Proteomics

Dataset Information

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Pithovirus particle proteome - Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology


ABSTRACT: 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.

INSTRUMENT(S): LTQ Orbitrap Velos, instrument model

ORGANISM(S): Unidentified

SUBMITTER: Yohann Couté  

PROVIDER: PXD000460 | Pride | 2014-02-12

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
PRIDE_Exp_Complete_Ac_31250.pride.mgf.gz Mgf
PRIDE_Exp_Complete_Ac_31250.pride.mztab.gz Mztab
PRIDE_Exp_Complete_Ac_31250.xml.gz Xml
Pithovirus.raw Raw
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Publications

Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology.

Legendre Matthieu M   Bartoli Julia J   Shmakova Lyubov L   Jeudy Sandra S   Labadie Karine K   Adrait Annie A   Lescot Magali M   Poirot Olivier O   Bertaux Lionel L   Bruley Christophe C   Couté Yohann Y   Rivkina Elizaveta E   Abergel Chantal C   Claverie Jean-Michel JM  

Proceedings of the National Academy of Sciences of the United States of America 20140303 11


The largest known DNA viruses infect Acanthamoeba and belong to two markedly different families. The Megaviridae exhibit pseudo-icosahedral virions up to 0.7 μm in diameter and adenine-thymine (AT)-rich genomes of up to 1.25 Mb encoding a thousand proteins. Like their Mimivirus prototype discovered 10 y ago, they entirely replicate within cytoplasmic virion factories. In contrast, the recently discovered Pandoraviruses exhibit larger amphora-shaped virions 1 μm in length and guanine-cytosine-ric  ...[more]

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