Immunoglobulin sub-class levels define inter-donor plasma variability: a longitudinal dual-lab study

Abstract Advancements in mass spectrometry have transformed plasma proteomics, allowing for high-throughput analysis of large cohorts. This study utilized the TIMES cohort, consisting of 51 healthy participants monitored monthly over 12 months, to evaluate intra- and inter-individual variability in the plasma proteome. Approximately 600 samples were analyzed in two independent laboratories, revealing strong correlations despite methodological differences. The study focused on the stability of the plasma proteome within donors over a year, with larger differences observed between donors. A support vector machine model achieved a 98% median classification accuracy, confirming stable, donor-specific proteomic profiles. Immunoglobulins, often overlooked in plasma proteomics, were found to contribute significantly to donor-specific signatures, showing pronounced inter-individual variability but remarkable intra-donor stability. In contrast, C-reactive protein and other inflammation markers exhibited significant temporal fluctuations and donor-specific baseline levels. This inter-laboratory study highlights the importance of longitudinal sampling for biomarker discovery, the robustness of MS-based proteomic workflows, and provides new insights into immunoglobulin dynamics and variability in human plasma. Synopsis: Longitudinal analysis of individual plasma proteomes over a one-year period revealed low intra-individual variability albeit high inter-individual differences. Cross-site laboratory comparisons confirmed strong concordance in analytical performance and measurement consistency. Conversion of relative protein intensities to absolute concentrations revealed immunoglobulin levels on par with established clinical reference ranges. Donors were distinguishable based on their unique plasma proteome. The immunoglobulin sub-classes are key discriminators defining inter- and intra-donor variability