PXD027535

PXD027535 is an original dataset announced via ProteomeXchange.

Title	Data-Independent Acquisition Mass Spectrometry Identification of Serum-derived Extracellular Vesicle Proteomics for Gastric Adenocarcinoma
Description	Timely diagnosis of gastric adenocarcinoma (GAC) can effectively prevent the deterioration of the disease and significantly improve the survival rate of patients. Currently, tumor markers used in clinical practice cannot meet the needs of patients, and it is urgent to develop biomarkers with high sensitivity and specificity to guide clinical diagnosis. In this study, serum samples from 33 patients with GAC and 19 healthy persons were collected. EVs were extracted by ultracentrifugation and EV protein expression profiles were obtained by DIA quantitative mass spectrometry. Multi-group differential protein expression analysis showed that 23 intersecting proteins had the same expression trend, among which 15 EV proteins were chosen as candidate biomarkers for GAC diagnosis. Afterward, a subset of 2 to 6 proteins was randomly selected as features for logistic regression modeling. To verify the diagnostic performance of these models, serums from a new cohort of 12 patients with gastric cancer and 18 healthy controls were collected, and the EV protein were quantified using the same method. We finally found a panel consisting of six proteins that performed the best as classifier. We also tried to discover biomarkers for diagnosis of advanced stage in GAC, and the results showed a three-protein panel had the best classification performance. In conclusion, we identified new protein biomarker panels from serum EVs for early diagnosis of gastric cancer that worth further validation.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:40:49.470.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yunyun Fu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-07-25 14:33:47	ID requested
1	2023-03-11 02:36:38	announced
⏵ 2	2023-11-14 08:40:51	announced	2023-11-14: Updated project metadata.

Gu L, Chen J, Yang Y, Zhang Y, Tian Y, Jiang J, Zhou D, Liao L, Data-independent acquisition mass spectrometry identification of extracellular vesicle biomarkers for gastric adenocarcinoma. Front Oncol, 12():1051450(2022) [pubmed]

submitter keyword: proteomics, extracellular vesicles, serum, gastric adenocarcinoma

Lujian Liao
contact affiliation	East China Normal University
contact email	ljliao@bio.ecnu.edu.cn
lab head
Yunyun Fu
contact affiliation	East China Normal University
contact email	fuyun1999@163.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/2023/03/PXD027535

PRIDE project URI

• PRIDE
  1. PXD027535
     1. Label: PRIDE project
     2. Name: Data-Independent Acquisition Mass Spectrometry Identification of Serum-derived Extracellular Vesicle Proteomics for Gastric Adenocarcinoma