{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,19]],"date-time":"2026-04-19T05:31:34Z","timestamp":1776576694481,"version":"3.51.2"},"reference-count":67,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,11,18]],"date-time":"2021-11-18T00:00:00Z","timestamp":1637193600000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"DFG","doi-asserted-by":"publisher","award":["SFB924"],"award-info":[{"award-number":["SFB924"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"DFG","doi-asserted-by":"publisher","award":["SFB1309"],"award-info":[{"award-number":["SFB1309"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"DFG","doi-asserted-by":"publisher","award":["SFB1321"],"award-info":[{"award-number":["SFB1321"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002347","name":"BMBF","doi-asserted-by":"publisher","award":["031L0168"],"award-info":[{"award-number":["031L0168"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>ProteomicsDB (https:\/\/www.ProteomicsDB.org) is a multi-omics and multi-organism resource for life science research. In this update, we present our efforts to continuously develop and expand ProteomicsDB. The major focus over the last two years was improving the findability, accessibility, interoperability\u00a0and reusability (FAIR) of the data as well as its implementation. For this purpose, we release a new application programming interface (API) that provides systematic access to essentially all data in ProteomicsDB. Second, we release a new open-source user interface (UI) and show the advantages the scientific community gains from such software. With the new interface, two new visualizations of protein primary, secondary and tertiary structure as well an updated spectrum viewer were added. Furthermore, we integrated ProteomicsDB with our deep-neural-network Prosit that can predict the fragmentation characteristics and retention time of peptides. The result is an automatic processing pipeline that can be used to reevaluate database search engine results stored in ProteomicsDB. In addition, we extended the data content with experiments investigating different human biology as well as a newly supported organism.<\/jats:p>","DOI":"10.1093\/nar\/gkab1026","type":"journal-article","created":{"date-parts":[[2021,10,16]],"date-time":"2021-10-16T10:07:08Z","timestamp":1634378828000},"page":"D1541-D1552","source":"Crossref","is-referenced-by-count":77,"title":["ProteomicsDB: toward a FAIR open-source resource for life-science research"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1540-5911","authenticated-orcid":false,"given":"Ludwig","family":"Lautenbacher","sequence":"first","affiliation":[{"name":"Technical University of Munich, Computational Mass Spectrometry, 85354\u00a0Freising, Bavaria, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6042-1585","authenticated-orcid":false,"given":"Patroklos","family":"Samaras","sequence":"additional","affiliation":[{"name":"Technical University of Munich, Chair of Proteomics and Bioanalytics, 85354\u00a0Freising, Bavaria, Germany"}]},{"given":"Julian","family":"Muller","sequence":"additional","affiliation":[{"name":"Technical University of Munich, Chair of Proteomics and Bioanalytics, 85354\u00a0Freising, Bavaria, Germany"}]},{"given":"Andreas","family":"Grafberger","sequence":"additional","affiliation":[{"name":"Technical University of Munich, Chair of Proteomics and Bioanalytics, 85354\u00a0Freising, Bavaria, Germany"}]},{"given":"Marwin","family":"Shraideh","sequence":"additional","affiliation":[{"name":"Technical University of Munich, Chair for Information Systems,\u00a085748 Garching, Bavaria, Germany"},{"name":"Technical University of Munich, SAP University Competence Center, 85748\u00a0Garching, Bavaria, Germany"}]},{"given":"Johannes","family":"Rank","sequence":"additional","affiliation":[{"name":"Technical University of Munich, Chair for Information Systems,\u00a085748 Garching, Bavaria, Germany"},{"name":"Technical University of Munich, SAP University Competence Center, 85748\u00a0Garching, Bavaria, Germany"}]},{"given":"Simon T","family":"Fuchs","sequence":"additional","affiliation":[{"name":"Technical University of Munich, Chair for Information Systems,\u00a085748 Garching, Bavaria, Germany"},{"name":"Technical University of Munich, SAP University Competence Center, 85748\u00a0Garching, Bavaria, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1883-6514","authenticated-orcid":false,"given":"Tobias K","family":"Schmidt","sequence":"additional","affiliation":[{"name":"Technical University of Munich, Chair of Proteomics and Bioanalytics, 85354\u00a0Freising, Bavaria, Germany"}]},{"given":"Matthew","family":"The","sequence":"additional","affiliation":[{"name":"Technical University of Munich, Chair of Proteomics and Bioanalytics, 85354\u00a0Freising, Bavaria, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4650-6181","authenticated-orcid":false,"given":"Christian","family":"Dallago","sequence":"additional","affiliation":[{"name":"Technical University of Munich, Department for Bioinformatics and Computational Biology, 85748\u00a0Garching, Bavaria, Germany"},{"name":"Technical University of Munich, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), 85748\u00a0Garching, Bavaria, Germany"}]},{"given":"Holger","family":"Wittges","sequence":"additional","affiliation":[{"name":"Technical University of Munich, Chair for Information Systems,\u00a085748 Garching, Bavaria, Germany"},{"name":"Technical University of Munich, SAP University Competence Center, 85748\u00a0Garching, Bavaria, Germany"}]},{"given":"Burkhard","family":"Rost","sequence":"additional","affiliation":[{"name":"Technical University of Munich, Department for Bioinformatics and Computational Biology, 85748\u00a0Garching, Bavaria, Germany"},{"name":"Technical University of Munich, Institute for Advanced Study (TUM-IAS), 85748 Freising,\u00a0Bavaria, Germany"}]},{"given":"Helmut","family":"Krcmar","sequence":"additional","affiliation":[{"name":"Technical University of Munich, Chair for Information Systems,\u00a085748 Garching, Bavaria, Germany"},{"name":"Technical University of Munich, SAP University Competence Center, 85748\u00a0Garching, Bavaria, Germany"}]},{"given":"Bernhard","family":"Kuster","sequence":"additional","affiliation":[{"name":"Technical University of Munich, Chair of Proteomics and Bioanalytics, 85354\u00a0Freising, Bavaria, Germany"},{"name":"Technical University of Munich, Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), 85354 Freising, Bavaria, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9224-3258","authenticated-orcid":false,"given":"Mathias","family":"Wilhelm","sequence":"additional","affiliation":[{"name":"Technical University of Munich, Computational Mass Spectrometry, 85354\u00a0Freising, Bavaria, Germany"}]}],"member":"286","published-online":{"date-parts":[[2021,11,17]]},"reference":[{"key":"2022010507371484800_B1","first-page":"D1153","article-title":"ProteomicsDB: a multi-omics and multi-organism resource for life science research","volume":"48","author":"Samaras","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2022010507371484800_B2","first-page":"28","article-title":"The SAP HANA Database\u2013An architecture overview","volume":"35","author":"F\u00e4rber","year":"2012","journal-title":"IEEE Data Eng. Bull."},{"key":"2022010507371484800_B3","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1038\/nature13319","article-title":"Mass-spectrometry-based draft of the human proteome","volume":"509","author":"Wilhelm","year":"2014","journal-title":"Nature"},{"key":"2022010507371484800_B4","doi-asserted-by":"crossref","first-page":"D1271","DOI":"10.1093\/nar\/gkx1029","article-title":"ProteomicsDB","volume":"46","author":"Schmidt","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2022010507371484800_B5","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1038\/s41586-020-2094-2","article-title":"Mass-spectrometry-based draft of the Arabidopsis proteome","volume":"579","author":"Mergner","year":"2020","journal-title":"Nature"},{"key":"2022010507371484800_B6","first-page":"1.30.1","article-title":"The GeneCards Suite: from gene data mining to disease genome sequence analyses","volume":"54","author":"Stelzer","year":"2016","journal-title":"Curr. Prot. Bioinform."},{"key":"2022010507371484800_B7","doi-asserted-by":"crossref","first-page":"D480","DOI":"10.1093\/nar\/gkaa1100","article-title":"UniProt: the universal protein knowledgebase in 2021","volume":"49","author":"The UniProt Consortium","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022010507371484800_B8","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1038\/nmeth.4077","article-title":"OmniPath: guidelines and gateway for literature-curated signaling pathway resources","volume":"13","author":"T\u00fcrei","year":"2016","journal-title":"Nat. Methods"},{"key":"2022010507371484800_B9","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1038\/s41592-019-0477-9","article-title":"Gene Information eXtension (GIX): effortless retrieval of gene product information on any website","volume":"16","author":"Knight","year":"2019","journal-title":"Nat. Methods"},{"key":"2022010507371484800_B10","doi-asserted-by":"crossref","first-page":"D246","DOI":"10.1093\/nar\/gkx1158","article-title":"Expression Atlas: gene and protein expression across multiple studies and organisms","volume":"46","author":"Papatheodorou","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2022010507371484800_B11","doi-asserted-by":"crossref","first-page":"M111.014068","DOI":"10.1074\/mcp.M111.014068","article-title":"Analysis of high accuracy, quantitative proteomics data in the MaxQB database","volume":"11","author":"Schaab","year":"2012","journal-title":"Mol. Cell. Proteomics"},{"key":"2022010507371484800_B12","doi-asserted-by":"crossref","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR guiding principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci. Data"},{"key":"2022010507371484800_B13","doi-asserted-by":"crossref","first-page":"37","DOI":"10.3233\/DS-190026","article-title":"Towards FAIR principles for research software","volume":"3","author":"Lamprecht","year":"2020","journal-title":"DS"},{"key":"2022010507371484800_B14","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1007\/978-3-030-82405-1_26","article-title":"A microservice-based reference architecture for digital platforms in the proteomics domain","volume-title":"The Next Wave of Sociotechnical Design","author":"Shraideh","year":"2021"},{"key":"2022010507371484800_B15","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1038\/s41592-019-0426-7","article-title":"Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning","volume":"16","author":"Gessulat","year":"2019","journal-title":"Nat. Methods"},{"key":"2022010507371484800_B16","doi-asserted-by":"crossref","first-page":"3346","DOI":"10.1038\/s41467-021-23713-9","article-title":"Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics","volume":"12","author":"Wilhelm","year":"2021","journal-title":"Nat. Commun."},{"key":"2022010507371484800_B17","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1145\/2872427.2883029","article-title":"Foundations of JSON Schema","volume-title":"Proceedings of the 25th International Conference on World Wide Web, WWW \u201916. International World Wide Web Conferences Steering Committee","author":"Pezoa","year":"2016"},{"key":"2022010507371484800_B18","author":"World Wide Web Consortium","year":"2006"},{"key":"2022010507371484800_B19","doi-asserted-by":"crossref","first-page":"W535","DOI":"10.1093\/nar\/gkab354","article-title":"PredictProtein - predicting protein structure and function for 29 Years","volume":"49","author":"Bernhofer","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022010507371484800_B20","doi-asserted-by":"crossref","first-page":"S1","DOI":"10.1186\/1471-2164-16-S8-S1","article-title":"Better prediction of functional effects for sequence variants","volume":"16","author":"Hecht","year":"2015","journal-title":"BMC Genomics"},{"key":"2022010507371484800_B21","doi-asserted-by":"crossref","first-page":"D458","DOI":"10.1093\/nar\/gkaa937","article-title":"SMART: recent updates, new developments and status in 2020","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022010507371484800_B22","doi-asserted-by":"crossref","first-page":"D437","DOI":"10.1093\/nar\/gkaa1038","article-title":"RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences","volume":"49","author":"Burley","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022010507371484800_B23","doi-asserted-by":"crossref","first-page":"3388","DOI":"10.1021\/acs.jproteome.1c00096","article-title":"Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource spectrum comparison","volume":"20","author":"Schmidt","year":"2021","journal-title":"J. Proteome Res."},{"key":"2022010507371484800_B24","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1038\/nmeth.4153","article-title":"Building ProteomeTools based on a complete synthetic human proteome","volume":"14","author":"Zolg","year":"2017","journal-title":"Nat. Methods"},{"key":"2022010507371484800_B25","doi-asserted-by":"crossref","first-page":"100076","DOI":"10.1016\/j.mcpro.2021.100076","article-title":"Spectral prediction features as a solution for the search space size problem in proteogenomics","volume":"20","author":"Verbruggen","year":"2021","journal-title":"Mol. Cell. Proteomics"},{"key":"2022010507371484800_B26","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1016\/j.tibs.2017.01.001","article-title":"A golden age for working with public proteomics data","volume":"42","author":"Martens","year":"2017","journal-title":"Trends Biochem. Sci."},{"key":"2022010507371484800_B27","first-page":"D1145","article-title":"The ProteomeXchange consortium in 2020: enabling \u2018big data\u2019 approaches in proteomics","volume":"48","author":"Deutsch","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2022010507371484800_B28","doi-asserted-by":"crossref","first-page":"D442","DOI":"10.1093\/nar\/gky1106","article-title":"The PRIDE database and related tools and resources in 2019: improving support for quantification data","volume":"47","author":"Perez-Riverol","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2022010507371484800_B29","doi-asserted-by":"crossref","first-page":"e8503","DOI":"10.15252\/msb.20188503","article-title":"A deep proteome and transcriptome abundance atlas of 29 healthy human tissues","volume":"15","author":"Wang","year":"2019","journal-title":"Mol. Syst. Biol."},{"key":"2022010507371484800_B30","doi-asserted-by":"crossref","first-page":"2394","DOI":"10.1074\/mcp.M114.046995","article-title":"A scalable approach for protein false discovery rate estimation in large proteomic data sets","volume":"14","author":"Savitski","year":"2015","journal-title":"Mol. Cell Proteomics"},{"key":"2022010507371484800_B31","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1016\/j.brainres.2016.04.008","article-title":"Protein profile changes in the frontotemporal lobes in human severe traumatic brain injury","volume":"1642","author":"Xu","year":"2016","journal-title":"Brain Res."},{"key":"2022010507371484800_B32","doi-asserted-by":"crossref","first-page":"2143","DOI":"10.1021\/pr501243m","article-title":"Comparative proteomics of human and macaque milk reveals species-specific nutrition during postnatal development","volume":"14","author":"Beck","year":"2015","journal-title":"J. Proteome Res."},{"key":"2022010507371484800_B33","doi-asserted-by":"crossref","first-page":"3583","DOI":"10.1021\/acs.jproteome.5b00435","article-title":"Tissue-Based proteogenomics reveals that human testis endows plentiful missing proteins","volume":"14","author":"Zhang","year":"2015","journal-title":"J. Proteome Res."},{"key":"2022010507371484800_B34","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1021\/acs.jproteome.5b00972","article-title":"Proteome profiling and ultrastructural characterization of the human RCMH cell line: Myoblastic properties and suitability for myopathological studies","volume":"15","author":"Kollipara","year":"2016","journal-title":"J. Proteome Res."},{"key":"2022010507371484800_B35","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1038\/nmeth.3811","article-title":"Plug-and-play analysis of the human phosphoproteome by targeted high-resolution mass spectrometry","volume":"13","author":"Lawrence","year":"2016","journal-title":"Nat. Methods"},{"key":"2022010507371484800_B36","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1002\/pmic.201500214","article-title":"A proteomic glimpse into human ureter proteome","volume":"16","author":"Magdeldin","year":"2016","journal-title":"Proteomics"},{"key":"2022010507371484800_B37","doi-asserted-by":"crossref","first-page":"1583","DOI":"10.1016\/j.celrep.2014.07.036","article-title":"Ultradeep human phosphoproteome reveals a distinct regulatory nature of tyr and Ser\/Thr-Based signaling","volume":"8","author":"Sharma","year":"2014","journal-title":"Cell Rep."},{"key":"2022010507371484800_B38","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/s12014-016-9113-1","article-title":"Synovial fluid proteome in rheumatoid arthritis","volume":"13","author":"Bhattacharjee","year":"2016","journal-title":"Clin. Proteome"},{"key":"2022010507371484800_B39","doi-asserted-by":"crossref","first-page":"5469","DOI":"10.1038\/ncomms6469","article-title":"Integrated omic analysis of lung cancer reveals metabolism proteome signatures with prognostic impact","volume":"5","author":"Li","year":"2014","journal-title":"Nat. Commun."},{"key":"2022010507371484800_B40","doi-asserted-by":"crossref","first-page":"150022","DOI":"10.1038\/sdata.2015.22","article-title":"Proteomic analysis of colon and rectal carcinoma using standard and customized databases","volume":"2","author":"Slebos","year":"2015","journal-title":"Sci. Data"},{"key":"2022010507371484800_B41","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1002\/pmic.201400171","article-title":"Refined phosphopeptide enrichment by phosphate additive and the analysis of human brain phosphoproteome","volume":"15","author":"Tan","year":"2015","journal-title":"Proteomics"},{"key":"2022010507371484800_B42","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1016\/j.neurobiolaging.2015.11.029","article-title":"Quantitative protein profiling of hippocampus during human aging","volume":"39","author":"Xu","year":"2016","journal-title":"Neurobiol. Aging"},{"key":"2022010507371484800_B43","doi-asserted-by":"crossref","first-page":"5461","DOI":"10.1021\/pr500845u","article-title":"Proteome-wide discovery of unknown ATP-binding proteins and kinase inhibitor target proteins using an ATP probe","volume":"13","author":"Adachi","year":"2014","journal-title":"J. Proteome Res."},{"key":"2022010507371484800_B44","doi-asserted-by":"crossref","first-page":"3606","DOI":"10.1021\/acs.jproteome.5b00170","article-title":"Human spermatozoa as a model for detecting missing proteins in the context of the chromosome-centric human proteome project","volume":"14","author":"Jumeau","year":"2015","journal-title":"J. Proteome Res."},{"key":"2022010507371484800_B45","doi-asserted-by":"crossref","first-page":"3998","DOI":"10.1021\/acs.jproteome.6b00400","article-title":"Looking for missing proteins in the proteome of human spermatozoa: An update","volume":"15","author":"Vandenbrouck","year":"2016","journal-title":"J. Proteome Res."},{"key":"2022010507371484800_B46","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1021\/acs.jproteome.6b00659","article-title":"In-Depth cerebrospinal fluid quantitative proteome and deglycoproteome analysis: Presenting a comprehensive picture of pathways and processes affected by multiple sclerosis","volume":"16","author":"Kroksveen","year":"2017","journal-title":"J. Proteome Res."},{"key":"2022010507371484800_B47","doi-asserted-by":"crossref","first-page":"1834","DOI":"10.1016\/j.celrep.2015.05.029","article-title":"An augmented multiple-protease-based human phosphopeptide atlas","volume":"11","author":"Giansanti","year":"2015","journal-title":"Cell Rep."},{"key":"2022010507371484800_B48","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1016\/j.jprot.2015.03.019","article-title":"Feasibility of label-free phosphoproteomics and application to base-line signaling of colorectal cancer cell lines","volume":"127","author":"Piersma","year":"2015","journal-title":"J. Proteomics"},{"key":"2022010507371484800_B49","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1002\/prca.201400007","article-title":"Deep proteomic profiling of human carotid atherosclerotic plaques using multidimensional LC-MS\/MS","volume":"8","author":"Hao","year":"2014","journal-title":"Proteome Clin. Appl."},{"key":"2022010507371484800_B50","doi-asserted-by":"crossref","first-page":"21507","DOI":"10.1038\/srep21507","article-title":"Comprehensive transcriptomic and proteomic characterization of human mesenchymal stem cells reveals source specific cellular markers","volume":"6","author":"Billing","year":"2016","journal-title":"Sci. Rep."},{"key":"2022010507371484800_B51","doi-asserted-by":"crossref","first-page":"6265","DOI":"10.1038\/ncomms7265","article-title":"Defining the phospho-adhesome through the phosphoproteomic analysis of integrin signalling","volume":"6","author":"Robertson","year":"2015","journal-title":"Nat. Commun."},{"key":"2022010507371484800_B52","doi-asserted-by":"crossref","first-page":"2803","DOI":"10.1074\/mcp.M114.038547","article-title":"Heterogeneity of pancreatic cancer metastases in a single patient revealed by quantitative proteomics","volume":"13","author":"Kim","year":"2014","journal-title":"Mol. Cell. Proteomics"},{"key":"2022010507371484800_B53","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1089\/omi.2015.0029","article-title":"Proteomics of human aqueous humor","volume":"19","author":"Murthy","year":"2015","journal-title":"OMICS"},{"key":"2022010507371484800_B54","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1002\/pmic.201400194","article-title":"Simultaneous dissection and comparison of IL-2 and IL-15 signaling pathways by global quantitative phosphoproteomics","volume":"15","author":"Osinalde","year":"2015","journal-title":"Proteomics"},{"key":"2022010507371484800_B55","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1021\/acs.jproteome.5b00420","article-title":"Quantitative tissue proteomics analysis reveals versican as potential biomarker for early-stage hepatocellular carcinoma","volume":"15","author":"Naboulsi","year":"2016","journal-title":"J. Proteome Res."},{"key":"2022010507371484800_B56","doi-asserted-by":"crossref","first-page":"2278","DOI":"10.1021\/acs.jproteome.5b00053","article-title":"Analysis of disease-associated protein expression using quantitative proteomics\u2014fibulin-5 is expressed in association with hepatic fibrosis","volume":"14","author":"Bracht","year":"2015","journal-title":"J. Proteome Res."},{"key":"2022010507371484800_B57","doi-asserted-by":"crossref","first-page":"29143","DOI":"10.18632\/oncotarget.5020","article-title":"Global phosphotyrosine survey in triple-negative breast cancer reveals activation of multiple tyrosine kinase signaling pathways","volume":"6","author":"Wu","year":"2015","journal-title":"Oncotarget"},{"key":"2022010507371484800_B58","doi-asserted-by":"crossref","first-page":"10259","DOI":"10.1038\/ncomms10259","article-title":"Proteomic maps of breast cancer subtypes","volume":"7","author":"Tyanova","year":"2016","journal-title":"Nat. Commun."},{"key":"2022010507371484800_B59","doi-asserted-by":"crossref","first-page":"2429","DOI":"10.1074\/mcp.O114.047555","article-title":"Deep, quantitative coverage of the lysine acetylome using novel anti-acetyl-lysine antibodies and an optimized proteomic workflow","volume":"14","author":"Svinkina","year":"2015","journal-title":"Mol. Cell. Proteomics"},{"key":"2022010507371484800_B60","doi-asserted-by":"crossref","first-page":"1174","DOI":"10.1016\/j.cell.2010.12.001","article-title":"A tissue-specific atlas of mouse protein phosphorylation and expression","volume":"143","author":"Huttlin","year":"2010","journal-title":"Cell"},{"key":"2022010507371484800_B61","first-page":"1","article-title":"Proteomic landscape of the primary somatosensory cortex upon sensory deprivation","volume":"6","author":"Kole","year":"2017","journal-title":"Gigascience"},{"key":"2022010507371484800_B62","doi-asserted-by":"crossref","first-page":"1819","DOI":"10.1038\/nn.4160","article-title":"Cell type- and brain region-resolved mouse brain proteome","volume":"18","author":"Sharma","year":"2015","journal-title":"Nat. Neurosci."},{"key":"2022010507371484800_B63","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.2732","article-title":"HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics","volume":"11","author":"Branca","year":"2014","journal-title":"Nat. Methods"},{"key":"2022010507371484800_B64","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1111\/jnc.13636","article-title":"Proteome rearrangements after auditory learning: high-resolution profiling of synapse-enriched protein fractions from mouse brain","volume":"138","author":"K\u00e4hne","year":"2016","journal-title":"J. Neurochem."},{"key":"2022010507371484800_B65","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1016\/j.exger.2015.11.016","article-title":"Temporal lobe in human aging: a quantitative protein profiling study of samples from Chinese Human Brain Bank","volume":"73","author":"Xu","year":"2016","journal-title":"Exp. Gerontol."},{"key":"2022010507371484800_B66","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1016\/j.nmd.2016.07.002","article-title":"Histological effects of givinostat in boys with Duchenne muscular dystrophy","volume":"26","author":"Bettica","year":"2016","journal-title":"Neuromuscul. Disord."},{"key":"2022010507371484800_B67","doi-asserted-by":"crossref","DOI":"10.21203\/rs.3.rs-646613\/v1","article-title":"Target deconvolution of HDAC pharmacopoeia highlights MBLAC2 as common off-target","author":"Lechner","year":"2021"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/D1\/D1541\/42058228\/gkab1026.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/D1\/D1541\/42058228\/gkab1026.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,1,5]],"date-time":"2022-01-05T08:10:11Z","timestamp":1641370211000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/50\/D1\/D1541\/6430496"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,11,17]]},"references-count":67,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2021,11,17]]},"published-print":{"date-parts":[[2022,1,7]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkab1026","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,1,7]]},"published":{"date-parts":[[2021,11,17]]}}}