Data-Independent Acquisition-Based Quantitative Proteomics for Pairwise Comparison of Serum and Plasma

Human blood contains proteins secreted by various organs,
but there
is no consensus on whether serum or plasma is preferable for proteome
studies. Mass spectrometry employing data-independent acquisition
has emerged as a transformative methodology in proteomics, enabling
reproducible large-scale quantification of proteomes during one LC–MS/MS
analytical run and facilitating identification of potential markers
and elucidation of biological processes. Here, we profiled the proteome
data of ten paired plasma and serum samples in the initial sample
set. Functional analysis revealed similarities and differences in
biological functions and the preference for different organs between
serum and plasma. Furthermore, comparative proteomic analysis highlighted
the different proteomic characteristics. Plasma-overrepresented pathways
were related to the phagosome and immune, while serum-overrepresented
pathways were associated with amino acid metabolism, which were further
validated by the follow-up sample set composed of eight paired plasma
and serum samples. We have detected potential markers in plasma and
serum for various cancers and explored their association with prognosis
using data from the TCGA pan-cancer cohort and HPA database. Further
assessment is required to validate the reproducibility of the quantification
for these markers. Overall, this study highlights the commonality
and specificity of plasma and serum at the molecular level, underscoring
their respective utility in biological exploration and clinical applications.