides a methodological basis for future comparative plasma proteomic studies of healthy individuals and patients for biomarker discovery and disease diagnostics.
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