PXD000213 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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 |
Publication List
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] |
Keyword List
submitter keyword: Pandoravirus |
proteins |
nanoLC-MS/MS |
Contact List
Yohann Couté |
contact affiliation | Laboratoire d'Etude de la Dynamique des Protéomes |
contact email | yohann.coute@cea.fr |
Full Dataset Link List
Dataset FTP location
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Repository Record List
[ + ]
[ - ]
- PRIDE
- 29261
- InstrumentRef: INSTRUMENT_1
- Label: Pandora proteome
- ModificationList: No applicable mass modifications,
- Name: Pandoravirus proteome analysis
- PublicationRef: PMID23869018