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PXD044787

PXD044787 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleDilute to Enrich for Deep Proteomics: Yolk-Depleted Carrier for a Limited Population of Embryonic (Frog) Cells
DescriptionThis 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.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_06:40:45.016.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD044787
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterPeter Nemes
SpeciesList scientific name: Xenopus laevis (African clawed frog); NCBI TaxID: 8355;
ModificationListTMT6plex-126 reporter+balance reagent acylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-08-23 04:09:42ID requested
12024-05-21 15:15:04announced
22024-10-22 06:40:45announced2024-10-22: 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 affiliationUniveristy of Maryland, College Park
contact emailnemes@umd.edu
lab head
Peter Nemes
contact affiliationUniversity of Maryland, College Park
contact emailnemes@umd.edu
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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