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PXD000926

PXD000926 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleDeep Proteomics of the Xenopus laevis Egg using an mRNA-derived Reference Database
DescriptionMass spectrometry based proteomics enables the global identification and quantification of proteins and their post-translational modifications in complex biological samples. Proteomic analysis requires a complete and accurate reference set of proteins, and is therefore largely restricted to model organisms with sequenced genomes. Here, we demonstrate the feasibility of deep genome-free proteomics using a reference proteome derived from heterogeneous mRNA data. We identify more than 11k proteins with 99% confidence from the unfertilized, X. laevis egg and estimate protein abundance with approximately two-fold precision. Our reference database outperforms the provisional gene models based on genomic DNA-sequencing and references generated by other methods. Surprisingly, we find that many proteins in the egg lack mRNA support and many of these proteins are found in blood or liver, suggesting that they are taken up from the blood plasma, together with yolk, during oocyte growth and maturation, potentially contributing to early embryogenesis. To facilitate proteomics in non-model organisms, we make our platform available as an online resource which converts heterogeneous mRNA data into a protein reference set. Thus, we demonstrate the feasibility and power of genome-free proteomics while shedding new light on embryogenesis in vertebrates.
HostingRepositoryPRIDE
AnnounceDate2014-10-23
AnnouncementXMLSubmission_2014-10-23_03:38:21.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterMartin Wuehr
SpeciesList scientific name: Xenopus laevis (African clawed frog); NCBI TaxID: 8355;
ModificationListmonohydroxylated residue
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02014-04-24 02:07:33ID requested
12014-05-30 06:53:09announced
22014-07-24 05:17:14announcedUpdated project metadata.
32014-08-01 03:20:24announcedUpdated project metadata.
42014-10-23 03:38:22announcedUpdated project metadata.
Publication List
W, ΓΌ, hr M, Freeman RM, Presler M, Horb ME, Peshkin L, Gygi S, Kirschner MW, Deep proteomics of the Xenopus laevis egg using an mRNA-derived reference database. Curr Biol, 24(13):1467-1475(2014) [pubmed]
Keyword List
curator keyword: Biological
submitter keyword: Xenopus laevis, genome-free, egg, metaphase, meiosis, development
Contact List
Steven Gygi
contact affiliationHarvard Medical School
contact emailsteven_gygi@hms.harvard.edu
lab head
Martin Wuehr
contact affiliationHarvard Medical School
contact emailmartin.wuehr@gmx.de
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
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