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This study aims to compare protein abundance (PA) of pre-treatment and during orthodontic treatment for root resorption and to determine potential early markers for root resorption.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Ten subjects (<jats:italic>n<\/jats:italic>\u2009=\u200910) who had upper and lower fixed appliances (MBT, 3\u2009M Unitek, 0.022\u2033\u2009\u00d7\u20090.028\u2033) were recruited for this study. Human gingival crevicular fluid (GCF) was obtained using periopaper strips at pre-treatment (T0), 1 month (T1), 3 months (T3), and 6 months (T6) of orthodontic treatment. Periapical radiographs of the upper permanent central incisors were taken at T0 and T6 to measure the amount of root resorption. Identification of changes in PA was performed using liquid chromatography-tandem mass spectrometry. Student\u2019s t-test was then performed to determine the significance of the differences in protein abundance before and after orthodontic treatment.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Our findings showed that all ten subjects had mild root resorption, with an average resorption length of 0.56\u2009\u00b1\u20090.30\u2009mm. A total of 186 proteins were found to be commonly present at T0, T1, T3, and T6. There were significant changes in the abundance of 16 proteins (student\u2019s t-test,<jats:italic>p<\/jats:italic>\u2009\u2264\u20090.05). The increased PA of S100A9, immunoglobulin J chain, heat shock protein 1A, immunoglobulin heavy variable 4\u201334 and vitronectin at T1 suggested a response to stress that involved inflammation during the early phase of orthodontic treatment. On the other hand, the increased PA of thymidine phosphorylase at T3 suggested growth promotion and, angiogenic and chemotactic activities.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>The identified proteins can be potential early markers for root resorption based on the increase in their respective PA and predicted roles during the early phase of orthodontic treatment. Non-invasive detection of root resorption using protein markers as early as possible is extremely important as it can aid orthodontists in successful orthodontic treatment.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12903-020-01246-9","type":"journal-article","created":{"date-parts":[[2020,9,11]],"date-time":"2020-09-11T13:04:39Z","timestamp":1599829479000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Label-free quantitative proteomic analysis of gingival crevicular fluid to identify potential early markers for root resorption"],"prefix":"10.1186","volume":"20","author":[{"given":"Farah Amirah","family":"Mohd Nasri","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shahrul Hisham","family":"Zainal Ariffin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saiful Anuar","family":"Karsani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8354-5131","authenticated-orcid":false,"given":"Rohaya","family":"Megat Abdul Wahab","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,9,11]]},"reference":[{"issue":"9\u201310","key":"1246_CR1","first-page":"1","volume":"11","author":"KE Kaczor-Urbanowicz","year":"2017","unstructured":"Kaczor-Urbanowicz KE, Deutsch O, Zaks B, Krief G, Chaushu S, Palmon A. 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