Plasma Proteomics of Colorectal Cancer Based on Data-Independent Acquisition

Colorectal cancer (CRC) is an aggressive malignant tumor
of the
digestive system that poses a serious threat to human health. Therefore,
there is an urgent need to discover early diagnostic markers and effective
therapeutic targets for CRC. In this study, data independent acquisition
(DIA) mass spectrometry quantitative technology combined with bioinformatics
analysis was used to carry out personalized quantitative proteomics
research on abundant protein depletion plasma samples from 48 CRC
patients at different TNM stages and healthy individuals. A total
of 1089 Protein Groups were identified. By comparing the plasma protein
expression profiles between CRC patients and healthy individuals,
differentially expressed proteins (DEPs) CRP, FABP1, FABP4 and OSTP
with significant changes were screened out, and GO functional, KEGG
pathway, and GSEA enrichment analysis were performed. Mfuzz clustering
analysis categorized the DEPs in CRC plasma into six expression patterns.
Among them, the OSTP protein level in proteomics data and the mRNA
level of the gene spp1 in TCGA database both showed
an upward trend with the progression of the disease, suggesting that
it may serve as a diagnostic and prognostic marker in plasma to reflect
the disease progression of CRC patients. ROC analysis showed robust
predictive performance, and PRM validation cohort correlated well
with DIA results, providing potential insights for CRC research.