Dataset Information

Proteomics analysis of B. bigemina

ABSTRACT: Protein from B. bigemina PR cell lysates was analysed by 1D SDS PAGE and in solution digestion. Digested peptides were analysed by on-line nanoflow liquid chromatography using the nanoACQUITY-nLC system (Waters MS technologies, Manchester, UK) coupled to an LTQ-Orbitrap Velos (ThermoFisher Scientific, Bremen, Germany). Collected data were then analysed by Mascot (version 2.3.02, Matrix Science) and Progenesis LC–MS (version 4.1, Nonlinear Dynamics, UK).

OTHER RELATED OMICS DATASETS IN: PRJEB5046

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Babesia Sp. Babesia Bigemina

TISSUE(S): Blood Cell

SUBMITTER: Dong Xia

LAB HEAD: Dong Xia

PROVIDER: PXD000629 | Pride | 2014-06-16

REPOSITORIES: Pride

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Publications

The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction.

Jackson Andrew P AP Otto Thomas D TD Darby Alistair A Ramaprasad Abhinay A Xia Dong D Echaide Ignacio Eduardo IE Farber Marisa M Gahlot Sunayna S Gamble John J Gupta Dinesh D Gupta Yask Y Jackson Louise L Malandrin Laurence L Malas Tareq B TB Moussa Ehab E Nair Mridul M Reid Adam J AJ Sanders Mandy M Sharma Jyotsna J Tracey Alan A Quail Mike A MA Weir William W Wastling Jonathan M JM Hall Neil N Willadsen Peter P Lingelbach Klaus K Shiels Brian B Tait Andy A Berriman Matt M Allred David R DR Pain Arnab A

Nucleic acids research 20140505 11

Babesia spp. are tick-borne, intraerythrocytic hemoparasites that use antigenic variation to resist host immunity, through sequential modification of the parasite-derived variant erythrocyte surface antigen (VESA) expressed on the infected red blood cell surface. We identified the genomic processes driving antigenic diversity in genes encoding VESA (ves1) through comparative analysis within and between three Babesia species, (B. bigemina, B. divergens and B. bovis). Ves1 structure diverges rapid ...[more]

PMID: 24799432

Similar Datasets

Project description:Cerebella from wild-type and cGKI knockout mice, on 129/Sv background, were subjected to protein digestion using trypsin o/n and chemically labeled with dimethyl labeling. After labeling the samples were mixed and subjected to both strong cation exchange and phosphopeptide enrichment. The SCX fractions and the enriched phosphopeptides were then analyzed on an Orbitrap mass spectrometer. Data analysis: For each raw data file recorded by the mass spectrometer, peak lists were generated using Proteome Discoverer (version 1.3, Thermo Scientific, Bremen, Germany) using a standardized workflow. Peak lists, generated in Proteome Discoverer, were searched against a Swiss-Prot database (version 2.3.02, taxonomy Mus musculus, 32402 protein entries) supplemented with frequently observed contaminants, using Mascot (version 2.3.02 Matrix Science, London, UK). The database search was performed by using the following paramenters: a mass tolerance of 50 ppm for the precursor masses and +/-0.6 Da for CID/ETD fragment ions and +/-0.05 Da for HCD fragments. Enzyme speciﬁcity was set to Trypsin with 2 missed cleavages allowed. Carbarmidomethylation of cysteines was set as fixed modification, oxidation of methionine and dimethyl labeling (L, I, H) of lysine residues and N termini, and phosphorylation (S, T, Y) (for the phosphoproteome analysis) were used as variable modifications. Percolator was used to ﬁlter the PSMs for <1% false discovery-rate. Phosphorylation sites were localized by applying phosphoRS (pRS) (v2.0). Triplex dimethyl labeling was used as quantification method, with a mass precision for the 2 ppm for consecutive precursor mass scan. A retention time tolerance of 0.5 min was used to account effect of deuterium on retention time. To further filter for high quality data we used the following parameters: high confidence peptide spectrum matches, minimal Mascot score of 20, minimal peptide length of 6 and only unique rank 1 peptide. For the phosphopeptides analysis, the search rank 1 peptide was added to the previous filters. For the identification and quantitation of the proteins, only the unique peptides were considered.

			Action	DRS
	BB-1D1.dat	Other
	BB-1D1.raw	Raw
	BB-1D2.dat	Other
	BB-1D2.raw	Raw
	BB-1D3.dat	Other