iProXProteomicsKanjian QuanGeotrichum Candidumhttp://www.iprox.org/page/project.html?id=IPX0016325000ganjianquan@swu.edu.cnSouthwest UniversityiProXfalseQuantitative analysis of mycelial protein in six samplesGeotrichum candidum XG1 was cultivated in potato dextrose broth (PDB) with or without 5 μg/mL patulin at 30 °C and 120 rpm for 48 h. Cells were harvested by centrifugation at 7,000 rpm for 5 min at 4 °C, washed with sterile water, flash‑frozen in liquid nitrogen, and stored at −80 °C. Total protein was extracted from 100 mg cell pellets using pre‑chilled lysis buffer, followed by mechanical lysis at 30 Hz for 1 min and ice‑bath incubation for 30 min with intermittent vortexing. After centrifugation at 8,000 rpm for 30 min at 4 °C, the supernatant was collected. Protein samples (10 μg) were denatured at 95 °C for 10 min and digested with trypsin at 37 °C for 2 h. Peptides were desalted, vacuum‑dried, and reconstituted for liquid chromatography‑tandem mass spectrometry (LC‑MS/MS) analysis. A combination of data‑dependent acquisition (DDA) and data‑independent acquisition (DIA) was employed on an UltiMate 3000 LC system coupled with a timsTOF Pro2 mass spectrometer. DDA was performed in PASEF mode to construct a high‑quality spectral library, while DIA in diaPASEF mode was used for quantitative proteomic profiling. Raw data were processed using Spectronaut 18 with a 1% false discovery rate (FDR) at both peptide and protein levels. Differentially expressed proteins (DEPs) were defined as those with fold change >1.2 or <0.83 and p < 0.05. Bioinformatic analyses including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment were conducted to annotate the functions of DEPs.Sun Mar 22 00:00:00 GMT 2026PXD0760061173061