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Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research.

Vizcaíno JA, Foster JM, Martens L - J Proteomics (2010)

Bottom Line: Additionally, the data contents from model organisms will be enumerated for each resource.There are other valuable smaller and/or more specialized repositories but they will not be covered in this review.Finally, the concept behind the ProteomeXchange consortium, a collaborative effort among the main resources in the field, will be introduced.

View Article: PubMed Central - PubMed

Affiliation: EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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Model organism representation by number of data depositions in PRIDE. * The asterisk represents 8 species: X. laevis, U. maydis, O. sativa, N. tabacum, N. crassa, M. mulatta, E. huxlei and A. gossypii.
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f0010: Model organism representation by number of data depositions in PRIDE. * The asterisk represents 8 species: X. laevis, U. maydis, O. sativa, N. tabacum, N. crassa, M. mulatta, E. huxlei and A. gossypii.

Mentions: The peptide level shows similar statistics, with H. sapiens having more than twice the peptide identifications assigned than the next nearest model organism D. melanogaster (Fig. 1B). It is interesting to note that when kingdoms are compared, there is large bias towards animals, with plants coming a distant second in both peptide and protein identifications. Data about the number of data depositions (groups of experiments submitted at different time points, Fig. 2) show that, as expected, H. sapiens comes with the largest number of distinct data depositions. Animal model organisms such as zebra fish, mouse and rat are all well represented (26, 24 and 15 data depositions respectively). Figures for plants (Arabidopsis and maize) are a bit lower (14 and 11 data depositions, respectively), and the numbers of distinct data submissions for some key model organisms such as Caenorhabditiselegans and D. melanogaster remain only sporadic.


Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research.

Vizcaíno JA, Foster JM, Martens L - J Proteomics (2010)

Model organism representation by number of data depositions in PRIDE. * The asterisk represents 8 species: X. laevis, U. maydis, O. sativa, N. tabacum, N. crassa, M. mulatta, E. huxlei and A. gossypii.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2958306&req=5

f0010: Model organism representation by number of data depositions in PRIDE. * The asterisk represents 8 species: X. laevis, U. maydis, O. sativa, N. tabacum, N. crassa, M. mulatta, E. huxlei and A. gossypii.
Mentions: The peptide level shows similar statistics, with H. sapiens having more than twice the peptide identifications assigned than the next nearest model organism D. melanogaster (Fig. 1B). It is interesting to note that when kingdoms are compared, there is large bias towards animals, with plants coming a distant second in both peptide and protein identifications. Data about the number of data depositions (groups of experiments submitted at different time points, Fig. 2) show that, as expected, H. sapiens comes with the largest number of distinct data depositions. Animal model organisms such as zebra fish, mouse and rat are all well represented (26, 24 and 15 data depositions respectively). Figures for plants (Arabidopsis and maize) are a bit lower (14 and 11 data depositions, respectively), and the numbers of distinct data submissions for some key model organisms such as Caenorhabditiselegans and D. melanogaster remain only sporadic.

Bottom Line: Additionally, the data contents from model organisms will be enumerated for each resource.There are other valuable smaller and/or more specialized repositories but they will not be covered in this review.Finally, the concept behind the ProteomeXchange consortium, a collaborative effort among the main resources in the field, will be introduced.

View Article: PubMed Central - PubMed

Affiliation: EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

Show MeSH