PXD018509-1

PXD018509 is an original dataset announced via ProteomeXchange.

Title	The analysis of SNT differential proteins after intervention UC based on proteomics
Description	Orbitrap Fusion (Thermo Fisher Scientific) LC-MS/MS analyses were performed on an Easy-nLC 1000 liquid chromatography system (Thermo Fisher Scientific) coupled to an Orbitrap Fusion via a nano-electrospray ion source. Tryptic peptides were dissolved with a loading buffer (acetonitrile and 0.1% formic acid), and were eluted with a flow rate of 350 nL/min. Survey scans were acquired after an accumulation of 5×105 ions in the Orbitrap for m/z 300-1,400 using a resolution of 120,000 at m/z. The top speed data-dependent mode was selected for fragmentation in the cell at a normalized collision energy of 32%, and fragment ions were then transferred into the ion trap analyzer with the AGC target at 5×103 and maximum injection time at 35 ms. The dynamic exclusion of previously acquired precursor ions was enabled at 18 s. The Proteome Discoverer 1.4.1.14 was used for analysis of the protein spectrum. Oxidation (Methionine) and acetylation (Protein-N term) were chosen as variable modifications, cysteine carbamidomethylation was chosen as a fixed modification. Two missed cleavage sites for trypsin were allowed. The intensity-based absolute quantification (iBAQ)-based protein quantification were performed by an in-house software. The interaction of SNT-related differentially expressed proteins was investigated by STRING 11.0 (https://string-db.org). The differentially expressed protein interaction network (high reliability, interaction score > 0.4, PPI enrichment P-value < 1.0×10 -16) was selected for the analysis.
HostingRepository	PRIDE
AnnounceDate	2021-09-09
AnnouncementXML	Submission_2021-09-09_01:46:09.847.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	enhui Ji
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	acetylated residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2020-04-14 01:52:38	ID requested
⏵ 1	2021-09-09 01:46:10	announced
2	2024-10-22 05:28:30	announced	2024-10-22: Updated project metadata.

Ji E, Wang T, Xu J, Fan J, Zhang Y, Guan Y, Yang H, Wei J, Zhang G, Huang L, Systematic Investigation of the Efficacy of Sinitang Decoction Against Ulcerative Colitis. Front Pharmacol, 11():1337(2020) [pubmed]

submitter keyword: Proteomics, Differential protein, SNT, UC

Hongjun Yang
contact affiliation	Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences
contact email	hongjun0420@vip.sina.com
lab head
enhui Ji
contact affiliation	Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences
contact email	2477651964@qq.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/09/PXD018509

PRIDE project URI

• PRIDE
  1. PXD018509
     1. Label: PRIDE project
     2. Name: The analysis of SNT differential proteins after intervention UC based on proteomics