A Cost-Effective High-Throughput Plasma and Serum Proteomics Workflow Enables Mapping of the Molecular Impact of Total Pancreatectomy with Islet Autotransplantation

Blood is an ideal body fluid for
the discovery or monitoring of
diagnostic and prognostic protein biomarkers. However, discovering
robust biomarkers requires the analysis of large numbers of samples
to appropriately represent interindividual variability. To address
this analytical challenge, we established a high-throughput and cost-effective
proteomics workflow for accurate and comprehensive proteomics at an
analytical depth applicable for clinical studies. For validation,
we processed 1 μL each from 62 plasma samples in 96-well plates
and analyzed the product by quantitative data-independent acquisition
liquid chromatography/mass spectrometry; the data were queried using
feature quantification with Spectronaut. To show
the applicability of our workflow to serum, we analyzed a unique set
of samples from 48 chronic pancreatitis patients, pre and post total
pancreatectomy with islet autotransplantation (TPIAT) surgery. We
identified 16 serum proteins with statistically significant abundance
alterations, which represent a molecular signature distinct from that
of chronic pancreatitis. In summary, we established a cost-efficient
high-throughput workflow for comprehensive proteomics using PVDF-membrane-based
digestion that is robust, automatable, and applicable to small plasma
and serum volumes, e.g., finger stick. Application of this plasma/serum
proteomics workflow resulted in the first mapping of the molecular
implications of TPIAT on the serum proteome.