PXD000460-2

PXD000460 is an original dataset announced via ProteomeXchange.

Title	Pithovirus particle proteome
Description	Proteomic analysis of purified Pithovirus particles. The virus was grown in A. castellanii amobea before being purified. Viral particules were enriched after centrifugation and proteins solubilised by SDS before being stacked in the top of a SDS-PAGE gel. After in-gel digestion, resulting peptides were injected for a 120min nanoLC-MS/MS analysis using an Ultimate U3000 system and a LTQ-Orbitrap Velos pro hybrid mass spectrometer (Top 20).Data processing and bioinformatics: Data were processed automatically using Mascot Daemon software (version 2.3.2, Matrix Science). Concomitant searches against Pithovirus and A. castellanii protein sequence databanks as well as classical contaminants database and the corresponding reversed databases were performed using Mascot (version 2.4). ESI-TRAP was chosen as the instrument, trypsin/P as the enzyme and 2 missed cleavage allowed. Precursor and fragment mass error tolerances were set respectively at 10 ppm and 0.6 Da. Peptide modifications allowed during the search were: carbamidomethyl (C, fixed) acetyl (N-ter, variable), oxidation (M, variable) and deamidation (NQ, variable). The IRMa software (Dupierris et al., Bioinformatics, 2009, 25:1980-1, version 1.30.4) was used to filter the results: selection of rank 1 peptides, peptide identification FDR < 1% (as calculated by employing the reverse database strategy), and minimum of 1 specific peptide per identified protein group.
HostingRepository	PRIDE
AnnounceDate	2014-02-13
AnnouncementXML	Submission_2014-03-17_03:23:33.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000460
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Yohann Coute
SpeciesList	scientific name: unidentified; NCBI TaxID: 32644;
ModificationList	No PTMs are included in the dataset
Instrument	instrument model: LTQ-Orbitrap Velos pro; LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2013-09-12 02:24:20	ID requested
1	2014-02-13 07:47:55	announced
⏵ 2	2014-03-17 03:23:35	announced	Updated publication reference for PubMed record(s): 24591590.
3	2014-07-28 00:47:55	announced	Updated project metadata.

Legendre M, Bartoli J, Shmakova L, Jeudy S, Labadie K, Adrait A, Lescot M, Poirot O, Bertaux L, Bruley C, Cout, é Y, Rivkina E, Abergel C, Claverie JM, Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. Proc Natl Acad Sci U S A, 111(11):4274-9(2014) [pubmed]

submitter keyword: Pithovirus

proteins

nanoLC-MS/MS

Yohann Coute
contact affiliation	Laboratoire d'Etude de la Dynamique des Proteomes
contact email	yohann.coute@cea.fr
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/2014/02/PXD000460

PRIDE project URI

• PRIDE
  1. PXD000460
     1. Label: PRIDE project
     2. Name: Pithovirus particle proteome