PXD075529

PXD075529 is an original dataset announced via ProteomeXchange.

Title	Salt adaptation mechanism of Vibrio natriegens strain VCOD-2 revealed by TMT-based quantitative proteomics
Description	This study investigates the molecular mechanism of high-salinity adaptation in Vibrio natriegens strain VCOD-2 (ATCC 14048) through Tandem Mass Tag (TMT)-based quantitative proteomics, analyzing protein expression profile changes under optimal salinity (3% NaCl) and high-salinity stress (8% NaCl) conditions. Experimental Design: V. natriegens strain VCOD-2 was cultured under optimal salinity (3% NaCl) and high-salinity stress (8% NaCl) conditions to logarithmic growth phase. Each salinity group had three biological replicates, totaling six samples (L3_1, L3_2, L3_3 for 3% NaCl group; H8_1, H8_2, H8_3 for 8% NaCl group). Experimental Workflow: Total proteins were extracted from harvested cells, quantified by BCA method, and quality-checked by SDS-PAGE. Proteins were reduced with DTT and alkylated with IAA, then digested with trypsin (protein:enzyme = 50:1) at 37℃ for 12-16 hours. Peptides were labeled using TMTpro 16plex kit (3% NaCl group: 126, 127N, 127C; 8% NaCl group: 129N, 129C, 130N). Labeled samples were mixed equally and fractionated by reverse-phase chromatography using Agilent 1260 Infinity II HPLC under high pH conditions, collecting 60 fractions. Mass Spectrometry Analysis: Samples were analyzed by nano-liquid chromatography-tandem mass spectrometry (nLC-MS/MS) using Thermo Scientific Easy nLC / Ultimate 3000 LC system coupled with Q Exactive HF-X mass spectrometer. Separation was performed on C18 column (1.9 μm, 150 μm×120 mm) with LC gradient from 94%-6% A (0.1% FA/H2O) to 60%-40% B (0.08% FA/80% ACN/H2O), flow rate 600 nL/min, analysis time 88 minutes. MS parameters: positive ion mode, MS1 resolution 120,000 (350-1500 m/z), MS2 resolution 60,000, HCD collision energy 32 eV. Data Analysis: Database search was performed using Proteome Discoverer 2.5 software with V. natriegens ATCC 14048 genomic database (GCF_001456255.1_ASM145625v1_protein.faa and 2811995373.genes.faa) as reference. Search parameters: enzyme trypsin, max missed cleavages 2, fixed modifications Carbamidomethyl (C), TMTpro (N-term), TMTpro (K), variable modifications Oxidation (M), Acetyl (Protein N-term), peptide mass tolerance ±10 ppm, fragment mass tolerance 0.02 Da, peptide identification FDR≤0.01. Results Summary: A total of 3077 protein groups and 31,646 peptides were identified. Differentially expressed proteins (DEPs) were screened with fold change ≥1.5 or ≤0.667 and q-value<0.05 using 3% NaCl as control and 8% NaCl as experimental group. In H8 vs L3 comparison group, 979 DEPs were identified, including 370 up-regulated and 609 down-regulated proteins. Differential proteins were further analyzed by COG, GO, and KEGG functional annotation and pathway enrichment analysis. PCA analysis and clustering heatmap were also completed.
HostingRepository	iProX
AnnounceDate	2026-03-11
AnnouncementXML	Submission_2026-03-11_18:28:11.112.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Xinyi Tao
SpeciesList	scientific name: Vibrio natriegens; NCBI TaxID: 691;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2026-03-11 18:27:04	ID requested
⏵ 1	2026-03-11 18:28:11	announced

Dataset with its publication pending

submitter keyword: Vibrio natriegens, salt stress, proteomics, TMT labeling, high-salinity adaptation, differentially expressed proteins, osmotic regulation

Baisuo Zhao
contact affiliation	Chinese Academy of Agricultural Sciences
contact email	bszhao@163.com
lab head
Xinyi Tao
contact affiliation	Chinese Academy of Agricultural Sciences
contact email	taoxinyi121dx@163.com
dataset submitter

iProX dataset URI