PXD043594

PXD043594 is an original dataset announced via ProteomeXchange.

Title	Proteomic profiling of IBD circulating exosomes
Description	Differential proteome profiling of IBD serum exosomes to find corresponding regulatory protein cargoes of serum exosomes in IBD progress. Exosomal proteins were extracted using SDT buffer lysis (4% SDS, 100mM Tris HCl, 1mM DTT, pH7.6), and the protein concentration was determined using the BCA protein quantification kit (Bio Rad, USA). The protein was digested with pancreatin and processed by ultrafiltration assisted sample preparation (FASP) method. The peptide segments obtained after treatment were desalinated using a C18 chromatographic column, concentrated by vacuum centrifugation, and then dissolved in 40 µL 0.1% formic acid. Identification and analysis were conducted using liquid chromatography tandem mass spectrometry (LC-MS/MS) technology. Each peptide sample was separated using a nanoliter flow rate high-performance liquid chromatography system, with mobile phase buffer A containing 0.1% formic acid aqueous solution and B containing 0.1% formic acid acetonitrile aqueous solution (84% acetonitrile). Using a 95% A-liquid equilibrium chromatographic column, the sample is loaded into a C18 chromatographic column using an automatic sampler, and separated by a C18-A2 analytical column at a flow rate of 300 nL/min. After chromatographic separation, the sample was subjected to mass spectrometry analysis using the timsTOF Pro mass spectrometer. The detection method is positive ions, the ion source voltage is set to 1.5kV, and TOF is used for detection and analysis in both mass spectrometry and tandem mass spectrometry. The scanning range of the mass spectrometry is set to 100-1700m/z. The data collection mode adopts the Parallel Accumulation Serial Fragmentation (PASEF) mode. After collection, the mother ion is collected in 10 PASEF modes, with a cycle window time of 1.17 seconds and a secondary mass spectrometry with a charge number in the range of 0-5, The dynamic exclusion time of tandem mass spectrometry scanning is set to 24 seconds to avoid repeated scanning of parent ions and generate original mass spectrometry detection data. The mass spectrometry raw data was identified and quantitatively analyzed using the LFQ (Label Free Quantification) algorithm using MaxQuant software (version 1.6.14).
HostingRepository	iProX
AnnounceDate	2023-07-07
AnnouncementXML	Submission_2023-08-14_00:26:22.472.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Bing Chen
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2023-07-06 20:44:49	ID requested
1	2023-07-06 20:44:58	announced
⏵ 2	2023-08-14 00:26:23	announced	2023-08-14: Update publication information.

Li Y, Xu M, Zhu Z, Xu F, Chen B, Transendothelial electrical resistance measurement by a microfluidic device for functional study of endothelial barriers in inflammatory bowel disease. Front Bioeng Biotechnol, 11():1236610(2023) [pubmed]

submitter keyword: Proteomic profiling, Inflammatory bowel disease, serum exosome

Bing Chen
contact affiliation	The First Affiliated Hospital of Zhengzhou University
contact email	chenbing_1121@163.com
lab head
Bing Chen
contact affiliation	The First Affiliated Hospital of Zhengzhou University
contact email	chenbing_1121@163.com
dataset submitter

iProX dataset URI