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The molecular pathology of calcification and especially events triggering calcification are poorly understood. Metagenomic and molecular microbial techniques have identified the presence of oral biofilm-producing and dental calculus-forming bacteria in atherosclerotic plaques, suggesting that they may be involved in calcification. To enable studying this at the proteome level, we compared four different protein extraction methods to find a robust and reliable method for the identification and quantification of human and bacterial proteins from 10 calcified arterial plaques. We identified 3 913 human proteins and 24 bacterial proteins. These findings provide further support for the presence of bacterial proteins in calcified areas of coronary artery plaques, with Fusobacteria being the most abundant bacterial protein source. Comparisons of the extraction methods showed that the urea-based extraction method was most optimal due to its simplicity and reproducible identification of a high number of proteins, which makes it suitable for further large-scale analysis of coronary artery plaque samples.<\/jats:p>","DOI":"10.1021\/acs.jproteome.6c00422","type":"journal-article","created":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T07:01:28Z","timestamp":1789369288000},"page":"5611-5623","source":"Crossref","is-referenced-by-count":0,"title":["Toward Optimized\nProteomics Analysis to Detect Bacterial\nand Host Proteins in Calcified Coronary Artery Plaques"],"prefix":"10.1021","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3940-442X","authenticated-orcid":true,"given":"Kirsikka","family":"Musta","sequence":"first","affiliation":[{"name":"Tampere University , , ,","place":["Tampere, Finland, 33520"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Markus J. T.","family":"Ojanen","sequence":"additional","affiliation":[{"name":"Tampere University , , ,","place":["Tampere, Finland, 33520"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Stensland","sequence":"additional","affiliation":[{"name":"University of Oslo and Oslo University Hospital , , ,","place":["Oslo, Norway, 0372"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonna","family":"Kankaanranta","sequence":"additional","affiliation":[{"name":"Tampere University , , ,","place":["Tampere, Finland, 33520"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Terho","family":"Lehtima\u0308ki","sequence":"additional","affiliation":[{"name":"Tampere University , , ,","place":["Tampere, Finland, 33520"]},{"name":"Fimlab laboratories , ,","place":["Tampere, Finland, 33520"]},{"name":"Tampere University , , ,","place":["Tampere, Finland, 33520"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pekka J.","family":"Karhunen","sequence":"additional","affiliation":[{"name":"Tampere University , , ,","place":["Tampere, Finland, 33520"]},{"name":"Fimlab Laboratories , ,","place":["Tampere, Finland, 33520"]},{"name":"Tampere University , , ,","place":["Tampere, Finland, 33520"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tuula A.","family":"Nyman","sequence":"additional","affiliation":[{"name":"University of Oslo and Oslo University Hospital , , ,","place":["Oslo, Norway, 0372"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9357-1480","authenticated-orcid":true,"given":"Vesa P.","family":"Hyto\u0308nen","sequence":"additional","affiliation":[{"name":"Tampere University , , ,","place":["Tampere, Finland, 33520"]},{"name":"Fimlab Laboratories , ,","place":["Tampere, Finland, 33520"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,14]]},"reference":[{"issue":"10440","key":"2026100208413555000_cit1","doi-asserted-by":"publisher","first-page":"2100","DOI":"10.1016\/S0140-6736(24)00367-2","article-title":"Global Burden of 288 Causes of Death and Life Expectancy\nDecomposition in 204 Countries and Territories and 811 Subnational\nLocations, 1990\u20132021: A Systematic Analysis for the Global\nBurden of Disease Study 2021","volume":"403","author":"Naghavi","year":"2024","journal-title":"Lancet"},{"key":"2026100208413555000_cit2","article-title":"Coronary\nArtery\nCalcification","volume-title":"StatPearls","author":"Mohan","year":"2024"},{"issue":"4","key":"2026100208413555000_cit3","doi-asserted-by":"publisher","first-page":"590","DOI":"10.1093\/cvr\/cvy010","article-title":"Role of Smooth Muscle Cells in Vascular Calcification:\nImplications in Atherosclerosis and Arterial Stiffness","volume":"114","author":"Durham","year":"2018","journal-title":"Cardiovasc. 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