Research
The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation
1 Department of Pre-clinical Veterinary Science, Faculty of Veterinary Science, University of Liverpool, Liverpool L69 7ZJ, UK
2 Department of Cell Biology, The Scripps Research Institute, North Torrey Pines Road, La Jolla, CA 92037, USA
3 Division of Microbiology, Institute for Animal Health, Compton, Berkshire, RG20 7NN, UK
4 The Division of Cell and Molecular Biology, Imperial College London, London, SW7 2AZ, UK
5 Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
6 Veterinary Pathology, Faculty of Veterinary Science, University of Liverpool, Liverpool L69 7ZJ, UK
Genome Biology 2008, 9:R116 doi:10.1186/gb-2008-9-7-r116
Published: 21 July 2008Additional files
Additional data file 1:
Soluble proteins from 2.53 × 108 tachyzoites (516 μg protein) resolved by IEF over a narrow linear pH 3-10 range followed by molecular mass on a 12.5% (w/v) acrylamide gel under denaturing conditions. Protein spots are visualized using colloidal Coomassie. Individual spots are numbered and the corresponding mass spectrometric data are detailed in Additional data file 3.
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Additional data file 2:
Soluble proteins from 1 × 108 tachyzoites (200 μg protein) resolved by IEF over a narrow linear pH 4-7 range followed by molecular mass on a 12.5% (w/v) acrylamide gel under denaturing conditions. Protein spots are visualized using colloidal Coomassie. Individual spots are numbered and the corresponding mass spectrometric data are detailed in Additional data file 4.
Format: EPS Size: 215KB Download file
Additional data file 3:
The spot number, matching gene annotation and description, Mascot score, sequence coverage and number of matching peptides are given. Further information concerning peptide sequences is available at ToxoDB. For consistency, where the release4 annotation is not identified by the peptide evidence, TwinScan gene annotation is given in preference to other alternative gene annotations assuming the returning Mascot score is equivalent (and in Additional data files 4, 5, 7, 8 and 9).
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Additional data file 4:
The spot number, matching gene annotation and description, Mascot score, sequence coverage and number of matching peptides are given. Further information concerning peptide sequences is available at ToxoDB. For consistency, where the release4 annotation is not identified by the peptide evidence, TwinScan gene annotation is given in preference to other alternative gene annotations assuming the returning Mascot score is equivalent.
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Additional data file 5:
Listed in the columns (from left to right) are: the gel slice number, ranking of each protein hit returned from the Mascot search for that gel slice, corresponding gene annotations and descriptions, Mascot scores, number of matching peptides to each protein and sequence coverage. Further information concerning peptide sequences is available at ToxoDB. For consistency, where the release4 annotation is not identified by the peptide evidence, TwinScan gene annotation is given in preference to other alternative gene annotations assuming the returning Mascot score is equivalent.
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Additional data file 6:
SDS-soluble proteins from 9.85 × 107 tachyzoites previously fractionated into Tris-soluble (120 μg) and Tris-insoluble (130 μg) fractions were resolved on a 12% (w/v) acrylamide gel under denaturing conditions as follows: protein standards (lane 1), Tris-insoluble protein (lane 2) and Tris-soluble protein (lane 4). Proteins were visualized using colloidal Coomassie. The masses of the protein standards and the position of every gel slice are shown.
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Additional data file 7:
Listed in the columns (from left to right) are: the gel slice number, ranking of each protein hit returned from the Mascot search for that gel slice, corresponding gene annotations and descriptions, Mascot scores, number of matching peptides to each protein and sequence coverage. Further information concerning peptide sequences is available at ToxoDB. For consistency, where the release4 annotation is not identified by the peptide evidence, TwinScan gene annotation is given in preference to other alternative gene annotations assuming the returning Mascot score is equivalent.
Format: XLS Size: 135KB Download file
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Additional data file 8:
Listed in the columns (from left to right) are: the gene annotations and descriptions of each protein, the highest individual Mascot score, sequence coverage and number of matching peptides returned for that protein from all the gel slices in which it appeared, and the gel slice number that this refers to. Individual peptide amino acid sequence, MS scores and a measure of the total sequence coverage obtained is available at ToxoDB. For consistency, where the release4 annotation is not identified by the peptide evidence, TwinScan gene annotation is given in preference to other alternative gene annotations assuming the returning Mascot score is equivalent.
Format: XLS Size: 181KB Download file
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Additional data file 9:
Listed in the columns (from left to right) are: the gene annotations and descriptions of each protein, the highest individual Mascot score, sequence coverage and number of matching peptides returned for that protein from all the gel slices in which it appeared, and the gel slice number that this refers to. Individual peptide amino acid sequence, MS scores and a measure of the total sequence coverage obtained is available at ToxoDB. For consistency, where the release4 annotation is not identified by the peptide evidence, TwinScan gene annotation is given in preference to other alternative gene annotations assuming the returning Mascot score is equivalent.
Format: XLS Size: 90KB Download file
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Additional data file 10:
The unprocessed results from MudPIT analysis lists: gene annotations and descriptions for each protein; alternative gene annotation for that region of the scaffold; total Xcorr scores for each protein hit; individual Xcorr scores theoretical mass and pI values and sequences for each individual matching peptide.
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Additional data file 11:
The unprocessed results from MudPIT analysis lists: gene annotations and descriptions for each protein; alternative gene annotation for that region of the scaffold; total Xcorr scores for each protein hit; individual Xcorr scores theoretical mass and pI values and sequences for each individual matching peptide.
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Additional data file 12:
List of protein identifiers according to subcellular localization category. Number of non-redundant proteins is shown in brackets.
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Additional data file 13:
List of protein identifiers according to functional category. Number of non-redundant proteins is shown in brackets.
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Additional data file 14:
The amino acid sequences of alternative genes and ORFs were submitted to BlastP and results returning e-values < e-30 were considered. Homology to apicomplexan proteins was prioritized when deciding the protein description to be used to assist the assignment of functional category. Sequences returning no significant BlastP result or with a description 'hypothetical protein' were searched against Amigo Blast [54] to determine the potential GO classification. The same e-value cut-off was applied. The above information was then used in conjunction with InterPro and independent literature searches to assign a MIPS category within the FunCatDB functional catalogue. Note: protein fate includes protein folding, modification and destination.
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