The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics
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Yasset Perez-Riverol | Michael J MacCoss | Henning Hermjakob | Brendan MacLean | Nuno Bandeira | Shujiro Okuda | Andrew F. Jarnuczak | Andrew F Jarnuczak | Eric W Deutsch | Yunping Zhu | Shin Kawano | Yu Watanabe | Vagisha Sharma | Julie Wertz | Zhi Sun | Juan A Vizcaíno | Jeremy J Carver | Benjamin S Pullman | Jeremy J. Carver | Suresh Hewapathirana | Yasushi Ishihama | Shujiro Okuda | Yun-ping Zhu | B. MacLean | M. MacCoss | H. Hermjakob | E. Deutsch | Y. Ishihama | J. Vizcaíno | Zhi Sun | N. Bandeira | S. Kawano | Yasset Pérez-Riverol | Yu Watanabe | Vagisha Sharma | Jeremy Carver | D. J. Kundu | D. García-Seisdedos | S. Hewapathirana | B. Pullman | J. Wertz | Deepti J Kundu | David García-Seisdedos | Suresh Hewapathirana
[1] Jun Fan,et al. The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience* , 2014, Molecular & Cellular Proteomics.
[2] J. Vizcaíno,et al. Exploring the potential of public proteomics data , 2015, Proteomics.
[3] Jian Wang,et al. Assembling the Community-Scale Discoverable Human Proteome , 2018, Cell systems.
[4] Helmut Krcmar,et al. ProteomicsDB , 2017, Nucleic Acids Res..
[5] The UniProt Consortium,et al. UniProt: a worldwide hub of protein knowledge , 2018, Nucleic Acids Res..
[6] F. Arnaud,et al. From core referencing to data re-use: two French national initiatives to reinforce paleodata stewardship (National Cyber Core Repository and LTER France Retro-Observatory) , 2017 .
[7] Aïda Ouangraoua,et al. OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes , 2018, Nucleic Acids Res..
[8] Eystein Oveland,et al. PeptideShaker enables reanalysis of MS-derived proteomics data sets , 2015, Nature Biotechnology.
[9] Nuno Bandeira,et al. ProteinExplorer: A Repository-Scale Resource for Exploration of Protein Detection in Public Mass Spectrometry Data Sets. , 2018, Journal of proteome research.
[10] Lindsay K. Pino,et al. The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics. , 2020, Mass spectrometry reviews.
[11] Lennart Martens,et al. Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques , 2019, Nucleic Acids Res..
[12] Johannes Griss,et al. Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets , 2016, Nature Methods.
[13] Mathias Wilhelm,et al. Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning , 2019, Nature Methods.
[14] Robertson Craig,et al. Open source system for analyzing, validating, and storing protein identification data. , 2004, Journal of proteome research.
[15] Martin Eisenacher,et al. Development of data representation standards by the human proteome organization proteomics standards initiative , 2015, J. Am. Medical Informatics Assoc..
[16] Juan Antonio Vizcaíno,et al. Introducing the PRIDE Archive RESTful web services , 2015, Nucleic Acids Res..
[17] Lennart Martens,et al. A Golden Age for Working with Public Proteomics Data , 2017, Trends in biochemical sciences.
[18] Lennart Martens,et al. Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1. , 2016, Journal of proteome research.
[19] Nuno A. Fonseca,et al. Expression Atlas: gene and protein expression across multiple studies and organisms , 2017, Nucleic Acids Res..
[20] Kristian Fog Nielsen,et al. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking , 2016, Nature Biotechnology.
[21] Roman A. Zubarev,et al. The SysteMHC Atlas project , 2017, Nucleic Acids Res..
[22] Jürgen Cox,et al. High-quality MS/MS spectrum prediction for data-dependent and data-independent acquisition data analysis , 2019, Nature Methods.
[23] Martin Eisenacher,et al. The PRIDE database and related tools and resources in 2019: improving support for quantification data , 2018, Nucleic Acids Res..
[24] Luis Mendoza,et al. PASSEL: The PeptideAtlas SRMexperiment library , 2012, Proteomics.
[25] Andrew R. Jones,et al. ProteomeXchange provides globally co-ordinated proteomics data submission and dissemination , 2014, Nature Biotechnology.
[26] Henry H. N. Lam,et al. PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows , 2008, EMBO reports.
[27] Juan Antonio Vizcaíno,et al. The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition , 2016, Nucleic Acids Res..
[28] Kenli Li,et al. iProX: an integrated proteome resource , 2018, Nucleic Acids Res..
[29] Juan Antonio Vizcaíno,et al. The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data , 2017, Genome Biology.
[30] Lennart Martens,et al. LNCipedia 5: towards a reference set of human long non-coding RNAs , 2018, Nucleic Acids Res..
[31] Masaki Matsumoto,et al. The jPOST environment: an integrated proteomics data repository and database , 2018, Nucleic Acids Res..
[32] Juan Antonio Vizcaíno,et al. ms-data-core-api: an open-source, metadata-oriented library for computational proteomics , 2015, Bioinform..
[33] Robert Petryszak,et al. Quantifying the impact of public omics data , 2018, Nature Communications.
[34] Martin Eisenacher,et al. PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets , 2015, Molecular & Cellular Proteomics.
[35] Gerben Menschaert,et al. An update on sORFs.org: a repository of small ORFs identified by ribosome profiling , 2017, Nucleic Acids Res..
[36] David Haussler,et al. The UCSC Genome Browser database: 2019 update , 2018, Nucleic Acids Res..
[37] Astrid Gall,et al. Ensembl 2019 , 2018, Nucleic Acids Res..
[38] R. Aebersold,et al. The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays. , 2017, Journal of proteome research.
[39] Martin Eisenacher,et al. Proteomics Standards Initiative: Fifteen Years of Progress and Future Work , 2017, Journal of proteome research.
[40] Robert Petryszak,et al. Discovering and linking public omics data sets using the Omics Discovery Index , 2017, Nature Biotechnology.
[41] Michael J MacCoss,et al. Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline* , 2018, Molecular & Cellular Proteomics.
[42] Amos Bairoch,et al. The neXtProt knowledgebase on human proteins: 2017 update , 2016, Nucleic Acids Res..
[43] Martin Eisenacher,et al. The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results , 2012, Molecular & Cellular Proteomics.