The PRIDE database and related tools and resources in 2019: improving support for quantification data

Nucleic Acids Research - Tập 47 Số D1 - Trang D442-D450 - 2019
Yasset Pérez‐Riverol1, Attila Csordás1, Jinwen Bai1, Manuel Bernal Llinares1, Suresh Hewapathirana1, Deepti Jaiswal1, Avinash Inuganti1, Johannes Griss2,1, Gerhard Mayer3, Martin Eisenacher3, Enrique Pérez1, Julian Uszkoreit3, Julianus Pfeuffer4, Timo Sachsenberg4, Şule Yılmaz5, Shivani Tiwary5, Jürgen Cox5, Enrique Audain6, Mathias Walzer1, Andrew F. Jarnuczak1, Tobias Ternent1, Alvis Brāzma1, Juan Antonio Vizcaíno1
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, Vienna, 1090, Austria
3Ruhr University Bochum, Medical Faculty, Medizinisches Proteom-Center, D-44801 Bochum, Germany
4Applied Bioinformatics, Department for Computer Science, University of Tuebingen, Sand 14, 72076 Tuebingen, Germany
5Computational Systems Biochemistry, Max Planck Institute for Biochemistry, Martinsried, 82152, Germany
6Department of Congenital Heart Disease and Pediatric Cardiology, Universitätsklinikum Schleswig–Holstein Kiel, Kiel, 24105, Germany

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Tài liệu tham khảo

Martens, 2005, PRIDE: the proteomics identifications database, Proteomics, 5, 3537, 10.1002/pmic.200401303

Vizcaino, 2016, 2016 update of the PRIDE database and its related tools, Nucleic Acids Res., 44, D447, 10.1093/nar/gkv1145

Deutsch, 2017, The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition, Nucleic Acids Res., 45, D1100, 10.1093/nar/gkw936

Deutsch, 2008, PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows, EMBO Rep., 9, 429, 10.1038/embor.2008.56

Farrah, 2012, PASSEL: the PeptideAtlas SRMexperiment library, Proteomics, 12, 1170, 10.1002/pmic.201100515

Okuda, 2017, jPOSTrepo: an international standard data repository for proteomes, Nucleic Acids Res., 45, D1107, 10.1093/nar/gkw1080

Sharma, 2018, Panorama Public: A public repository for quantitative data sets processed in skyline, Mol. Cell. Proteomics, 17, 1239, 10.1074/mcp.RA117.000543

Wang, 2015, Open source libraries and frameworks for biological data visualisation: a guide for developers, Proteomics, 15, 1356, 10.1002/pmic.201400377

Zerbino, 2018, Ensembl 2018, Nucleic Acids Res., 46, D754, 10.1093/nar/gkx1098

UniProt Consortium, T, 2018, UniProt: the universal protein knowledgebase, Nucleic Acids Res., 46, D158

Papatheodorou, 2018, Expression Atlas: gene and protein expression across multiple studies and organisms, Nucleic Acids Res., 46, D246, 10.1093/nar/gkx1158

Perez-Riverol, 2016, PRIDE inspector toolsuite: moving toward a universal visualization tool for proteomics data standard formats and quality assessment of ProteomeXchange datasets, Mol. Cell. Proteomics, 15, 305, 10.1074/mcp.O115.050229

Reisinger, 2015, Introducing the PRIDE Archive RESTful web services, Nucleic Acids Res., 43, W599, 10.1093/nar/gkv382

Perez-Riverol, 2015, ms-data-core-api: an open-source, metadata-oriented library for computational proteomics, Bioinformatics, 31, 2903, 10.1093/bioinformatics/btv250

Uszkoreit, 2015, PIA: an intuitive protein inference engine with a web-based user interface, J. Proteome Res., 14, 2988, 10.1021/acs.jproteome.5b00121

Audain, 2017, In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics, J. Proteomics, 150, 170, 10.1016/j.jprot.2016.08.002

Deutsch, 2017, Proteomics standards initiative: Fifteen years of progress and future work, J. Proteome Res., 16, 4288, 10.1021/acs.jproteome.7b00370

Craig, 2004, Open source system for analyzing, validating, and storing protein identification data, J. Proteome Res., 3, 1234, 10.1021/pr049882h

Edwards, 2015, The CPTAC Data Portal: a resource for cancer proteomics research, J. Proteome Res., 14, 2707, 10.1021/pr501254j

Schmidt, 2018, ProteomicsDB, Nucleic Acids Res., 46, D1271, 10.1093/nar/gkx1029

Reisinger, 2015, Introducing the PRIDE Archive RESTful web services, Nucleic Acids Res., 43, W599, 10.1093/nar/gkv382

Perez-Riverol, 2017, Discovering and linking public omics data sets using the Omics Discovery Index, Nat. Biotechnol., 35, 406, 10.1038/nbt.3790

Ternent, 2014, How to submit MS proteomics data to ProteomeXchange via the PRIDE database, Proteomics, 14, 2233, 10.1002/pmic.201400120

Griss, 2014, The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience, Mol. Cell. Proteomics, 13, 2765, 10.1074/mcp.O113.036681

Perkins, 1999, Probability-based protein identification by searching sequence databases using mass spectrometry data, Electrophoresis, 20, 3551, 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2

Pfeuffer, 2017, OpenMS—a platform for reproducible analysis of mass spectrometry data, J. Biotechnol., 261, 142, 10.1016/j.jbiotec.2017.05.016

Tyanova, 2016, The MaxQuant computational platform for mass spectrometry-based shotgun proteomics, Nat. Protoc., 11, 2301, 10.1038/nprot.2016.136

Perez-Riverol, 2017, OLS client and OLS Dialog: open source tools to annotate public omics datasets, Proteomics, 17, 1700244, 10.1002/pmic.201700244

Perez-Riverol, 2018, Future prospects of spectral clustering approaches in proteomics, Proteomics, 18, e1700454, 10.1002/pmic.201700454

Griss, 2016, Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets, Nat. Methods, 13, 651, 10.1038/nmeth.3902

Deutsch, 2016, Human proteome project mass spectrometry data interpretation guidelines 2.1, J. Proteome Res., 15, 3961, 10.1021/acs.jproteome.6b00392

Vaudel, 2016, Exploring the potential of public proteomics data, Proteomics, 16, 214, 10.1002/pmic.201500295

Heunis, 2017, Proteogenomic investigation of strain variation in clinical mycobacterium tuberculosis isolates, J. Proteome Res., 16, 3841, 10.1021/acs.jproteome.7b00483

Tardaguila, 2018, SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification, Genome Res., 28, 396, 10.1101/gr.222976.117

Martens, 2017, A golden age for working with public proteomics data, Trends Biochem. Sci., 42, 333, 10.1016/j.tibs.2017.01.001

Schlaffner, 2017, Fast, quantitative and variant enabled mapping of peptides to genomes, Cell Syst., 5, 152, 10.1016/j.cels.2017.07.007

Koscielny, 2017, Open Targets: a platform for therapeutic target identification and validation, Nucleic Acids Res., 45, D985, 10.1093/nar/gkw1055

Kolesnikov, 2015, ArrayExpress update–simplifying data submissions, Nucleic Acids Res., 43, D1113, 10.1093/nar/gku1057

da Veiga Leprevost, 2017, BioContainers: an open-source and community-driven framework for software standardization, Bioinformatics, 33, 2580, 10.1093/bioinformatics/btx192

Grüning, 2018, Bioconda: sustainable and comprehensive software distribution for the life sciences, Nat. Methods, 15, 475, 10.1038/s41592-018-0046-7

Durinx, 2016, Identifying ELIXIR core data resources [version2; referees: 2 approved], F1000Res, 5, 2422, 10.12688/f1000research.9656.1