Specimen Inactivation Methods for ProteomicsComparisons of Irradiation, Chemical, and Heat Treatments on Downstream Serum Analyses

Multiomic techniques, including proteomics, can provide
novel insights
for both pathogen detection and assessment of host responses to infection.
Numerous studies have described the efficacy of heat inactivation,
γ irradiation, or treatment with guanidinium-based chaotropic
salts (e.g., TRIzol) for pathogen inactivation of biological samples
to ensure biosafety and biosecurity. However, the effect of these
methods on the greater serum proteome is less studied. Here, we sought
to comprehensively measure the effects of four routinely used pathogen
inactivation methods on the serum proteome of Rhesus macaques by characterizing
the serum proteome pre-and-post inactivation treatment. Using the
R-package MS-DAP for statistical benchmarking, our analysis revealed
distinct changes in total peptide/protein detection and individual
protein abundances (e.g., ALB, APOA1, and CRP) across inactivation
methods and compared to their untreated controls. Specifically, we
observed improved quantitative reproducibility in γ-irradiated
samples across biological, technical, and experimental replicates
compared to chemical inactivation and different heat combinations.
These findings represent the first direct, experimental comparisons
of effective pathogen inactivation methods on the serologic profiles
of nonhuman primates and provide useful criteria for evaluating methods
for biological specimen inactivation prior to proteomic analysis.