Erratum: 2016 update of the PRIDE database and its related tools (Nucleic Acids Research (2016) 44:D1 (D447-D456) DOI: 10.1093/nar/gkv1145);2016 update of the PRIDE database and its related tools

Nucleic Acids Research

Volumn 44, Issue D1, 2016, Pages D447-D456

  Vizcaíno, Juan Antonio ^a   Csordas, Attila ^a   Del Toro, Noemi ^a   Dianes, José A ^a   Griss, Johannes ^a,b   Lavidas, Ilias ^a   Mayer, Gerhard ^a,c   Perez Riverol, Yasset ^a   Reisinger, Florian ^a   Ternent, Tobias ^a   Xu, Qing Wei ^a,d   Wang, Rui ^a   Hermjakob, Henning ^a,e  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b MEDICAL UNIVERSITY OF VIENNA   (Austria)

^c RUHR UNIVERSITY BOCHUM   (Germany)

^d HUBEI UNIVERSITY OF EDUCATION   (China)

^e BEIJING INSTITUTE OF LIFEOMICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME; PEPTIDE; PROTEIN;

ARTICLE; COMPUTER INTERFACE; DATA ANALYSIS; DATA ANALYSIS SOFTWARE; DOCUMENTATION; INFORMATION CENTER; INFORMATION STORAGE; MASS SPECTROMETRY; PRIDE DATABASE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; PUBLICATION; QUALITY CONTROL; REFERENCE DATABASE; SOFTWARE DESIGN; SOFTWARE VALIDATION; WEB BROWSER; CHEMISTRY; METABOLISM; PROTEIN DATABASE; SOFTWARE;

DATABASES, PROTEIN; MASS SPECTROMETRY; PEPTIDES; PROTEINS; PROTEOMICS; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 84976871411     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw880     Document Type: Erratum

References (60)

1. Martens, L., Hermjakob, H., Jones, P., Adamski, M., Taylor, C., States, D., Gevaert, K., Vandekerckhove, J. and Apweiler, R. (2005) PRIDE: the proteomics identifications database. Proteomics, 5, 3537-3545.
2. Jones, P., Cote, R.G., Martens, L., Quinn, A.F., Taylor, C.F., Derache, W., Hermjakob, H. and Apweiler, R. (2006) PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res., 34, D659-D663.
3. Jones, P., Cote, R.G., Cho, S.Y., Klie, S., Martens, L., Quinn, A.F., Thorneycroft, D. and Hermjakob, H. (2008) PRIDE: new developments and new datasets. Nucleic Acids Res., 36, D878-D883.
4. Vizcaino, J.A., Cote, R., Reisinger, F., Barsnes, H., Foster, J.M., Rameseder, J., Hermjakob, H. and Martens, L. (2010) The Proteomics Identifications database: 2010 update. Nucleic Acids Res., 38, D736-D742.
5. 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.
6. 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.
7. Deutsch, E.W., Lam, H. and Aebersold, R. (2008) PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep., 9, 429-434.
8. Farrah, T., Deutsch, E.W., Kreisberg, R., Sun, Z., Campbell, D.S., Mendoza, L., Kusebauch, U., Brusniak, M.Y., Huttenhain, R., Schiess, R. et al. (2012) PASSEL: the PeptideAtlas SRMexperiment library. Proteomics, 12, 1170-1175.
9. Deutsch, E.W., Mendoza, L., Shteynberg, D., Slagel, J., Sun, Z. and Moritz, R.L. (2015) Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics. Proteomics Clin. Appl., 9, 745-754.
10. Craig, R., Cortens, J.P. and Beavis, R.C. (2004) Open source system for analyzing, validating, and storing protein identification data. J. Proteome Res., 3, 1234-1242.
11. Wilhelm, M., Schlegl, J., Hahne, H., Moghaddas Gholami, A., Lieberenz, M., Savitski, M.M., Ziegler, E., Butzmann, L., Gessulat, S., Marx, H. et al. (2014) Mass-spectrometry-based draft of the human proteome. Nature, 509, 582-587.
12. Kim, M.S., Pinto, S.M., Getnet, D., Nirujogi, R.S., Manda, S.S., Chaerkady, R., Madugundu, A.K., Kelkar, D.S., Isserlin, R., Jain, S. et al. (2014) A draft map of the human proteome. Nature, 509, 575-581.
13. 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, M111 014068.
14. Wang, M., Herrmann, C.J., Simonovic, M., Szklarczyk, D. and von Mering, C. (2015) Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines. Proteomics, 15, 3163-3168.
15. Montague, E., Janko, I., Stanberry, L., Lee, E., Choiniere, J., Anderson, N., Stewart, E., Broomall, W., Higdon, R., Kolker, N. et al. (2015) Beyond protein expression, MOPED goes multi-omics. Nucleic Acids Res., 43, D1145-D1151.
16. Perez-Riverol, Y., Alpi, E., Wang, R., Hermjakob, H. and Vizcaino, J.A. (2015) Making proteomics data accessible and reusable: current state of proteomics databases and repositories. Proteomics, 15, 930-949.
17. The UniProt Consortium (2015) UniProt: a hub for protein information. Nucleic Acids Res., 43, D204-D212.
18. Gaudet, P., Michel, P.A., Zahn-Zabal, M., Cusin, I., Duek, P.D., Evalet, O., Gateau, A., Gleizes, A., Pereira, M., Teixeira, D. et al. (2015) The neXtProt knowledgebase on human proteins: current status. Nucleic Acids Res., 43, D764-D770.
19. Barsnes, H., Vizcaino, J.A., Eidhammer, I. and Martens, L. (2009) PRIDE Converter: making proteomics data-sharing easy. Nat. Biotechnol., 27, 598-599.
20. Cote, R.G., Griss, J., Dianes, J.A., Wang, R., Wright, J.C., van den Toorn, H.W., van Breukelen, B., Heck, A.J., Hulstaert, N., Martens, L. et al. (2012) The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium. Mol. Cell. Proteomics, 11, 1682-1689.
21. Wang, R., Fabregat, A., Rios, D., Ovelleiro, D., Foster, J.M., Cote, R.G., Griss, J., Csordas, A., Perez-Riverol, Y., Reisinger, F. et al. (2012) PRIDE Inspector: a tool to visualize and validate MS proteomics data. Nat. Biotechnol., 30, 135-137.
22. 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. et al. (2012) The mzIdentML data standard for mass spectrometry-based proteomics results. Mol. Cell. Proteomics, 11, M111 014381.
23. Rompp, A., Wang, R., Albar, J.P., Urbani, A., Hermjakob, H., Spengler, B. and Vizcaino, J.A. (2015) A public repository for mass spectrometry imaging data. Anal. Bioanal. Chem., 407, 2027-2033.
24. Csordas, A., Ovelleiro, D., Wang, R., Foster, J.M., Rios, D., Vizcaino, J.A. and Hermjakob, H. (2012) PRIDE: quality control in a proteomics data repository. Database (Oxford), 2012, bas004.
25. Reisinger, F., Krishna, R., Ghali, F., Rios, D., Hermjakob, H., Vizcaino, J.A. and Jones, A.R. (2012) jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data. Proteomics, 12, 790-794.
26. Cote, R.G., Reisinger, F. and Martens, L. (2010) jmzML, an open-source Java API for mzML, the PSI standard for MS data. Proteomics, 10, 1332-1335.
27. Martens, L., Chambers, M., Sturm, M., Kessner, D., Levander, F., Shofstahl, J., Tang, W.H., Rompp, A., Neumann, S., Pizarro, A.D. et al. (2011) mzML - a community standard for mass spectrometry data. Mol. Cell. Proteomics, 10, R110 000133.
28. Xu, Q.W., Griss, J., Wang, R., Jones, A.R., Hermjakob, H. and Vizcaino, J.A. (2014) jmzTab: a java interface to the mzTab data standard. Proteomics, 14, 1328-1332.
29. Griss, J., Reisinger, F., Hermjakob, H. and Vizcaino, J.A. (2012) jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats. Proteomics, 12, 795-798.
30. Perez-Riverol, Y., Uszkoreit, J., Sanchez, A., Ternent, T., Toro, N., Hermjakob, H., Vizcaino, J.A. and Wang, R. (2015) ms-data-core-api: an open-source, metadata-oriented library for computational proteomics. Bioinformatics, 31, 2903-2905.
31. Reisinger, F., Del-Toro, N., Ternent, T., Hermjakob, H. and Vizcaino, J.A. (2015) Introducing the PRIDE Archive RESTful web services. Nucleic Acids Res., 43, W599-W604.
32. Griss, J., Jones, A.R., Sachsenberg, T., Walzer, M., Gatto, L., Hartler, J., Thallinger, G.G., Salek, R.M., Steinbeck, C., Neuhauser, N. et al. (2014) The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience. Mol. Cell. Proteomics, 13, 2765-2775.
33. Walther, D.M., Kasturi, P., Zheng, M., Pinkert, S., Vecchi, G., Ciryam, P., Morimoto, R.I., Dobson, C.M., Vendruscolo, M., Mann, M. et al. (2015) Widespread Proteome Remodeling and Aggregation in Aging C. elegans. Cell, 161, 919-932.
34. Welker, F., Collins, M.J., Thomas, J.A., Wadsley, M., Brace, S., Cappellini, E., Turvey, S.T., Reguero, M., Gelfo, J.N., Kramarz, A. et al. (2015) Ancient proteins resolve the evolutionary history of Darwin's South American ungulates. Nature, 522, 81-84.
35. Hultman, J., Waldrop, M.P., Mackelprang, R., David, M.M., McFarland, J., Blazewicz, S.J., Harden, J., Turetsky, M.R., McGuire, A.D., Shah, M.B. et al. (2015) Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes. Nature, 521, 208-212.
36. Mohammed, H., Russell, I.A., Stark, R., Rueda, O.M., Hickey, T.E., Tarulli, G.A., Serandour, A.A., Birrell, S.N., Bruna, A., Saadi, A. et al. (2015) Progesterone receptor modulates ERalpha action in breast cancer. Nature, 523, 313-317.
37. Raschle, M., Smeenk, G., Hansen, R.K., Temu, T., Oka, Y., Hein, M.Y., Nagaraj, N., Long, D.T., Walter, J.C., Hofmann, K. et al. (2015) DNA repair. Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links. Science, 348, 1253671.
38. Haw, R., Hermjakob, H., D'Eustachio, P. and Stein, L. (2011) Reactome pathway analysis to enrich biological discovery in proteomics data sets. Proteomics, 11, 3598-3613.
39. Griss, J., Cote, R.G., Gerner, C., Hermjakob, H. and Vizcaino, J.A. (2011) Published and perished? The influence of the searched protein database on the long-term storage of proteomics data. Mol. Cell. Proteomics, 10, M111 008490.
40. Ternent, T., Csordas, A., Qi, D., Gomez-Baena, G., Beynon, R.J., Jones, A.R., Hermjakob, H. and Vizcaino, J.A. (2014) How to submit MS proteomics data to ProteomeXchange via the PRIDE database. Proteomics, 14, 2233-2241.
41. Gluck, F., Hoogland, C., Antinori, P., Robin, X., Nikitin, F., Zufferey, A., Pasquarello, C., Fetaud, V., Dayon, L., Muller, M. et al. (2013) EasyProt-an easy-to-use graphical platform for proteomics data analysis. J. Proteomics, 79, 146-160.
42. Kim, S. and Pevzner, P.A. (2014) MS-GF+ makes progress towards a universal database search tool for proteomics. Nat. Commun., 5, 5277.
43. Tabb, D.L., Fernando, C.G. and Chambers, M.C. (2007) MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J. Proteome Res., 6, 654-661.
44. Vaudel, M., Burkhart, J.M., Zahedi, R.P., Oveland, E., Berven, F.S., Sickmann, A., Martens, L. and Barsnes, H. (2015) PeptideShaker enables reanalysis of MS-derived proteomics data sets. Nat. Biotechnol., 33, 22-24.
45. Craig, R. and Beavis, R.C. (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics, 20, 1466-1467.
46. 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.
47. Griss, J., Foster, J.M., Hermjakob, H. and Vizcaino, J.A. (2013) PRIDE Cluster: building a consensus of proteomics data. Nat. Methods, 10, 95-96.
48. Vaudel, M., Verheggen, K., Csordas, A., Raeder, H., Berven, F.S., Martens, L., Vizcaino, J.A. and Barsnes, H. (2015) Exploring the potential of public proteomics data. Proteomics, doi: 10.1002/pmic.201500295.
49. Omenn, G.S., Lane, L., Lundberg, E.K., Beavis, R.C., Nesvizhskii, A.I. and Deutsch, E.W. (2015) Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification. J. Proteome Res., 14, 3452-3460.
50. Ezkurdia, I., Vazquez, J., Valencia, A. and Tress, M. (2014) Analyzing the first drafts of the human proteome. J. Proteome Res., 13, 3854-3855.
51. Fan, J., Mohareb, F., Bond, N.J., Lilley, K.S. and Bessant, C. (2012) MRMaid 2.0: mining PRIDE for evidence-based SRM transitions. OMICS, 16, 483-488.
52. Mohammed, Y., Domanski, D., Jackson, A.M., Smith, D.S., Deelder, A.M., Palmblad, M. and Borchers, C.H. (2014) PeptidePicker: a scientific workflow with web interface for selecting appropriate peptides for targeted proteomics experiments. J. Proteomics, 106, 151-161.
53. Mohammed, Y. and Borchers, C.H. (2015) An extensive library of surrogate peptides for all human proteins. J. Proteomics, doi: 10.1016/j.jprot.2015.07.025.
54. Degroeve, S. and Martens, L. (2013) MS2PIP: a tool for MS/MS peak intensity prediction. Bioinformatics, 29, 3199-3203.
55. Burkhart, J.M., Schumbrutzki, C., Wortelkamp, S., Sickmann, A. and Zahedi, R.P. (2012) Systematic and quantitative comparison of digest efficiency and specificity reveals the impact of trypsin quality on MS-based proteomics. J. Proteomics, 75, 1454-1462.
56. Swindell, W.R., Remmer, H.A., Sarkar, M.K., Xing, X., Barnes, D.H., Wolterink, L., Voorhees, J.J., Nair, R.P., Johnston, A., Elder, J.T. et al. (2015) Proteogenomic analysis of psoriasis reveals discordant and concordant changes in mRNA and protein abundance. Genome Med., 7, 86.
57. Walzer, M., Qi, D., Mayer, G., Uszkoreit, J., Eisenacher, M., Sachsenberg, T., Gonzalez-Galarza, F.F., Fan, J., Bessant, C., Deutsch, E.W. et al. (2013) The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics. Mol. Cell. Proteomics, 12, 2332-2340.
58. Walzer, M., Pernas, L.E., Nasso, S., Bittremieux, W., Nahnsen, S., Kelchtermans, P., Pichler, P., van den Toorn, H.W., Staes, A., Vandenbussche, J. et al. (2014) qcML: an exchange format for quality control metrics from mass spectrometry experiments. Mol. Cell. Proteomics, 13, 1905-1913.
59. Matic, I., Ahel, I. and Hay, R.T. (2012) Reanalysis of phosphoproteomics data uncovers ADP-ribosylation sites. Nat. Methods, 9, 771-772.
60. Griss, J., Perez-Riverol, Y., Hermjakob, H. and Vizcaino, J.A. (2015) Identifying novel biomarkers through data mining - A realistic scenario? Proteomics Clin. Appl., 9, 437-443.