{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T05:26:20Z","timestamp":1783488380324,"version":"3.55.0"},"reference-count":68,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,11,18]],"date-time":"2022-11-18T00:00:00Z","timestamp":1668729600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1U01HG012680-01"],"award-info":[{"award-number":["1U01HG012680-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1R21CA261642-01A1"],"award-info":[{"award-number":["1R21CA261642-01A1"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["5R35GM133416"],"award-info":[{"award-number":["5R35GM133416"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100019102","name":"University of Illinois Cancer Center","doi-asserted-by":"publisher","award":["2020-PP-07"],"award-info":[{"award-number":["2020-PP-07"]}],"id":[{"id":"10.13039\/100019102","id-type":"DOI","asserted-by":"publisher"}]},{"name":"LAS Undergraduate Research Initiative"},{"name":"Summer Research Opportunities Program"},{"name":"Graduate Pathways to Success"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The extracellular matrix (ECM) is a complex assembly of proteins that constitutes the scaffold organizing cells, tissues, and organs. Over the past decade, mass-spectrometry-based proteomics has become the method of choice to profile the composition of the ECM, or the matrisome, of tissues. To assist non-specialists with the reuse of ECM proteomic datasets, we released MatrisomeDB (https:\/\/matrisomedb.org) in 2020. Here, we report the expansion of the database to include 25 new curated studies on the ECM of 24 new tissues in addition to datasets on tissues previously included, more than doubling the size of the original database and achieving near-complete coverage of the in-silico predicted matrisome. We further enhanced data visualization by maps of peptides and post-translational-modifications detected onto domain-based representations and 3D structures of ECM proteins. We also referenced external resources to facilitate the design of targeted mass spectrometry assays. Last, we implemented an abstract-mining tool that generates an enrichment word cloud from abstracts of studies in which a queried protein is found with higher confidence and higher abundance relative to other studies in MatrisomeDB.<\/jats:p>","DOI":"10.1093\/nar\/gkac1009","type":"journal-article","created":{"date-parts":[[2022,11,18]],"date-time":"2022-11-18T18:30:42Z","timestamp":1668796242000},"page":"D1519-D1530","source":"Crossref","is-referenced-by-count":200,"title":["MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database"],"prefix":"10.1093","volume":"51","author":[{"given":"Xinhao","family":"Shao","sequence":"first","affiliation":[{"name":"Department of Pharmaceutical Sciences, University of Illinois at Chicago , Chicago , IL \u00a060612, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clarissa D","family":"Gomez","sequence":"additional","affiliation":[{"name":"Department of Physiology and Biophysics, University of Illinois at Chicago , Chicago , IL \u00a060612, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nandini","family":"Kapoor","sequence":"additional","affiliation":[{"name":"Department of Physiology and Biophysics, University of Illinois at Chicago , Chicago , IL \u00a060612, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James M","family":"Considine","sequence":"additional","affiliation":[{"name":"Department of Physiology and Biophysics, University of Illinois at Chicago , Chicago , IL \u00a060612, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"Grams","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences, University of Illinois at Chicago , Chicago , IL \u00a060612, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu (Tom)","family":"Gao","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences, University of Illinois at Chicago , Chicago , IL \u00a060612, USA"},{"name":"University of Illinois Cancer Center , Chicago , IL \u00a060612, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4796-5614","authenticated-orcid":false,"given":"Alexandra","family":"Naba","sequence":"additional","affiliation":[{"name":"Department of Physiology and Biophysics, University of Illinois at Chicago , Chicago , IL \u00a060612, USA"},{"name":"University of Illinois Cancer Center , Chicago , IL \u00a060612, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,11,18]]},"reference":[{"key":"2023010804193474500_B1","volume-title":"Extracellular Matrix Biology. Cold Spring Harbor Perspectives in Biology","author":"Hynes","year":"2012"},{"key":"2023010804193474500_B2","doi-asserted-by":"crossref","first-page":"6850","DOI":"10.1111\/febs.15776","article-title":"A guide to the composition and functions of the extracellular matrix","volume":"288","author":"Karamanos","year":"2021","journal-title":"FEBS J."},{"key":"2023010804193474500_B3","doi-asserted-by":"crossref","first-page":"dev175596","DOI":"10.1242\/dev.175596","article-title":"The extracellular matrix in development","volume":"147","author":"Walma","year":"2020","journal-title":"Development"},{"key":"2023010804193474500_B4","doi-asserted-by":"crossref","first-page":"101530","DOI":"10.1016\/j.jbc.2021.101530","article-title":"The interplay of fibroblasts, the extracellular matrix, and inflammation in scar formation","volume":"298","author":"Moretti","year":"2022","journal-title":"J. Biol. Chem."},{"key":"2023010804193474500_B5","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1002\/aac2.12013","article-title":"A glitch in the matrix: age-dependent changes in the extracellular matrix facilitate common sites of metastasis","volume":"1","author":"Marino","year":"2020","journal-title":"Aging Cancer"},{"key":"2023010804193474500_B6","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1159\/000504295","article-title":"The matrisome during aging and longevity: a systems-level approach toward defining matreotypes promoting healthy aging","volume":"66","author":"Ewald","year":"2020","journal-title":"Gerontology"},{"key":"2023010804193474500_B7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.matbio.2018.08.007","article-title":"Matrix modeling and remodeling: a biological interplay regulating tissue homeostasis and diseases","volume":"75\u201376","author":"Karamanos","year":"2019","journal-title":"Matrix Biol."},{"key":"2023010804193474500_B8","doi-asserted-by":"crossref","first-page":"2830","DOI":"10.1111\/febs.14818","article-title":"The extracellular matrix as a multitasking player in disease","volume":"286","author":"Theocharis","year":"2019","journal-title":"FEBS J."},{"key":"2023010804193474500_B9","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1016\/j.semcdb.2018.06.005","article-title":"The cancer matrisome: from comprehensive characterization to biomarker discovery","volume":"89","author":"Socovich","year":"2019","journal-title":"Semin. Cell Dev. Biol."},{"key":"2023010804193474500_B10","doi-asserted-by":"crossref","first-page":"1527","DOI":"10.1002\/ar.24086","article-title":"Genetic disorders of the extracellular matrix","volume":"303","author":"Lamand\u00e9","year":"2020","journal-title":"Anat Rec (Hoboken)"},{"key":"2023010804193474500_B11","doi-asserted-by":"crossref","first-page":"100079","DOI":"10.1016\/j.mcpro.2021.100079","article-title":"Evaluation and refinement of sample preparation methods for extracellular matrix proteome coverage","volume":"20","author":"McCabe","year":"2021","journal-title":"Mol. Cell. Proteomics"},{"key":"2023010804193474500_B12","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1042\/EBC20190001","article-title":"Exploring the extracellular matrix in health and disease using proteomics","volume":"63","author":"Taha","year":"2019","journal-title":"Essays Biochem."},{"key":"2023010804193474500_B13","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/bs.ctm.2015.06.001","article-title":"Applying proteomics to investigate extracellular matrix in health and disease","volume":"76","author":"Randles","year":"2015","journal-title":"Curr. Top. Membr."},{"key":"2023010804193474500_B14","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1080\/14789450.2021.1984885","article-title":"Advances in the proteomic profiling of the matrisome and adhesome","volume":"18","author":"Krasny","year":"2021","journal-title":"Expert Rev. Proteomics"},{"key":"2023010804193474500_B15","doi-asserted-by":"crossref","first-page":"M111.014647","DOI":"10.1074\/mcp.M111.014647","article-title":"The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices","volume":"11","author":"Naba","year":"2012","journal-title":"Mol. Cell. 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