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PXD000938 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleTARA Oceans Viral Proteins
DescriptionA grand challenge in biology is the lack of annotation for much of global sequence space. In particular, while microbes and their viruses are critical to Earth System functioning, surveys of their communities in nature routinely return genes of unknown function, particularly for viruses. This hampers understanding and predictive capability, and reflects a number of database limitations. Here we apply high-resolution environmental metaproteomics to 4 purified viral concentrates from the Tara Oceans Expedition to identify in situ proteins extracted from uncultivated viral particles. Using matched metagenomic databases, we identified 1875 proteins belonging to 549 non-redundant protein clusters that are predominantly of unknown function. These data help identify function for structure-associated proteins in known abundant tailed viruses (e.g., pelagiphages and cyanophages) and validate newly-identified uncultured viral sequences linked to abundant novel hosts. One protein cluster alone comprised 22% of the identified structure-associated proteins, with ~46% of the observed spectra. Structural modeling of this highly abundant viral protein cluster indicates its likely role as a novel, previously unknown capsid. Together these analyses provide much-needed, culture-independent structure-associated protein annotations critical for identifying viral signals across diverse datasets to better elucidate viral roles in nature.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterRobert Jones
SpeciesList scientific name: environmental samples; NCBI TaxID: 135062;
ModificationListcarbamoylated residue
InstrumentLTQ Orbitrap; LTQ Orbitrap Velos; Q Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02014-04-29 01:03:56ID requested
12016-02-25 04:56:34announced
Publication List
Brum JR, Ignacio-Espinoza JC, Kim EH, Trubl G, Jones RM, Roux S, VerBerkmoes NC, Rich VI, Sullivan MB, Illuminating structural proteins in viral "dark matter" with metaproteomics. Proc Natl Acad Sci U S A, 113(9):2436-41(2016) [pubmed]
Keyword List
curator keyword: Metaproteomics, Biological
submitter keyword: Viral, Virus, Proteins, Proteomics, TARA, Viral Proteomics
Contact List
Matthew B. Sullivan
contact affiliationUniversity of Arizona, Department of Ecology and Evolutionary Biology, Tucson Marine Phage Lab.
contact emailmbsulli@email.arizona.edu
lab head
Robert Jones
contact affiliationUniversity of Arizona
contact emailrmj3@email.arizona.edu
dataset submitter
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