PXD044787

PXD044787 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Dilute to Enrich for Deep Proteomics: Yolk-Depleted Carrier for a Limited Population of Embryonic (Frog) Cells
Description	This project developed a proteomic methodology that deepens the detectable and quantifiable proteome from limited proteomes where abundant proteins pose interference. As proof-of-principle, this study used Xenopus laevis, where ~90% of the proteome is dominated by abundant yolk proteins in the early developing embryo. We pooled Xenopus embryos and depleted the proteome to ~30% yolk protein content to prepare a carrier proteome. This yolk-depleted carrier proteome digest was spiked into isobarically tagged proteome digests that were prepared from limited tissues and cells isolated by fluorescence-activated cell sorting (FACS). The resulting samples were analyzed using liquid chromatography (LC) high resolution mass spectrometry (HRMS). We demonstrated that the yolk depleted carrier dilutes abundant yolk peptides and boosts the overall depth of proteome coverage, including many biologically important non-yolk proteins present in low abundance.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:40:45.016.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD044787
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Peter Nemes
SpeciesList	scientific name: Xenopus laevis (African clawed frog); NCBI TaxID: 8355;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-23 04:09:42	ID requested
1	2024-05-21 15:15:04	announced
⏵ 2	2024-10-22 06:40:45	announced	2024-10-22: Updated project metadata.

Publication List

10.6019/PXD044787;
10.1021/acs.jproteome.3c00541;
Pade LR, Lombard-Banek C, Li J, Nemes P, Dilute to Enrich for Deeper Proteomics: A Yolk-Depleted Carrier for Limited Populations of Embryonic (Frog) Cells. J Proteome Res, 23(2):692-703(2024) [pubmed]

10.6019/PXD044787;

10.1021/acs.jproteome.3c00541;

Pade LR, Lombard-Banek C, Li J, Nemes P, Dilute to Enrich for Deeper Proteomics: A Yolk-Depleted Carrier for Limited Populations of Embryonic (Frog) Cells. J Proteome Res, 23(2):692-703(2024) [pubmed]

Keyword List

submitter keyword: liquid chromatography, proteomics, Xenopus,Ultrasensitive, mass spectrometry., yolk

submitter keyword: liquid chromatography, proteomics, Xenopus,Ultrasensitive, mass spectrometry., yolk

Contact List

Peter Nemes
contact affiliation	Univeristy of Maryland, College Park
contact email	nemes@umd.edu
lab head
Peter Nemes
contact affiliation	University of Maryland, College Park
contact email	nemes@umd.edu
dataset submitter

Full Dataset Link List

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/2024/05/PXD044787
PRIDE project URI

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/2024/05/PXD044787

PRIDE project URI

Repository Record List

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