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