2016 update of the PRIDE database and its related tools

Nucleic Acids Research - Tập 44 Số D1 - Trang D447-D456 - 2016
Juan Antonio Vizcaíno1, Attila Csordás1, Noemi del-Toro1, José A. Dianes1, Johannes Griss2,1, Ilias Lavidas1, Gerhard Mayer1,3, Yasset Pérez‐Riverol1, Florian Reisinger1, Tobias Ternent1, Qing-Wei Xu4,1, Rui Wang1, Henning Hermjakob1,5
1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
2Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Austria
3Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany
4Department of Computer Science and Technology, Hubei University of Education, Wuhan, China
5National Center for Protein Sciences, Beijing, China

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Tài liệu tham khảo

10.1002/pmic.200401303

10.1093/nar/gkj138

10.1093/nar/gkm1021

10.1093/nar/gkp964

10.1093/nar/gks1262

10.1038/nbt.2839

10.1038/embor.2008.56

10.1002/pmic.201100515

10.1002/prca.201400164

10.1021/pr049882h

10.1038/nature13319

10.1038/nature13302

Schaab C. Geiger T. Stoehr G. Cox J. Mann M. Analysis of high accuracy, quantitative proteomics data in the MaxQB database. Mol. Cell. Proteomics 2012;11. M111 014068.

10.1002/pmic.201400441

10.1093/nar/gku1175

10.1002/pmic.201400302

10.1093/nar/gku989

10.1093/nar/gku1178

10.1038/nbt0709-598

10.1074/mcp.O112.021543

10.1038/nbt.2112

Jones A.R. Eisenacher M. Mayer G. Kohlbacher O. Siepen J. Hubbard S.J. Selley J.N. Searle B.C. Shofstahl J. Seymour S.L. . The mzIdentML data standard for mass spectrometry-based proteomics results. Mol. Cell. Proteomics 2012;11. M111 014381.

10.1007/s00216-014-8357-8

Csordas A. Ovelleiro D. Wang R. Foster J.M. Rios D. Vizcaino J.A. Hermjakob H. PRIDE: quality control in a proteomics data repository. Database (Oxford) 2012;2012. bas004.

10.1002/pmic.201100577

10.1002/pmic.200900719

Martens L. Chambers M. Sturm M. Kessner D. Levander F. Shofstahl J. Tang W.H. Rompp A. Neumann S. Pizarro A.D. . mzML–a community standard for mass spectrometry data. Mol. Cell. Proteomics 2011;10. R110 000133.

10.1002/pmic.201300560

10.1002/pmic.201100578

10.1093/bioinformatics/btv250

10.1093/nar/gkv382

10.1074/mcp.O113.036681

10.1016/j.cell.2015.03.032

10.1038/nature14249

10.1038/nature14238

10.1038/nature14583

10.1126/science.1253671

10.1002/pmic.201100066

Griss J. Cote R.G. Gerner C. Hermjakob H. Vizcaino J.A. Published and perished? The influence of the searched protein database on the long-term storage of proteomics data. Mol. Cell. Proteomics 2011;10. M111 008490.

10.1002/pmic.201400120

10.1016/j.jprot.2012.12.012

10.1038/ncomms6277

10.1021/pr0604054

10.1038/nbt.3109

10.1093/bioinformatics/bth092

10.1038/nbt.1511

10.1038/nmeth.2343

Vaudel M. Verheggen K. Csordas A. Raeder H. Berven F.S. Martens L. Vizcaino J.A. Barsnes H. Exploring the potential of public proteomics data. Proteomics 2015. doi: 10.1002/pmic.201500295.

10.1021/acs.jproteome.5b00499

10.1021/pr500572z

10.1089/omi.2011.0143

10.1016/j.jprot.2014.04.018

Mohammed Y. Borchers C.H. An extensive library of surrogate peptides for all human proteins. J. Proteomics 2015. doi: 10.1016/j.jprot.2015.07.025.

10.1093/bioinformatics/btt544

10.1016/j.jprot.2011.11.016

10.1186/s13073-015-0208-5

10.1074/mcp.O113.028506

10.1074/mcp.M113.035907

10.1038/nmeth.2106

10.1002/prca.201400107