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] |
Keyword List
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 |
Repository Record List
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