Standardized Workflow for Precise Mid- and High-Throughput Proteomics of Blood Biofluids.

BACKGROUND: Accurate discovery assay workflows are critical for identifying authentic circulating protein biomarkers in diverse blood matrices. Maximizing the commonalities in the proteomic workflows between different biofluids simplifies the approach and increases the likelihood for reproducibility. We developed a workflow that can accommodate 3 blood-based proteomes: naive plasma, depleted plasma and dried blood. METHODS: Optimal conditions for sample preparation and data independent acquisition-mass spectrometry analysis were established in plasma then automated for depleted plasma and dried blood. The mass spectrometry workflow was modified to facilitate sensitive high-throughput analysis or deeper profiling with mid-throughput analysis. Analytical performance was evaluated by the linear response of peptides and proteins to a 6- or 7-point dilution curve and the reproducibility of the relative peptide and protein intensity for 5 digestion replicates per day on 3 different days for each biofluid. RESULTS: Using the high-throughput workflow, 74% (plasma), 93% (depleted), and 87% (dried blood) displayed an inter-day CV <30%. The mid-throughput workflow had 67% (plasma), 90% (depleted), and 78% (dried blood) of peptides display an inter-day CV <30%. Lower limits of detection and quantification were determined for peptides and proteins observed in each biofluid and workflow. Based on each protein and peptide's analytical performance, we could describe the observable, reliable, reproducible, and quantifiable proteomes for each biofluid and workflow. CONCLUSION: The standardized workflows established here allows for reproducible and quantifiable detection of proteins covering a broad dynamic range. We envisage that implementation of this standard workflow should simplify discovery approaches and facilitate the translation of candidate markers into clinical use.

Discovery Proteomics for COVID-19: Where We Are Now.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible coronavirus responsible for the pandemic coronavirus disease 2019 (COVID-19), which has had a devastating impact on society. Here, we summarize proteomic research that has helped elucidate hallmark proteins associated with the disease with respect to both short- and long-term diagnosis and prognosis. Additionally, we review the highly variable humoral response associated with COVID-19 and the increased risk of autoimmunity.

Earthquake-induced structural deformations enhance long-term solute fluxes from active volcanic systems.

Evidence for relationships between seismotectonic activity and dissolved weathering fluxes remains limited. Motivated by the occurrence of new springs emerging after the 2016 Kumamoto earthquake and supported by historical groundwater data, this study focuses on the long-term effect of near-surface structural deformation on the contribution of deep, highly saline fluids to the solute fluxes from the Aso caldera, Kyushu, Japan. Available hydrologic and structural data suggest that concentrated, over-pressured groundwaters migrate to the surface when new hydraulic pathways open during seismic deformation. These new springs have a hydrochemical fingerprint (including δDH2O, δ18OH2O, δ7Li, δ11B, δ18OSO4, and δ34SSO4) indistinguishable from long-established confined groundwater that likely reflects a mixture of infiltrated meteoric water with high-sulfate hydrothermal fluids. A comparison of historical hydrochemistry data and patterns of past seismicity suggests that discharge of deep fluids is associated with similar deformation structures to those observed during the Kumamoto earthquake, and that seismic activity plays an important role over historic timescales in delivering the majority of the solutes to the caldera outlet, sustaining fluxes that are amongst the world's highest. This upwelling mechanism might be relevant for other systems too, and could contribute to the over-proportional share of active volcanic areas in global weathering fluxes.