Automated Platform for Mass-Spectrometry-Based Multiomics Analysis from Small Volumes of Biofluids

Proteins
and metabolites directly reflect biological states, yet
traditional mass-spectrometry-based sample preparation remains labor-intensive,
manual, and necessitates separate workflows for different molecules,
hindering large-scale studies and risking microsample depletion. We
developed an integrated multiomics workflowdesigned for the
sequential enrichment of extracellular vesicle proteins (EVPs), secreted
proteins (SPs, enriched via protein corona formation), and metabolites
from a single biofluid sampleby leveraging an automated liquid-handling
and sample-preparation system. Applied to 1 mL of urine, it identified
2,287 EVPs, 1,759 SPs, and 1,122 metabolites, with >82% protein
overlap
in at least two replicates, a coefficient of variation <6%, and
Pearson correlations >0.86. In 100 μL of respiratory syncytial
virus-stimulated immune organoid culture media, we observed multiomics
patterns that were consistent with three typical immune response stages.
The automated system-based multiomics workflow provides a scalable
and reliable solution for high-throughput sample preparation, offering
broad utility in clinical research, biomarker discovery, and translational
studies.