PXD045146

PXD045146 is an original dataset announced via ProteomeXchange.

Title	In-depth Endogenous Phosphopeptidomics of Serum with Zirconium (IV)-Grafted Mesoporous Silica Enrichment
Description	In this study, we developed an approach using Zirconium (IV)-grafted mesoporous beads to enrich phosphopeptides followed by analysis with a high resolution nanoRPLC-MS/MS system. The new method was first tested with tryptic digests of standard phosphoproteins and HeLa cell lysates, with excellent enrichment performance achieved. The method was further used for endogenous phosphopeptidomic analysis of serum samples from pancreatic ductal adenocarcinoma (PDAC) patients and controls. In total, 329 endogenous phosphopeptides (containing 113 high confidence sites) were identified across samples, by far the largest endogenous phosphorylation dataset catalogued to date. In addition, the method was readily applied for phosphoproteomics of the same set of samples, with 172 phosphopeptides identified and significant changes in dozens of phosphopeptides observed. Taken together, this method serves as a benchmark for analyzing serum phosphorylation events. Given the simplicity and robustness of the proposed method, we envision that it can be readily used for comprehensive phosphorylation studies (i.e., simultaneous endogenous phosphopeptidomics and phosphoproteomics) of serum and other biofluid samples.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:45:21.775.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ci Wu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-09-06 02:03:20	ID requested
1	2024-06-15 23:21:10	announced
⏵ 2	2024-10-22 06:45:23	announced	2024-10-22: Updated project metadata.

10.1021/acs.analchem.3c02150;

submitter keyword: phosphoproteome, serum,human, LC-MS/MS

Ci Wu
contact affiliation	Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University
contact email	wuci1111@126.com
lab head
Ci Wu
contact affiliation	Research specialist
contact email	wuci1111@126.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/2024/06/PXD045146

PRIDE project URI

• PRIDE
  1. PXD045146
     1. Label: PRIDE project
     2. Name: In-depth Endogenous Phosphopeptidomics of Serum with Zirconium (IV)-Grafted Mesoporous Silica Enrichment