PXD076006

PXD076006 is an original dataset announced via ProteomeXchange.

Title	Quantitative analysis of mycelial protein in six samples
Description	Geotrichum 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.
HostingRepository	iProX
AnnounceDate	2026-03-22
AnnouncementXML	Submission_2026-03-23_01:25:59.690.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Funglan Zhou
SpeciesList	scientific name: Geotrichum candidum; NCBI TaxID: 1173061;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2026-03-23 01:23:27	ID requested
⏵ 1	2026-03-23 01:26:00	announced

Dataset with its publication pending

submitter keyword: Geotrichum candidum XG1, potato dextrose broth (PDB), data‑dependent acquisition

Kanjian Quan
contact affiliation	Southwest University
contact email	ganjianquan@swu.edu.cn
lab head
Funglan Zhou
contact affiliation	Southwest University
contact email	chowfunglan@163.com
dataset submitter

iProX dataset URI