PXD048742

PXD048742 is an original dataset announced via ProteomeXchange.

Title	Analysis of Differential Expression Proteins of in Liver injury Rats Reveal Hepatoprotective Effects of Gypenosides Using Label-free Global Proteome (Lael-free)
Description	All animals were randomly separated into three groups (n=5) after one week of acclimation: the control group (CON group), the liver injury group (MOD group), and the GPs treatment group (GP group). The rats in the MOD and GP groups received 40% (v/v) CCl4 (dissolved in soybean oil) orally administration twice a week for 13 weeks, whereas the CON rats received the same dose of soybean oil via the same manner. The rats in the GPs group have been given GPs at a dose of 200 mg/kg once daily for 8 weeks, while the rats in the CON and MOD groups have been given an equivalent amount of normal saline. The tryptic peptides were dissolved in 0.1% formic acid and 2% acetonitrile (solvent A) and directly put onto an Agilent 300Extend C18 column (250 mm4.6 mm, 5 m; Agilent, USA). The gradient consisted of an increase from 6% to 23% solvent B (0.1% formic acid in 98% acetonitrile) over 68 minutes, 23% to 32% in 14 minutes, 80% in 4 minutes, and 80% for the last 4 minutes, all at a constant flow rate of 500 nL/min using an EASY-nLC 1000 UPLC system. The peptides were analyzed using an NSI source, followed by tandem mass spectrometry (MS/MS) in a Q ExactiveTM Plus (Thermo) linked online to the UPLC. The electrospray voltage was set to 2.3 kV, and the FAIMS compensation voltage (CV) was -45V, -65V. The m/z scan range for the full scan was 400 to 1200, and intact peptides were detected at a resolution of 60,000. Peptides were then selected for MS/MS analysis with NCE set to 27, and fragments were detected at a resolution of 15,000. A data-depsendent acquisition approach in which a MS scan was followed by 25 MS/MS scans. The AGC was set to 5E4 ions/s, and the maximum IT was set to Auto. The raw data were retrieved using Proteome Discoverer (v2.4.1.15). The database was Rattus_norvegicus_10116_PR_20210721.fasta (29934 sequences). Retrieve parameters: enzyme was set as Trypsin (Full), Max missed cleavage set as 2. The minimum peptide length was set as 6. Variable modification was set as Oxidation (M), Acetyl (N-terminus), Met-loss (M), Met-loss+acetyl (M), and max variable modifications was set as 3. The precursor mass tolerance was set as 10 ppm, the product mass tolerance was set as 0.02 Da. The FDR for protein identification and PSM identification were set to 1%.
HostingRepository	iProX
AnnounceDate	2024-01-21
AnnouncementXML	Submission_2025-09-29_02:39:26.842.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Miao Wang
SpeciesList	scientific name: Rattus rattus; NCBI TaxID: 10117;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2024-01-22 00:17:27	ID requested
⏵ 1	2025-09-29 02:39:27	announced

Dataset with its publication pending

submitter keyword: Liver injury, Gypenosides, Proteomics, Label-free

Miao Wang
contact affiliation	Pharmaceutical University
contact email	wm18341401092@163.com
lab head
Miao Wang
contact affiliation	Shenyang Pharmaceutical University
contact email	wm18341401092@163.com
dataset submitter

iProX dataset URI