ABSTRACT: This project employed a data-independent acquisition (DIA, also known as SWATH) quantitative proteomics approach coupled with the advanced diaPASEF scanning mode to investigate the global proteomic alterations in human cells following GPR120 gene knockdown. A total of 6 human-derived samples were analyzed, comprising the si-GPR120 treatment group and the si-NC control group. Protein extraction, reduction, alkylation, and tryptic digestion were performed using the iST Sample Preparation Kit (PreOmics), followed by peptide desalting and cleanup. The digested peptides were separated on an UltiMate 3000 LC system and analyzed on a timsTOF HT mass spectrometer (Bruker) operating in diaPASEF mode. The raw DIA data were processed using Spectronaut 19 against the UniProt Homo sapiens proteome database (version 2025, containing 220,644 entries). The false discovery rate (FDR) was strictly controlled at < 1% at the precursor, peptide, and protein levels. The analysis identified a total of 8,984 protein groups and 141,824 peptides across all samples. Differential expression analysis (cutoff criteria: Fold Change > 2 and P-value < 0.05) between the si_gpr120 and si_nc comparison pair revealed 912 differentially expressed proteins (DEPs), of which 470 were significantly upregulated and 442 were downregulated. Comprehensive bioinformatics analyses were subsequently performed on the DEPs, including Gene Ontology (GO) functional enrichment (covering Biological Process, Cellular Component, and Molecular Function), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, STRING protein-protein interaction (PPI) network construction, eggNOG orthologous functional classification, and subcellular localization prediction. These analyses provide a systematic insight into the potential biological functions, key signaling cascades, and molecular interaction networks modulated by GPR120.
Zhenhua Ren 
