PXD000213

PXD000213 is an original dataset announced via ProteomeXchange.

Title	Pandoravirus proteome
Description	Proteome analysis of a novel type of virus. 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-PGE 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 Pandoravirus 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, fixes) 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	2013-07-23
AnnouncementXML	Submission_2013-07-23_02:01:38.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000213
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Yohann Couté
SpeciesList	scientific name: unidentified; NCBI TaxID: 32644;
ModificationList	No applicable mass modifications
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2013-04-11 07:21:26	ID requested
1	2013-07-19 07:13:19	announced
1	2014-07-28 00:34:25	announced
2	2013-07-19 07:26:12	announced	missing
3	2013-07-19 07:28:51	announced	missing
⏵ 4	2013-07-23 02:01:38	announced	Add reference

Philippe N, Legendre M, Doutre G, Cout, é Y, Poirot O, Lescot M, Arslan D, Seltzer V, Bertaux L, Bruley C, Garin J, Claverie JM, Abergel C, Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes. Science, 341(6143):281-6(2013) [pubmed]

submitter keyword: Pandoravirus

proteins

nanoLC-MS/MS

Yohann Couté
contact affiliation	Laboratoire d'Etude de la Dynamique des Protéomes
contact email	yohann.coute@cea.fr

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• PRIDE
  1. 29261
     1. InstrumentRef: INSTRUMENT_1
     2. Label: Pandora proteome
     3. ModificationList: No applicable mass modifications,
     4. Name: Pandoravirus proteome analysis
     5. PublicationRef: PMID23869018