Age-Associated Plasma Protein Signatures and Proteomic Age Estimation by Data-Independent Acquisition Mass Spectrometry in a Russian Cross-Sectional Cohort

Abstract

Chronological age can be estimated from molecular profiles; however, predictive accuracy alone does not establish a biologically validated ageing clock. We therefore evaluated whether plasma protein intensities measured by data-independent acquisition mass spectrometry (DIA-MS) support chronological-age estimation in a cross-sectional cohort from Moscow, Russia, while explicitly examining acquisition-order and MS-batch confounding. Plasma samples from 350 adult participants aged 19.8 to 99.1 years were analyzed as single-shot, single-injection DIA-MS acquisitions on a Q Exactive HFX platform. The final matrix comprised 222 protein groups and was generated with DIA-NN version 1.8.1 using a two-pass predicted-library-assisted workflow, cross-run precursor-level normalization, normalized MaxLFQ-like protein–group quantification, and 1% precursor and protein–group false-discovery-rate thresholds. Descriptive associations were assessed using Spearman rank correlation with Bonferroni correction. Feature selection and missing-value imputation were confined to each training subset. Generalization was assessed primarily by holding out complete MS batches, with repeated, nested, and random five-fold analyses retained as internal comparators. Of the 222 proteins, 148 were associated with chronological age at the nominal threshold p < 0.05, and 98 remained significant after Bonferroni correction. The strongest descriptive associations involved fibrinogen beta chain (FGB; rs = 0.590), SERPINA3 (rs = 0.560), ITIH4 (rs = 0.542), complement C5 (rs = 0.538), and ceruloplasmin (rs = 0.518). In internal random-split analyses, a 50-feature Gradient Boosting strategy yielded MAE = 8.90 ± 1.06 years in repeated five-fold cross-validation and MAE = 9.10 ± 1.10 years in nested cross-validation. However, when complete MS batches were held out, aggregate MAE increased to 10.56 years (R2 = 0.554) using a batch-stratified assignment and 11.87 years (R2 = 0.461) using GroupKFold. These batch-held-out results constitute the primary estimate of generalization from the present dataset. To assess the trade-off between error and assay complexity, strategies using 5, 8, 10, 12, 15, 20, 30, and 50 proteins selected within each training fold were compared. The 8-feature strategy yielded MAE = 11.83 years in repeated random cross-validation, whereas the 50-feature strategy yielded MAE = 8.90 years. These estimates concern feature-number strategies, not fixed panels. The post hoc eight-protein list is reported only as an exploratory candidate set for future independent validation. Acquisition order was associated with chronological age (rs = 0.336, p = 1.03 × 10−10), and age and sex distributions differed strongly across 27 MS batches. Order alone predicted age with MAE = 3.98 years in a negative-control model, demonstrating that age information was encoded in the acquisition design. Accordingly, the present findings support only a proof-of-concept for plasma-proteomic prediction of chronological age within this dataset; they do not establish a batch-independent model, a clinical tool, or a biologically validated ageing clock.