PXD000938-1

PXD000938 is an original dataset announced via ProteomeXchange.

Title	TARA Oceans Viral Proteins
Description	A 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.
HostingRepository	PRIDE
AnnounceDate	2016-02-25
AnnouncementXML	Submission_2016-02-25_04:56:32.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Robert Jones
SpeciesList	scientific name: environmental samples; NCBI TaxID: 135062;
ModificationList	carbamoylated residue
Instrument	LTQ Orbitrap; LTQ Orbitrap Velos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2014-04-29 01:03:56	ID requested
⏵ 1	2016-02-25 04:56:34	announced

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]

curator keyword: Metaproteomics, Biological

submitter keyword: Viral, Virus, Proteins, Proteomics, TARA, Viral Proteomics

Matthew B. Sullivan
contact affiliation	University of Arizona, Department of Ecology and Evolutionary Biology, Tucson Marine Phage Lab.
contact email	mbsulli@email.arizona.edu
lab head
Robert Jones
contact affiliation	University of Arizona
contact email	rmj3@email.arizona.edu
dataset submitter

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/2016/02/PXD000938

PRIDE project URI

• PRIDE
  1. PXD000938
     1. Label: PRIDE project
     2. Name: TARA Oceans Viral Proteins