The Encyclopedia of Proteome Dynamics: A big data ecosystem for (prote)omics

Nucleic Acids Research

Volumn 46, Issue D1, 2018, Pages D1202-D1209

  Brenes, Alejandro ^a   Afzal, Vackar ^a   Kent, Robert ^a   Lamond, Angus I ^a  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME;

ACCESS TO INFORMATION; ARTICLE; DATA ANALYSIS; DATA BASE; DATA SYNTHESIS; ENCYCLOPEDIA OF PROTEOME DYNAMICS; GENOMICS; INFORMATION PROCESSING; INFORMATION STORAGE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEOMICS; SOFTWARE; ANIMAL; COMPUTER INTERFACE; FACTUAL DATABASE; GENETICS; HUMAN; INTERNET; MASS SPECTROMETRY; METABOLISM; PROCEDURES;

ANIMALS; BIG DATA; DATA DISPLAY; DATABASES, FACTUAL; HUMANS; INTERNET; MASS SPECTROMETRY; PROTEOME; PROTEOMICS; USER-COMPUTER INTERFACE;

EID: 85040927657     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkx807     Document Type: Article

References (25)

1. Larance,M. and Lamond,A.I. (2015) Multidimensional proteomics for cell biology. Nat. Rev. Mol. Cell. Biol., 16, 269-280.
2. Larance,M., Ahmad,Y., Kirkwood,K.J., Ly,T. and Lamond,A.I. (2013) Global subcellular characterization of protein degradation using quantitative proteomics. Mol. Cell. Proteomics, 12, 638-650.
3. Vizcaino,J.A., Cote,R.G., Csordas,A., Dianes,J.A., Fabregat,A., Foster,J.M., Griss,J., Alpi,E., Birim,M., Contell,J. et al. (2013) The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res., 41, D1063-D1069.
4. Vizcaino,J.A., Deutsch,E.W., Wang,R., Csordas,A., Reisinger,F., Rios,D., Dianes,J.A., Sun,Z., Farrah,T., Bandeira,N. et al. (2014) ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat. Biotechnol., 32, 223-226.
5. Ly,T., Ahmad,Y., Shlien,A., Soroka,D.,Mills,A., Emanuele,M.J., Stratton,M.R. and Lamond,A.I. (2014) A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells. Elife, 3, e01630.
6. Ly,T., Endo,A. and Lamond,A.I. (2015) Proteomic analysis of the response to cell cycle arrests in human myeloid leukemia cells. Elife, 4, doi:10.7554/eLife.04534.
7. Kirkwood,K.J., Ahmad,Y., Larance,M. and Lamond,A.I. (2013) Characterization of native protein complexes and protein isoform variation using size-fractionation-based quantitative proteomics. Mol. Cell. Proteomics, 12, 3851-3873.
8. Larance,M., Kirkwood,K.J., Tinti,M., Brenes Murillo,A., Ferguson,M.A. and Lamond,A.I. (2016) Global membrane protein interactome analysis using in vivo crosslinking and mass spectrometry-based protein correlation profiling. Mol. Cell. Proteomics, 15, 2476-2490.
9. Boisvert,F.M., Ahmad,Y., Gierlinski,M., Charriere,F., Lamont,D., Scott,M., Barton,G. and Lamond,A.I. (2012) A quantitative spatial proteomics analysis of proteome turnover in human cells. Mol. Cell. Proteomics, 11, doi:10.1074/mcp.M111.011429.
10. Hukelmann,J.L., Anderson,K.E., Sinclair,L.V., Grzes,K.M., Murillo,A.B., Hawkins,P.T., Stephens,L.R., Lamond,A.I. and Cantrell,D.A. (2016) The cytotoxic T cell proteome and its shaping by the kinase mTOR. Nat. Immunol., 17, 104-112.
11. Larance,M., Pourkarimi,E., Wang,B., Brenes Murillo,A., Kent,R., Lamond,A.I. and Gartner,A. (2015) Global proteomics analysis of the response to starvation in C. elegans. Mol. Cell. Proteomics, 14, 1989-2001.
12. Narayan,V., Ly,T., Pourkarimi,E., Murillo,A.B., Gartner,A., Lamond,A.I. and Kenyon,C. (2016) Deep proteome analysis identifies age-related processes in C. elegans. Cell Syst., 3, 144-159.
13. Bensaddek,D., Narayan,V., Nicolas,A., Murillo,A.B., Gartner,A., Kenyon,C.J. and Lamond,A.I. (2016) Micro-proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level. Proteomics, 16, 381-392.
14. Offenburger,S.L., Bensaddek,D., Murillo,A.B., Lamond,A.I. and Gartner,A. (2017) Comparative genetic, proteomic and phosphoproteomic analysis of C. elegans embryos with a focus on ham-1/STOX and pig-1/MELK in dopaminergic neuron development. Sci. Rep., 7, 4314.
15. The UniProt Consortium (2017) UniProt: the universal protein knowledgebase. Nucleic Acids Res., 45, D158-D169.
16. Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S., Eppig,J.T. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
17. Ruepp,A., Brauner,B., Dunger-Kaltenbach,I., Frishman,G., Montrone,C., Stransky,M., Waegele,B., Schmidt,T., Doudieu,O.N., Stumpflen,V. et al. (2008) CORUM: the comprehensive resource of mammalian protein complexes. Nucleic Acids Res., 36, D646-D650.
18. Joshi-Tope,G., Gillespie,M., Vastrik,I., D'Eustachio,P., Schmidt,E., de Bono,B., Jassal,B., Gopinath,G.R., Wu,G.R., Matthews,L. et al. (2005) Reactome: a knowledgebase of biological pathways. Nucleic Acids Res., 33, D428-D432.
19. Berman,H.M.,Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
20. Szklarczyk,D., Franceschini,A., Wyder,S., Forslund,K., Heller,D., Huerta-Cepas,J., Simonovic,M., Roth,A., Santos,A., Tsafou,K.P. et al. (2015) STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res., 43, D447-D452.
21. Cox,J., Neuhauser,N., Michalski,A., Scheltema,R.A., Olsen,J.V. and Mann,M. (2011) Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res., 10, 1794-1805.
22. Nightingale,A., Antunes,R., Alpi,E., Bursteinas,B., Gonzales,L., Liu,W., Luo,J., Qi,G., Turner,E. and Martin,M. (2017) The Proteins API: accessing key integrated protein and genome information. Nucleic Acids Res., doi:10.1093/nar/gkx237.
23. Schaab,C., Geiger,T., Stoehr,G., Cox,J. and Mann,M. (2012) Analysis of high accuracy, quantitative proteomics data in the MaxQB database. Mol. Cell. Proteomics, 11, doi:10.1074/mcp.M111.014068.
24. Cox,J. and Mann,M. (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol., 26, 1367-1372.
25. Kilpinen,H., Goncalves,A., Leha,A., Afzal,V., Alasoo,K., Ashford,S., Bala,S., Bensaddek,D., Casale,F.P., Culley,O.J. et al. (2017) Common genetic variation drives molecular heterogeneity in human iPSCs. Nature, 546, 370-375.