Advances of Proteomic Sciences in Dentistry
Identifieur interne : 000798 ( Pmc/Corpus ); précédent : 000797; suivant : 000799Advances of Proteomic Sciences in Dentistry
Auteurs : Zohaib Khurshid ; Sana Zohaib ; Shariq Najeeb ; Muhammad Sohail Zafar ; Rabia Rehman ; Ihtesham Ur RehmanSource :
- International Journal of Molecular Sciences [ 1422-0067 ] ; 2016.
Abstract
Applications of proteomics tools revolutionized various biomedical disciplines such as genetics, molecular biology, medicine, and dentistry. The aim of this review is to highlight the major milestones in proteomics in dentistry during the last fifteen years. Human oral cavity contains hard and soft tissues and various biofluids including saliva and crevicular fluid. Proteomics has brought revolution in dentistry by helping in the early diagnosis of various diseases identified by the detection of numerous biomarkers present in the oral fluids. This paper covers the role of proteomics tools for the analysis of oral tissues. In addition, dental materials proteomics and their future directions are discussed.
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DOI: 10.3390/ijms17050728
PubMed: 27187379
PubMed Central: 4881550
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Advances of Proteomic Sciences in Dentistry</title><author><name sortKey="Khurshid, Zohaib" sort="Khurshid, Zohaib" uniqKey="Khurshid Z" first="Zohaib" last="Khurshid">Zohaib Khurshid</name><affiliation><nlm:aff id="af1-ijms-17-00728">Department of Prosthodontics and Dental Materials, School of Dentistry, King Faisal University, Al-Hofuf 31982, Saudi Arabia;<email>drzohaibkhurshid@gmail.com</email></nlm:aff></affiliation></author><author><name sortKey="Zohaib, Sana" sort="Zohaib, Sana" uniqKey="Zohaib S" first="Sana" last="Zohaib">Sana Zohaib</name><affiliation><nlm:aff id="af2-ijms-17-00728">Department of Biomedical Engineering, College of Engineering, King Faisal University, Al-Hofuf 31982, Saudi Arabia;<email>szohaib@kfu.edu.sa</email> (S.Z.);<email>rimtiaz@kfu.edu.sa</email> (R.R.)</nlm:aff></affiliation></author><author><name sortKey="Najeeb, Shariq" sort="Najeeb, Shariq" uniqKey="Najeeb S" first="Shariq" last="Najeeb">Shariq Najeeb</name><affiliation><nlm:aff id="af3-ijms-17-00728">Department of Restorative Dental Sciences, Al Farabi Colleges, Riyadh 11313, Saudi Arabia;<email>shariqnajeeb@gmail.com</email></nlm:aff></affiliation></author><author><name sortKey="Zafar, Muhammad Sohail" sort="Zafar, Muhammad Sohail" uniqKey="Zafar M" first="Muhammad Sohail" last="Zafar">Muhammad Sohail Zafar</name><affiliation><nlm:aff id="af4-ijms-17-00728">Department of Restorative Dentistry, College of Dentistry, Taibah University, Madina Munawwarrah 41311, Saudi Arabia;<email>MZAFAR@taibahu.edu.sa</email></nlm:aff></affiliation></author><author><name sortKey="Rehman, Rabia" sort="Rehman, Rabia" uniqKey="Rehman R" first="Rabia" last="Rehman">Rabia Rehman</name><affiliation><nlm:aff id="af2-ijms-17-00728">Department of Biomedical Engineering, College of Engineering, King Faisal University, Al-Hofuf 31982, Saudi Arabia;<email>szohaib@kfu.edu.sa</email> (S.Z.);<email>rimtiaz@kfu.edu.sa</email> (R.R.)</nlm:aff></affiliation></author><author><name sortKey="Rehman, Ihtesham Ur" sort="Rehman, Ihtesham Ur" uniqKey="Rehman I" first="Ihtesham Ur" last="Rehman">Ihtesham Ur Rehman</name><affiliation><nlm:aff id="af5-ijms-17-00728">Department of Materials Science and Engineering, The Kroto Research Institute, The University of Sheffield, North Campus, Broad Lane, Sheffield S3 7HQ, UK</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27187379</idno><idno type="pmc">4881550</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4881550</idno><idno type="RBID">PMC:4881550</idno><idno type="doi">10.3390/ijms17050728</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000798</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000798</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Advances of Proteomic Sciences in Dentistry</title><author><name sortKey="Khurshid, Zohaib" sort="Khurshid, Zohaib" uniqKey="Khurshid Z" first="Zohaib" last="Khurshid">Zohaib Khurshid</name><affiliation><nlm:aff id="af1-ijms-17-00728">Department of Prosthodontics and Dental Materials, School of Dentistry, King Faisal University, Al-Hofuf 31982, Saudi Arabia;<email>drzohaibkhurshid@gmail.com</email></nlm:aff></affiliation></author><author><name sortKey="Zohaib, Sana" sort="Zohaib, Sana" uniqKey="Zohaib S" first="Sana" last="Zohaib">Sana Zohaib</name><affiliation><nlm:aff id="af2-ijms-17-00728">Department of Biomedical Engineering, College of Engineering, King Faisal University, Al-Hofuf 31982, Saudi Arabia;<email>szohaib@kfu.edu.sa</email> (S.Z.);<email>rimtiaz@kfu.edu.sa</email> (R.R.)</nlm:aff></affiliation></author><author><name sortKey="Najeeb, Shariq" sort="Najeeb, Shariq" uniqKey="Najeeb S" first="Shariq" last="Najeeb">Shariq Najeeb</name><affiliation><nlm:aff id="af3-ijms-17-00728">Department of Restorative Dental Sciences, Al Farabi Colleges, Riyadh 11313, Saudi Arabia;<email>shariqnajeeb@gmail.com</email></nlm:aff></affiliation></author><author><name sortKey="Zafar, Muhammad Sohail" sort="Zafar, Muhammad Sohail" uniqKey="Zafar M" first="Muhammad Sohail" last="Zafar">Muhammad Sohail Zafar</name><affiliation><nlm:aff id="af4-ijms-17-00728">Department of Restorative Dentistry, College of Dentistry, Taibah University, Madina Munawwarrah 41311, Saudi Arabia;<email>MZAFAR@taibahu.edu.sa</email></nlm:aff></affiliation></author><author><name sortKey="Rehman, Rabia" sort="Rehman, Rabia" uniqKey="Rehman R" first="Rabia" last="Rehman">Rabia Rehman</name><affiliation><nlm:aff id="af2-ijms-17-00728">Department of Biomedical Engineering, College of Engineering, King Faisal University, Al-Hofuf 31982, Saudi Arabia;<email>szohaib@kfu.edu.sa</email> (S.Z.);<email>rimtiaz@kfu.edu.sa</email> (R.R.)</nlm:aff></affiliation></author><author><name sortKey="Rehman, Ihtesham Ur" sort="Rehman, Ihtesham Ur" uniqKey="Rehman I" first="Ihtesham Ur" last="Rehman">Ihtesham Ur Rehman</name><affiliation><nlm:aff id="af5-ijms-17-00728">Department of Materials Science and Engineering, The Kroto Research Institute, The University of Sheffield, North Campus, Broad Lane, Sheffield S3 7HQ, UK</nlm:aff></affiliation></author></analytic><series><title level="j">International Journal of Molecular Sciences</title><idno type="eISSN">1422-0067</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Applications of proteomics tools revolutionized various biomedical disciplines such as genetics, molecular biology, medicine, and dentistry. The aim of this review is to highlight the major milestones in proteomics in dentistry during the last fifteen years. Human oral cavity contains hard and soft tissues and various biofluids including saliva and crevicular fluid. Proteomics has brought revolution in dentistry by helping in the early diagnosis of various diseases identified by the detection of numerous biomarkers present in the oral fluids. This paper covers the role of proteomics tools for the analysis of oral tissues. In addition, dental materials proteomics and their future directions are discussed.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bhattacharyya, M" uniqKey="Bhattacharyya M">M. Bhattacharyya</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Alberts, B" uniqKey="Alberts B">B. Alberts</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Murzin, A G" uniqKey="Murzin A">A.G. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Int J Mol Sci</journal-id><journal-id journal-id-type="iso-abbrev">Int J Mol Sci</journal-id><journal-id journal-id-type="publisher-id">ijms</journal-id><journal-title-group><journal-title>International Journal of Molecular Sciences</journal-title></journal-title-group><issn pub-type="epub">1422-0067</issn><publisher><publisher-name>MDPI</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">27187379</article-id><article-id pub-id-type="pmc">4881550</article-id><article-id pub-id-type="doi">10.3390/ijms17050728</article-id><article-id pub-id-type="publisher-id">ijms-17-00728</article-id><article-categories><subj-group subj-group-type="heading"><subject>Review</subject></subj-group></article-categories><title-group><article-title>Advances of Proteomic Sciences in Dentistry</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Khurshid</surname><given-names>Zohaib</given-names></name><xref ref-type="aff" rid="af1-ijms-17-00728">1</xref></contrib><contrib contrib-type="author"><name><surname>Zohaib</surname><given-names>Sana</given-names></name><xref ref-type="aff" rid="af2-ijms-17-00728">2</xref></contrib><contrib contrib-type="author"><name><surname>Najeeb</surname><given-names>Shariq</given-names></name><xref ref-type="aff" rid="af3-ijms-17-00728">3</xref></contrib><contrib contrib-type="author"><name><surname>Zafar</surname><given-names>Muhammad Sohail</given-names></name><xref ref-type="aff" rid="af4-ijms-17-00728">4</xref></contrib><contrib contrib-type="author"><name><surname>Rehman</surname><given-names>Rabia</given-names></name><xref ref-type="aff" rid="af2-ijms-17-00728">2</xref></contrib><contrib contrib-type="author"><name><surname>Rehman</surname><given-names>Ihtesham Ur</given-names></name><xref ref-type="aff" rid="af5-ijms-17-00728">5</xref><xref rid="c1-ijms-17-00728" ref-type="corresp">*</xref></contrib></contrib-group><contrib-group><contrib contrib-type="editor"><name><surname>Rahaman</surname><given-names>Mohamed N.</given-names></name><role>Academic Editor</role></contrib></contrib-group><aff id="af1-ijms-17-00728"><label>1</label>Department of Prosthodontics and Dental Materials, School of Dentistry, King Faisal University, Al-Hofuf 31982, Saudi Arabia;<email>drzohaibkhurshid@gmail.com</email></aff><aff id="af2-ijms-17-00728"><label>2</label>Department of Biomedical Engineering, College of Engineering, King Faisal University, Al-Hofuf 31982, Saudi Arabia;<email>szohaib@kfu.edu.sa</email> (S.Z.);<email>rimtiaz@kfu.edu.sa</email> (R.R.)</aff><aff id="af3-ijms-17-00728"><label>3</label>Department of Restorative Dental Sciences, Al Farabi Colleges, Riyadh 11313, Saudi Arabia;<email>shariqnajeeb@gmail.com</email></aff><aff id="af4-ijms-17-00728"><label>4</label>Department of Restorative Dentistry, College of Dentistry, Taibah University, Madina Munawwarrah 41311, Saudi Arabia;<email>MZAFAR@taibahu.edu.sa</email></aff><aff id="af5-ijms-17-00728"><label>5</label>Department of Materials Science and Engineering, The Kroto Research Institute, The University of Sheffield, North Campus, Broad Lane, Sheffield S3 7HQ, UK</aff><author-notes><corresp id="c1-ijms-17-00728"><label>*</label>Correspondence: <email>i.u.rehman@sheffield.ac.uk</email>; Tel.: +44-114-222-5946; Fax: +44-114-222-5945</corresp></author-notes><pub-date pub-type="epub"><day>13</day><month>5</month><year>2016</year></pub-date><pub-date pub-type="collection"><month>5</month><year>2016</year></pub-date><volume>17</volume><issue>5</issue><elocation-id>728</elocation-id><history><date date-type="received"><day>18</day><month>4</month><year>2016</year></date><date date-type="accepted"><day>09</day><month>5</month><year>2016</year></date></history><permissions><copyright-statement>© 2016 by the authors; licensee MDPI, Basel, Switzerland.</copyright-statement><copyright-year>2016</copyright-year><license><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC-BY) license (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>).</license-p></license></permissions><abstract><p>Applications of proteomics tools revolutionized various biomedical disciplines such as genetics, molecular biology, medicine, and dentistry. The aim of this review is to highlight the major milestones in proteomics in dentistry during the last fifteen years. Human oral cavity contains hard and soft tissues and various biofluids including saliva and crevicular fluid. Proteomics has brought revolution in dentistry by helping in the early diagnosis of various diseases identified by the detection of numerous biomarkers present in the oral fluids. This paper covers the role of proteomics tools for the analysis of oral tissues. In addition, dental materials proteomics and their future directions are discussed.</p></abstract><kwd-group><kwd>proteomics</kwd><kwd>dentistry</kwd><kwd>enamel</kwd><kwd>dentin</kwd><kwd>saliva</kwd><kwd>gingival crevicular fluids and dental materials</kwd></kwd-group></article-meta></front><body><sec id="sec1-ijms-17-00728"><title>1. Introduction</title><p>Every living thing contains fascinating molecules called proteins [<xref rid="B1-ijms-17-00728" ref-type="bibr">1</xref>]. Proteins are building blocks for the living matrix and perform various functions [<xref rid="B2-ijms-17-00728" ref-type="bibr">2</xref>]. The human body contains a number of different proteins which are structural, catalytic, regulatory, transport and storage, and transducer proteins. Each of these proteins plays a specific functional role [<xref rid="B3-ijms-17-00728" ref-type="bibr">3</xref>]. Proteins belong to biological macromolecules that exist as three-dimensional structures because of the sequences involving the twenty different amino acids [<xref rid="B4-ijms-17-00728" ref-type="bibr">4</xref>,<xref rid="B5-ijms-17-00728" ref-type="bibr">5</xref>]. These amino acids are linked with each other by peptide bonds. The word “proteome”, first coined by Mark Wilkins in 1961, is used to describe a mixture of proteins [<xref rid="B6-ijms-17-00728" ref-type="bibr">6</xref>]. All proteomes arise from mRNA and can be used to describe a cell’s protein content [<xref rid="B7-ijms-17-00728" ref-type="bibr">7</xref>]. In simple terms, proteomics is the study of the distribution and interaction of proteins in time and space in a cell, organisms, or an ecosystem. In recent years, a number of proteomical studies on human body fluid and tissues (diseased and non-diseased) have been carried out by several researchers to analyze the chemistry in order to understand the life processes at the molecular as well as the cellular levels [<xref rid="B8-ijms-17-00728" ref-type="bibr">8</xref>,<xref rid="B9-ijms-17-00728" ref-type="bibr">9</xref>].</p><p>Proteomic tools have the ability to analyze human body samples such as blood, saliva, serums, urine, cervico-vaginal fluid (CVF), sperm cells, gingival crevicular fluids (GCF), microorganisms, and different tissues (enamel, dentine, cementum, pulp, gingiva, bone ligaments, stem cells, and mucosa) in both pathological and normal physiological states [<xref rid="B10-ijms-17-00728" ref-type="bibr">10</xref>,<xref rid="B11-ijms-17-00728" ref-type="bibr">11</xref>,<xref rid="B12-ijms-17-00728" ref-type="bibr">12</xref>]. Quite a few studies have reported the analysis of dental tissues by means of proteomic tools. Approximately, 64% of human oral tissues samples have been studied for proteomics analysis as compared to 11% of animal dental tissues which signifies the clinical importance of proteomics [<xref rid="B13-ijms-17-00728" ref-type="bibr">13</xref>]. A number of studies have explored human saliva due to its ease of accessibility and non-invasive method of collection. A significant number of studies (30%) have explored the salivary proteome during oral pathological conditions e.g., caries, periodontitis, gingivitis, dental abscess, endodontic lesions, and oral carcinomas [<xref rid="B14-ijms-17-00728" ref-type="bibr">14</xref>]. Two methods exist to conduct proteomics of body fluids. In top down proteomics, intact proteins are analyzed by Electrospray Ionization (ESI) or Matrix-Assisted Laser Desorption/Ionization (MALDI) and the peptides are generated by a gas phase fragmentation method [<xref rid="B15-ijms-17-00728" ref-type="bibr">15</xref>]. In contrast, bottom-up approach of proteomics is commonly used to analyze peptides produced through chemical or enzymatic cleavage of proteins, and with post-translational modification as well as through liquid chromatography (LC) in conjunction with mass spectrometry (MS). The bottom-up analysis, the more conventional method, has been sometimes also called “shotgun proteomics” [<xref rid="B16-ijms-17-00728" ref-type="bibr">16</xref>]. Both approaches are commonly used in proteomics procedures utilizing mass spectrometry.</p><p><xref ref-type="table" rid="ijms-17-00728-t001">Table 1</xref> presents a description of proteomics studies carried out on whole mouth saliva (WS), unstimulated whole mouth saliva (USWS) parotid gland secretions, submandibular and sublingual gland secretions, salivary gland ductal secretions, enamel, dentine, pulp tissues, gingival crevicular fluid (GCF), cementum, alveolar bone, periodontal fibers (PDL), and dental materials through top-down and bottom up approaches.</p><p>Recent developments in dental proteomic have helped uncover previously unknown details regarding the unique protein structures and their function for the diagnosis, defense mechanisms, and regeneration of dental tissues, tissue calcification, and repairing of dental tissues [<xref rid="B40-ijms-17-00728" ref-type="bibr">40</xref>]. The aim of this paper is to elaborate on the currently available techniques, their reported applications for dental tissues. Furthermore, the current status of dental proteomical analysis and the discovered biomarkers is discussed in detail.</p></sec><sec id="sec2-ijms-17-00728"><title>2. Dental Hard Tissue Proteomics</title><p>The tooth is the strongest calcified tissue of the human body due to its special architecture and compositions. It is composed of three distinct mineralized hard tissues: enamel, dentine, and cementum. Enamel is the hardest tissue of the human body and contains 96% minerals, 1% proteins and the remainder being water. The adequate mechanical properties of enamel suit its primary function: mastication of food. Enamel, the only dental hard tissue formed before eruption of teeth, is formed by cells called ameloblasts. Histologically, the inorganic component of enamel is composed of micro-rods and inter-rods of hydroxyapatite (HA) crystals embedded in protein matrix, the organic phase [<xref rid="B41-ijms-17-00728" ref-type="bibr">41</xref>]. To date, the major enamel proteins that have been recognized are amelogenin, ameloblastin, enamelin, and tuftelin [<xref rid="B42-ijms-17-00728" ref-type="bibr">42</xref>]. Additionally, a total of 42 proteins has been identified during enamel formation (secretory phase and maturation phase) by two dimensional electrophoresis (2-DE) and MS. These proteins include ERp29 which is involved in secretory protein synthesis and calcium binding protein (calbindin) and play a role in tooth maturation [<xref rid="B43-ijms-17-00728" ref-type="bibr">43</xref>,<xref rid="B44-ijms-17-00728" ref-type="bibr">44</xref>,<xref rid="B45-ijms-17-00728" ref-type="bibr">45</xref>,<xref rid="B46-ijms-17-00728" ref-type="bibr">46</xref>]. It has been concluded that amelogenin takes part in enamel formation and cementum development by guiding cells. It also regulates initiation and growth of HA crystals during the mineralization front across the carboxyl terminals [<xref rid="B47-ijms-17-00728" ref-type="bibr">47</xref>,<xref rid="B48-ijms-17-00728" ref-type="bibr">48</xref>]. Very recently, a novel organic protein containing enamel matrix was reported in an adult human tooth with thickness of 100–400 µm which could provide important protein transportation or biochemical linkage between enamel and dentin [<xref rid="B49-ijms-17-00728" ref-type="bibr">49</xref>]. Ameloblasts secrete enamel specific extracellular matrix protein called ameloblastin and its expression is also detected during the initial development of craniofacial bones and dental hard tissues of mesenchymal origin [<xref rid="B50-ijms-17-00728" ref-type="bibr">50</xref>]. The precise role of ameloblastin is not known but it has been hypothesized that it may control the enamel mineralization process during tooth development alongside growth of enamel mineral crystals [<xref rid="B51-ijms-17-00728" ref-type="bibr">51</xref>].</p><p>The bulk structure of a tooth is made from dentin which possesses neurogenic and regenerative capabilities. By weight, dentin contains 70% minerals (mainly hydroxyapatite), 20% organic component, and 10% water. In proteomics, dentin has been particularly found useful for the identification of collagenous and non-collagenous proteins [<xref rid="B52-ijms-17-00728" ref-type="bibr">52</xref>]. Its formation and biomineralization (dentinogenesis) is dynamically complex. Odontoblasts develop and secrete extracellular matrix followed by mineralization in an organized fashion [<xref rid="B53-ijms-17-00728" ref-type="bibr">53</xref>]. Most abundant collagenous proteins present in dentin matrix are collagen (type I, III, V, VI, and XII) providing a three dimensional (3D) template for the mineralization of apatite crystals. Fibronectin and matrix metalloproteinase (MMP) 2, 9, and 20 are associated with predentin collagen fibrils [<xref rid="B36-ijms-17-00728" ref-type="bibr">36</xref>]. Park <italic>et al.</italic> [<xref rid="B36-ijms-17-00728" ref-type="bibr">36</xref>] performed Sodium-Dodecyl-Sulfate-Polyacrylamide Gel Electrophoresis (SDS-PAGE) followed by an LC-MS/MS method for identifying dentin proteins. The outcome of these experiments revealed the presence of 233 proteins and was confirmed using Western blot technique and immunohistochemical staining. This study was the first to provide dentin protein classification such as: metabolic enzymes, signal transduction, cellular organization, transport, immune response, transcription factor activity, cell growth/maintenance, chaperone/stress response, nucleic acid binding, and unknowns function. Another study reported by Jagr <italic>et al.</italic> [<xref rid="B54-ijms-17-00728" ref-type="bibr">54</xref>], 2-DE and nano-LC-MS/MS was used to identify 289 proteins overall of which 90 had been previously unknown. In this study nine novel proteins were identified and were classified as immunoglobulins which help in the formation of extracellular matrix, formation of the cytoskeleton, cell adhesion molecule activity, cytoskeleton protein binding, immune responses, and peptidase activity. These findings may provide deep insight for the regenerative and rehabilitation of dental tissues. Moreover, only a few studies reported the proteomics analysis of cementum and alveolar bone. A total of 235 and 213 proteins have been recognized in the alveolar bone and cementum respectively using LC-MS/MS with LTQ-FT (Ultra) due to their high resolution and high accuracy [<xref rid="B33-ijms-17-00728" ref-type="bibr">33</xref>]. Previously, proteins including osteocalcin (BGLAP), TNN, FN, VIM, CHAD, vitronectin VTN, and LUM were identified as non-collagenous extracellular proteins in cementum and alveolar bone [<xref rid="B55-ijms-17-00728" ref-type="bibr">55</xref>,<xref rid="B56-ijms-17-00728" ref-type="bibr">56</xref>,<xref rid="B57-ijms-17-00728" ref-type="bibr">57</xref>].</p></sec><sec id="sec3-ijms-17-00728"><title>3. Oral Fluid Proteomics</title><p>Compared to dental hard tissues, whole mouth saliva (WMS) and GCF have been studied more for proteomical analysis due to their non-invasive collection technique, minimal patient discomfort and anxiety as compare to blood collection for serum or plasma [<xref rid="B14-ijms-17-00728" ref-type="bibr">14</xref>]. WMS is not only composed of major and minor salivary glands secretions but also contains mucosal transudates from all surfaces of the mouth, lymphoid tissues, oropharynx, and GCFs [<xref rid="B58-ijms-17-00728" ref-type="bibr">58</xref>]. Proteomics studies on human saliva revealed 1000 plus proteins and peptides (<xref ref-type="fig" rid="ijms-17-00728-f001">Figure 1</xref>).</p><p>Numerous studies have been conducted on WMS to evaluate various body physiological and pathological conditions and have proven it as a diagnostic as well as a maintenance test fluid. The WMS was isolated from different diseases such as dental caries, Sjögren’s syndrome, diabetic patients, breast cancer patients, squamous cell carcinoma patients, and graft-versus-host disease patients. The WMS has been analyzed successfully by proteomical tools (electrophorically and chromatographically) [<xref rid="B59-ijms-17-00728" ref-type="bibr">59</xref>,<xref rid="B60-ijms-17-00728" ref-type="bibr">60</xref>,<xref rid="B61-ijms-17-00728" ref-type="bibr">61</xref>,<xref rid="B62-ijms-17-00728" ref-type="bibr">62</xref>].</p><p>Human gingival crevicular fluid (GCF) has been analyzed extensively. GCF has a variable protein composition based on periodontal health and diseases. GCF contains serum transudate (found in gingival sulcus), broken products of host epithelial or connective tissues, subgingival microbial plaque, extracellular proteins, host inflammatory mediators and cells [<xref rid="B63-ijms-17-00728" ref-type="bibr">63</xref>]. GCF provides medium for the transportation of bacterial byproducts into the periodontal microenvironment and also helps to drive off host derived products [<xref rid="B64-ijms-17-00728" ref-type="bibr">64</xref>]. It has been reported that GCF volume for biochemical and proteomics analysis is limited due to severity of tissue inflammation [<xref rid="B65-ijms-17-00728" ref-type="bibr">65</xref>]. Many methods are available for the collection of GCF such as paper strips, capillary tubes, gingival wash, and paper cones [<xref rid="B63-ijms-17-00728" ref-type="bibr">63</xref>]. In the last decade researchers have favored using paper strip in their research work due to easy insertion into the gingival crevice up to 1 mm of depth without bleeding from periodontal pockets [<xref rid="B35-ijms-17-00728" ref-type="bibr">35</xref>]. After collection of the GCF sample it goes through different steps for proteomics analysis, as illustrated in <xref ref-type="fig" rid="ijms-17-00728-f002">Figure 2</xref>.</p><p>Variety of proteolytic enzymes are identified in GCF, such as collagenase, elastase, and cathepsin B, D, H, and L [<xref rid="B66-ijms-17-00728" ref-type="bibr">66</xref>]. These proteolytic enzymes have been reported as destructors of periodontal tissues and have the capability to degrade type-I collagen and glycoproteins [<xref rid="B67-ijms-17-00728" ref-type="bibr">67</xref>]. <xref ref-type="table" rid="ijms-17-00728-t002">Table 2</xref> describes detailed profiling of GCF proteins, proteomic tools used, and the number of proteins identified. Most commonly reported identified proteins from GCF are actin, keratins, histones, annexins, proteins S100-A9, apolipoprotein A-1, albumin, salivary gland antimicrobial peptides (histatins, HNP-1, -2 & -3, LL-37, statherin), and cystatin B [<xref rid="B68-ijms-17-00728" ref-type="bibr">68</xref>,<xref rid="B69-ijms-17-00728" ref-type="bibr">69</xref>]. Some immune related proteins present in GCF such as; Ig γ-1 chain C region, Ig γ-3 chain C region, lactoferroxin-C, leukocyte elastase inhibitor, α 1 antitrypsin, heat shock protein β-1, and coronin-1A [<xref rid="B70-ijms-17-00728" ref-type="bibr">70</xref>].</p><p>A protein based oral biofilm, the acquired enamel pellicle (AEP), is formed on tooth surfaces within seconds after mechanical cleaning of the tooth surfaces [<xref rid="B75-ijms-17-00728" ref-type="bibr">75</xref>]. It consists predominantly of proteins secreted from major and minor salivary glands, carbohydrates, ions, exogenous proteins, and lipids [<xref rid="B76-ijms-17-00728" ref-type="bibr">76</xref>]. Lee and co-workers investigated AEP layer on enamel and quantified 50 proteins through Liquid Chromatography- Electrospray Ionization-Mass Spectrometry(LC-ESI-MS/MS) [<xref rid="B77-ijms-17-00728" ref-type="bibr">77</xref>]. This layer amount is approximately 0.5–1 µg per tooth surface and its formation is crucial and the dynamic process is influenced by many factors such as; circadian cycle, biochemical properties of tooth surfaces, proteolytic capacity of the oral micro environment, and the oral microbiota [<xref rid="B78-ijms-17-00728" ref-type="bibr">78</xref>]. The fatty acids (FAs) identified in AEP play an essential role in the pellicle formation, bacterial adhesion and protection against pellicle [<xref rid="B79-ijms-17-00728" ref-type="bibr">79</xref>]. <italic>In-situ</italic> study reveals qualitatively and quantitatively a wide range of FAs (C<sub>12</sub>–C<sub>24</sub>) through gas-chromatography- electrospray ionization/ mass spectrometry (GC-EI/MS), in this study pellicle were formed <italic>in-situ</italic> on bovine enamel slabs mounted on upper jaw splints and inserted in the mouth of 10 subjects for 3–240 min. Several methods have been used for the collection of AEP over the last four decades e.g., palatal appliances, chemical solubilization techniques, mechanical techniques and soaked membranes method [<xref rid="B80-ijms-17-00728" ref-type="bibr">80</xref>]. All these methods reported different compositions due to different routes of collection. Mayhall <italic>et al.</italic> [<xref rid="B81-ijms-17-00728" ref-type="bibr">81</xref>] remounted freshly extracted discs of teeth crowns in a palatal appliance worn by the subject for 1 h. After AEP formation on the specimens, they dipped the appliances in 2% HCl and detected glutamic acid, serine, and glycine but a low amount of proline [<xref rid="B81-ijms-17-00728" ref-type="bibr">81</xref>]. In another <italic>in vivo</italic> study on AEP composition it revealed a high level of glutamic acid and alanine but a significant amount of hexosamines. This study also determined that a different approach of AEP collection varies the composition of AEP [<xref rid="B82-ijms-17-00728" ref-type="bibr">82</xref>]. AEP has many function in the oral cavity such as lubrication, regulation of mineral homeostasis, providing defense against microbes and microbial colonization through specific receptors. Siqueira <italic>et al.</italic> [<xref rid="B75-ijms-17-00728" ref-type="bibr">75</xref>] identified 100 plus proteins and peptides from <italic>in vivo</italic> AEP, and suggested that all play an active role in maintaining oral health. Similarly, histatin peptide has shown protective mechanism against demineralization of the tooth [<xref rid="B83-ijms-17-00728" ref-type="bibr">83</xref>]. A total of 130 proteins were identified from AEP using LC-ESI-MS/MS with high confidence which allowed the classification of AEP proteins according to nature of origin, chemical properties, and biological function as shown in <xref ref-type="fig" rid="ijms-17-00728-f003">Figure 3</xref> [<xref rid="B39-ijms-17-00728" ref-type="bibr">39</xref>]. Very recently, another group of researchers has identified 76 proteins from <italic>in vivo</italic> AEP present on deciduous teeth through mass spectrometry which opens up a diagnostic frontier in pediatric dentistry [<xref rid="B84-ijms-17-00728" ref-type="bibr">84</xref>].</p></sec><sec id="sec4-ijms-17-00728"><title>4. Dental Soft Tissue Proteomics</title><p>This dental pulp is a soft connective tissue that is composed of cells (mesenchymal, odontoblasts, fibroblasts) neural fibers, blood vessels, and lymphatics [<xref rid="B85-ijms-17-00728" ref-type="bibr">85</xref>]. Tooth development, nourishment, sensitivity, defense reactions, repair, and regeneration are the main functions of dental pulp [<xref rid="B86-ijms-17-00728" ref-type="bibr">86</xref>]. Its unique composition helps in nutrition as well as sensation for external stimuli [<xref rid="B87-ijms-17-00728" ref-type="bibr">87</xref>]. Robertson <italic>et al.</italic> [<xref rid="B88-ijms-17-00728" ref-type="bibr">88</xref>] investigated the calcification response from dental pulp against various external stimuli including dental trauma, caries, abrasion or attrition, and tooth retransplantation. Similarly, Yamazoe <italic>et al.</italic> [<xref rid="B89-ijms-17-00728" ref-type="bibr">89</xref>] harvested dental pulp cells in subcutaneous tissues and analyzed its calcified tissues through proteomics. The reason behind this is that stem cells have the potential to form deciduous or permanent pulp cells. In the last decade, dental pulp stem cells have proven value in repairing dentin-pulp complex [<xref rid="B90-ijms-17-00728" ref-type="bibr">90</xref>]. Dental pulp contains unique tissue specific proteins and small leucine-rich proteoglycans (biglycan, lumican, and mimecan) [<xref rid="B91-ijms-17-00728" ref-type="bibr">91</xref>]. Pääkkönen <italic>et al.</italic> [<xref rid="B92-ijms-17-00728" ref-type="bibr">92</xref>] analyzed gene and protein expression in healthy and carious dental pulp organs for the first time using cDNA microarray and 2D-gel electrophoresis. In their study, slight expression changes were reported due to the high amount of healthy pulp in both conditions. In addition, a total of 96 proteins were identified through 2-DE gel followed by MS/MS techniques. In the same experiment, cDNA microarrays explored the difference of gene expression in carious tissues and no gene differences were detected in 96 detected proteins. In another <italic>in vitro</italic> study on proteome mapping of odontoblasts-like dental pulp revealed 23 total proteins by 2-DE gel followed by MS [<xref rid="B93-ijms-17-00728" ref-type="bibr">93</xref>]. These proteins are comprised of various types of peptides such as cell membrane bound molecules, cytoskeleton, and nuclear proteins and are involved in matrix synthesis and enzyme metabolism. The expression of various recognized proteins (annexin VI, heteronuclear ribonuclear proteins C, collagen type VI, matrilin-2) were confirmed using western blotting (WB) technique and real time- polymerase chain reaction (RT-PCR) analysis. The RNA amplification technique was successfully used to analyze gene expression and protein encoding linked to physiology of dental pulp. Microarray analysis disclosed a total of 362 genes related to pulp expression specifically hence, further classified as protoncogenes, tooth morphogenesis, genes of collagen, DNAse, metallopeptidases, and growth factors [<xref rid="B94-ijms-17-00728" ref-type="bibr">94</xref>]. McLachlan <italic>et al.</italic> [<xref rid="B95-ijms-17-00728" ref-type="bibr">95</xref>] studied dental pulp tissues for detailed characterization and molecular changes due to dental caries. A total of 445 genes were identified with two fold or greater difference in the expression level. At least 85 genes were reported abundant in health and 360 more abundant in disease suggesting that this approach may contribute to improved future diagnosis and treatment. Another comprehensive study on human tooth pulp was done by 2D-gel electrophoresis followed by nano-liquid chromatography tandem mass spectrometry (LC/MS). This approach detected 342 proteins in total with a high confidence, and two proteins were distinguished in human samples [<xref rid="B37-ijms-17-00728" ref-type="bibr">37</xref>]. Very recently, Eckhard <italic>et al.</italic> [<xref rid="B96-ijms-17-00728" ref-type="bibr">96</xref>] attempted in depth dental pulp proteome with N-Terminome by the help of the terminal amine isotropic labelling of substrates (TAILS) approach and identified 17 missing protein candidates for the Chromosome-centric Human Proteome Project (C-HPP; <uri xlink:type="simple" xlink:href="www.c-hpp.og">www.c-hpp.og</uri>). Missing proteins can be defined as proteins that show only transcriptomic evidences and an expected sequence (or suggested by homology) or partly detected proteins. Furthermore, there are transcript evidences for the survival of the corresponding proteins available without conclusive mass spectrometry data [<xref rid="B97-ijms-17-00728" ref-type="bibr">97</xref>].</p><p>Periodontal ligament (PDL) is another fibrous connective tissue containing heterogeneous cell population and type 1collagen fibers abundantly. They play a key role in maintaining PDL space, homeostasis, and anchorage, as well as maintaining and providing regeneration or repair of periodontium in response to disease and mechanical trauma. Only a few studies reported on PDL cellular components at genomics and proteomics level but it is very essential to understand the unique features and functions. Reichenberg <italic>et al.</italic> [<xref rid="B38-ijms-17-00728" ref-type="bibr">38</xref>] reported a first study on periodontal ligament (PDL) fibroblast proteome for understanding physiology and regulation of PDL and identifying disease related protein markers. In this study 900 spots were detected and 117 proteins spot identified with 74 different genes. In another study on exploring the early osteogenic differential protein-profile in human PDL cells [<xref rid="B98-ijms-17-00728" ref-type="bibr">98</xref>], 29 differentially expressed proteins during osteogenic differentiations were reported [<xref rid="B98-ijms-17-00728" ref-type="bibr">98</xref>] which have been primarily linked to the cell membrane-binding, cytoskeleton, nuclear regulations, matrix synthesis signal conduction and metabolic enzymes [<xref rid="B99-ijms-17-00728" ref-type="bibr">99</xref>]. Proteomics may shed light on these complex functional details of these intra- and inter-cellular processes.</p></sec><sec id="sec5-ijms-17-00728"><title>5. Dental Materials Proteomics</title><p>Concurrent application of genomics and proteomics have revolutionized dentistry by allowing the identification and characterization of oral tissues (soft, hard, and liquid), and also help in understanding them on the molecular level [<xref rid="B10-ijms-17-00728" ref-type="bibr">10</xref>]. By definition, dental materials are those materials or devices which interact with the oral environment in physio-chemical, mechanical, and biological aspects [<xref rid="B100-ijms-17-00728" ref-type="bibr">100</xref>,<xref rid="B101-ijms-17-00728" ref-type="bibr">101</xref>,<xref rid="B102-ijms-17-00728" ref-type="bibr">102</xref>,<xref rid="B103-ijms-17-00728" ref-type="bibr">103</xref>,<xref rid="B104-ijms-17-00728" ref-type="bibr">104</xref>,<xref rid="B105-ijms-17-00728" ref-type="bibr">105</xref>,<xref rid="B106-ijms-17-00728" ref-type="bibr">106</xref>]. Hence, dental materials should be biocompatible and interact without causing any toxicity. Many approaches have been used previously to analyze the success of dental materials and failure at a cellular level. Very recently, Ryta <italic>et al.</italic> [<xref rid="B107-ijms-17-00728" ref-type="bibr">107</xref>] studied elution of unreacted triethylene glycol dimethacrylate (TEGDMA) from Smart Dentine Replacement (SDR™), Dentsply International, UK bulk-fill dental composite by using HPLC. In this study, polymerized specimens were treated with four solutions (100% ethanol, 75% ethanol, distilled water, and 100% methanol) with different concentration to evaluate direct dental pulp toxicity of unreacted TEGDMA monomer. It was confirmed through HPLC that the toxicity of unreacted TEGDMA towards dental pulp established during the first hour after the placement of resin. Dental adhesive systems were analyzed by a research group for the quantification of monomer elution and carbon–carbon double bonds in dental adhesive system using reverse-phase HPLC, and observed that no correlation exists between the resin dentin bonding of adhesives and the elution of unreacted monomers [<xref rid="B108-ijms-17-00728" ref-type="bibr">108</xref>]. However, further proteomic analysis of materials on the molecular level is needed to understand the changes in proteomes of failed or successful implants. Some of the studies reported in the last decade on proteomics of dental materials are listed in <xref ref-type="table" rid="ijms-17-00728-t003">Table 3</xref>.</p></sec><sec id="sec6-ijms-17-00728"><title>6. Conclusions</title><p>With the help of “omics” (genomics, transcriptomics, proteomics, metabolomics, and metagenomics) many hidden compositions, behavior and metabolisms of dental tissues and oral fluids have been analyzed in the last fifteen years. These scientific disciplines helped the gathering of valuable information of the human proteome and will complete the Human Proteome Project (HPP) [<xref rid="B117-ijms-17-00728" ref-type="bibr">117</xref>]. Proteomics tools have provided remarkable information regarding dental tissues and oral fluids [<xref rid="B118-ijms-17-00728" ref-type="bibr">118</xref>]. The overall analysis on proteomics in dentistry shows that more studies directed toward structural formation, diagnosis, and pathogenesis but very limited studies on evaluation of treatment, prevention of diseases, and prognosis of interventions. To sum up, all proteomic tools can help to fill the gaps of the unexplored aspects of oral health and dental sciences.</p></sec></body><back><notes><title>Author Contributions</title><p>Zohaib Khurshid performed the literature search, wrote the manuscript. The information to create <xref ref-type="table" rid="ijms-17-00728-t001">Table 1</xref> and <xref ref-type="table" rid="ijms-17-00728-t002">Table 2</xref> was done by Sana Zohaib. Shariq Najeeb helped in the development of all figures and also in manuscript write up. Muhammad Sohail Zafar and Rabia Rehman performed literature search, and helped in the compilation of <xref ref-type="table" rid="ijms-17-00728-t003">Table 3</xref>. Ihtesham Ur Rehman performed literature search, provide the guidelines in order to prepare the manuscript and finalized the manuscript.</p></notes><notes><title>Conflicts of Interest</title><p>The authors declare no conflict of interest.</p></notes><glossary><title>Abbreviations</title><array><tbody><tr><td align="left" valign="top" rowspan="1" colspan="1">BGLAP</td><td align="left" valign="top" rowspan="1" colspan="1">Bone Gamma Carboxyglutamate Protein</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">cDNA</td><td align="left" valign="top" rowspan="1" colspan="1">Complementary Deoxyribonucleic Acid</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">CHAD</td><td align="left" valign="top" rowspan="1" colspan="1">Chondroadherin</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">C-HPP</td><td align="left" valign="top" rowspan="1" colspan="1">Chromosome-Centric Human Proteome Project</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">CsA</td><td align="left" valign="top" rowspan="1" colspan="1">Cyclosporin A</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">DNAse</td><td align="left" valign="top" rowspan="1" colspan="1">Deoxyribonuclease</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">EMD</td><td align="left" valign="top" rowspan="1" colspan="1">Enamel Matrix Derivative</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">ESI</td><td align="left" valign="top" rowspan="1" colspan="1">Electrospray Ionization</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">FN</td><td align="left" valign="top" rowspan="1" colspan="1">Fibronectin</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">FNA</td><td align="left" valign="top" rowspan="1" colspan="1">Fine Needle Aspiration</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">HGF</td><td align="left" valign="top" rowspan="1" colspan="1">Hepatocyte Growth Factor</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">GCF</td><td align="left" valign="top" rowspan="1" colspan="1">Gingival Crevicular Fluid</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">GVHD</td><td align="left" valign="top" rowspan="1" colspan="1">Graft Versus Host Disease</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">HA</td><td align="left" valign="top" rowspan="1" colspan="1">Hydroxyapatite</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">HPP</td><td align="left" valign="top" rowspan="1" colspan="1">Human Proteome Project</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">LC/MS</td><td align="left" valign="top" rowspan="1" colspan="1">Liquid chromatography/mass spectrometry</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">LTQ-FT</td><td align="left" valign="top" rowspan="1" colspan="1">Linear Ion Trap Mass Spectrometer</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">LUM</td><td align="left" valign="top" rowspan="1" colspan="1">Lumican</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">mRNA</td><td align="left" valign="top" rowspan="1" colspan="1">messenger Ribonucleic Acid</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">MS</td><td align="left" valign="top" rowspan="1" colspan="1">Mass-Spectrometry</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">MALDI</td><td align="left" valign="top" rowspan="1" colspan="1">Matrix-Assisted Laser Desorption/Ionization</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">PDL</td><td align="left" valign="top" rowspan="1" colspan="1">Periodontal Ligament</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">PEEK</td><td align="left" valign="top" rowspan="1" colspan="1">Polyetheretherketone</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">R-PCR</td><td align="left" valign="top" rowspan="1" colspan="1">Realtime-Polymerase Chain Reaction</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">SDS-PAGE</td><td align="left" valign="top" rowspan="1" colspan="1">Sodium dodecyl sulfate polyacrylamide gel electrophoresis</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">TAILS</td><td align="left" valign="top" rowspan="1" colspan="1">Terminal Amine Isotropic Labelling of Substrates</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">TNN</td><td align="left" valign="top" rowspan="1" colspan="1">Tenascin</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">USWS</td><td align="left" valign="top" rowspan="1" colspan="1">Unstimulated Whole-Mouth Saliva</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">VIM</td><td align="left" valign="top" rowspan="1" colspan="1">Vimentin</td></tr><tr><td align="left" valign="top" rowspan="1" colspan="1">VTN</td><td align="left" valign="top" rowspan="1" 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xlink:href="ijms-17-00728-g003"></graphic></fig><table-wrap id="ijms-17-00728-t001" position="float"><object-id pub-id-type="pii">ijms-17-00728-t001_Table 1</object-id><label>Table 1</label><caption><p>Detailed discussion of oral diseases protein analysis using proteomic tools.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Sample</th><th align="left" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Disease Condition</th><th align="left" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Proteomic Tools</th><th align="left" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Identified Markers</th><th align="left" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">References</th></tr></thead><tbody><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Whole mouth saliva (WS)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Oral squamous cell carcinoma</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Shotgun proteome analysis, Western blotting (WB) and Enzyme Linked Immuno-Sorbent Assay (ELISA)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">MRP14, M2BP, CD59, catalase, profilin, M2BP, involucrin, histone H1, S100A12, and S100P</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B17-ijms-17-00728" ref-type="bibr">17</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">WS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Denture stomatitis</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Surface-Enhanced Laser Desorption/Ionization (SELDI) time-of-flight-(TOF)/ mass spectrometry (MS), liquid chromatography (LC)- Matrix-Assisted Laser Desorption/Ionization (MALDI)-TOF-MS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Statherin, desmocollin-2, kininogen-1, carbonic anhydrase-6, cystatin SN, cystatin c, peptidyl-prolyl cis-trans isomerase and immunoglobulin fragments</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B18-ijms-17-00728" ref-type="bibr">18</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">WS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Primary Sjögren’s syndrome</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">two dimensional electrophoresis (2-DE), MALDI-TOF/MS, WB and ELISA</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Carbonic anhydrase VI, α-amylases precursor, epidermal fatty acid binding protein (E-FABP), macroglobulin (b-2), immunoglobulin k light chain (IGK-light chain) and glyceraldehydes-3-phosphate dehydrogenase (G3PDH)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B19-ijms-17-00728" ref-type="bibr">19</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">WS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Secondary Sjögren’s syndrome</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">2-DE, MALDI-TOF-MS, WB and ELISA</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Decrease ↓ Proline rich proteins (PRPs), ↓ Cystatin C, ↓ Lysozyme C and histatin, Increase ↑ Kallikrein and defensins</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B20-ijms-17-00728" ref-type="bibr">20</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">WS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">GVHD</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Tandem MS & ELISA</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">IL-1 receptor antagonist and cystatin B</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B21-ijms-17-00728" ref-type="bibr">21</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">WS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Protein-energy undernutrition</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">2-DE Gel and Image Master two dimensional 2D</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Cyclic-dependent protein kinase</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B22-ijms-17-00728" ref-type="bibr">22</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">WS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Squamous cell carcinoma (head and neck region)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">C4 Reverse Phase-High Pressure Liquid Chromatography (RP-HPLC), and LC-MS/MS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">MRP14, Profilin, CD59, catalase and M2BP</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B23-ijms-17-00728" ref-type="bibr">23</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">WS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Diabetes (type-2)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">2D-LC-MS/MS, WB and ELISA</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">α-1-antitrypsin (A1AT), α-2 macroglobulin (A2MG), transthyretin (TTR), salivary α -amylase (AMYS), cystatin C (Cys-C)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B24-ijms-17-00728" ref-type="bibr">24</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">WS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Edentulous patient with type-2 diabetes</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">2D-LC-MS/MS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Serum amyloid-A and glyceraldehyde-3-phosphate dehydrogenase are increased, serotransferrin and amylase, palate, lung and nasal epithelium associated proteins (PLUNC) are reduced</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B25-ijms-17-00728" ref-type="bibr">25</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Unstimulated whole mouth saliva (USWS)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Squamous cell carcinoma (oral mucosa)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Ultra-Pressure Liquid Chromatography (UPLC-MS), Hydrophilic Interaction Liquid Chromatography (HILIC)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"><sc>l</sc>-carnitine, choline, betaine and pipecolinic acid</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B26-ijms-17-00728" ref-type="bibr">26</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Saliva (parotid glands)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Caries</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">HPLC-MS/MS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">matrix metalloproteinase-9 (MMP9), mucin-7 (MUC7), lactotransferrin (LTF), carbonic anhydrase 6 (CA6), azurocidin (AZU), and cold agglutinin</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B27-ijms-17-00728" ref-type="bibr">27</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">WS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Orthodontic tooth movement</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">2-DE, MALDI-TOF/tandem mass spectrometry (TEM)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Protein S100-A9, CRISP-3, Immunoglobulin J chain and Ig α-1 chain C region</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B28-ijms-17-00728" ref-type="bibr">28</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">USWS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Aggressive periodontitis</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">2-DE/HPLC–Electrospray Ionization (ESI)-MS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Increase in serum albumin, immunoglobulin Ig γ2, α2 chain C region, zinc-α2 glycoprotein, salivary α-amylase and vitamin D-binding proteins.<break></break> Decrease in lactotransferrin, carbonic anhydrase 6, elongation factor 2, 14-3-3 sigma, short palate, lung and nasal epithelium carcinoma-associated protein-2</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B29-ijms-17-00728" ref-type="bibr">29</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">USWS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Periodontitis chronic</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">2-DE/MALDI-TOF/TOF MS and nLC-Q-TOF</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Rise in serum albumin, hemoglobin, immunoglobulin and α-amylase</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B30-ijms-17-00728" ref-type="bibr">30</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">WS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Periodontitis in obese patient</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">SELDI-TOF-MS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Albumin, haemoglobin (α and β chains) and α-defensins (1, 2 & 3)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B31-ijms-17-00728" ref-type="bibr">31</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">USWS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Gingivitis</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">2-DE/MALDI-TOF/TOF MS and nLC-Q-TOF</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Zymogen granule protein-16 homolog B mucin, S100-A9, histatin, proline-rich-protein, 3, lipocalin-1 precursor, carbonic anhydrase 6, prolactin-induced protein, cystatin, keratins</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B32-ijms-17-00728" ref-type="bibr">32</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Dental cementum</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">-</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Nano-Acuity HPLC and LTQ-FT ultra</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Osteomodulin (OMD), biglycan (BGN), insulin-like growth factor II (IGF2), pigment epithelium-derived factor (SERPINF1) and POSTN</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B33-ijms-17-00728" ref-type="bibr">33</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Fine Needle Aspiration (FNA) fluid</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Parotid gland tumor (Benign origin)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Nano LC-ESI-MS/MS and LTQ-Qrbitrap velos analysis and Western blot analysis</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Ig γ-1 and kappa chain and Ig α-1 chain C regions, S100A9, macrophage capping proteins, apolipoprotein E and α crystalline B chain, annexin (A1 and A4)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B34-ijms-17-00728" ref-type="bibr">34</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Gingival crevicular fluids (GCF)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Gingivitis and chronic periodontitis</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">2-DE-LC-ESI-MS and Nano-LC-ESI-MS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Fibronectin, keratin, neutrophil, defensin3, Immunoglobulins, lactotransferrin precursor, 14-3-3 protein ζ/δ and α-actinin</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B35-ijms-17-00728" ref-type="bibr">35</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Dentin</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">-</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">LC-MS/MS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Biglycan, osteoglycin, osteopontin, osteocalcin, asporin, lumican, mimecan, DSPP and SOD3</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B36-ijms-17-00728" ref-type="bibr">36</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Dental pulp</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">-</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">2-DE, Nano-LCMS/MS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">342 proteins identified</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B37-ijms-17-00728" ref-type="bibr">37</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Periodontal fibers (PDL)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">-</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">2-DE, MALDI-TOF, Western blot,</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">117 proteins identified</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B38-ijms-17-00728" ref-type="bibr">38</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Acquired enamel pellicle (AEP)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">-</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">LC-ESI-MS/MS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">130 proteins identified</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B39-ijms-17-00728" ref-type="bibr">39</xref>]</td></tr></tbody></table></table-wrap><table-wrap id="ijms-17-00728-t002" position="float"><object-id pub-id-type="pii">ijms-17-00728-t002_Table 2</object-id><label>Table 2</label><caption><p>Profiling and proteomic tools used for the detection and characterization of gingival crevicular fluid (GCF) proteins.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Author </th><th align="left" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Sample Collection Sites</th><th align="left" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Collection Method</th><th align="left" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Proteomic Tool</th><th align="left" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Number of Identified Proteins</th><th align="left" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Outcome of Study</th><th align="left" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Reference</th></tr></thead><tbody><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Baliban <italic>et al.</italic></td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Collected from pre-selected sites with probing depth >6 mm and <8 mm in periodontitis patients and for periodontaly health from mesio-buccal sites of first molar</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Filter strips (Periopapers<sup>®</sup>, Interstate Drug. Exchange, Amityville, NY, USA)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Protein digest with trypsin, HPLC, fragmented analysis with tandem mass spectrometry (MS/MS)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">432 human proteins identified (120 new)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Study identified novel biomarkers from GCF of periodontaly healthy and chronic periodontitis patients</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B68-ijms-17-00728" ref-type="bibr">68</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Tsuchida <italic>et al.</italic></td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Labial side of maxillary incisors without crown and restoration</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Absorbent paper points (ZIPPERER<sup>®</sup>, Munich, Germany)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">2-DE, Sodium-Dodecyl-Sulfate-Polyacrylamide Gel Electrophoresis (SDS-PAGE), WB analysis, HPLC with LTQ-XL, HPLC with LTQ-Orbitrap XL, LC-MS/MS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">327 proteins identified</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">SOD1 and DCD were significantly increase ↑ in GCF of periodontal patients</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B64-ijms-17-00728" ref-type="bibr">64</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Carneiro <italic>et al.</italic></td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Healthy gingival sulcus of the second and third molar teeth</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Periopapers<sup>®</sup>, USA</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Trypsin digested followed by nano-flow liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) analysis and ELISA for human albumin analysis</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">199 proteins identified </td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Provide proteins analysis of healthy periodontium and explore GCF composition with new groups of proteins specific to GCF microenvironment</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B71-ijms-17-00728" ref-type="bibr">71</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Ngo <italic>et al.</italic></td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Five deepest sites and molar sites except mesial surface were excluded</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Microcaps (glass micocapillary tubes); Drummed Scientific, Brookmall, PA, USA</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Matrix-assisted laser desposition/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"></td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">GCF mass spectra could be best for analyzing attachment loss and diagnosis of periodontal diseases</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B69-ijms-17-00728" ref-type="bibr">69</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Carina, <italic>et al.</italic></td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Chronic Periodontitis patients sample were taken from different sites (5 deep sites, 5 shallow sites with gingivitis, and 4 without bleeding on probing sites)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Periopaper strip (ProFlow Inc., Amityville, NY, USA)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Reversed- phase (RP) LC-ESi-MS/MS and ELISA</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">230 proteins identified</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Concluded marked differences in GCF proteomics in different disease profiles</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B70-ijms-17-00728" ref-type="bibr">70</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Carneiro <italic>et al.</italic></td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">The pre-selected specific sites with moderate and severe chronic periodontal disease were defined by pocket depth of 5–7 mm (24 patients) and >7 mm (16 patients)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Periopaper strips (Oraflow, Plainview, NY, USA)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">SDS-PAGE, Isotope-Coded-Affinity-Tag (ICAT) labelling, mTRAQ labelling, Nano-LC-ESI-MS/MS, Human Albumin ELISA Kit, and S100-A9 protein quantification by ELISA</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">238 proteins Identified</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Innovative approach concluded the novel changes in host and microbial derived GCF proteome of periodontal patients</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B72-ijms-17-00728" ref-type="bibr">72</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Rody Jr <italic>et al.</italic></td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Collected from a deciduous second molar with radiographic evidence of root resorption on 1 quadrant (experimental site) and from the permanent first molar on the contralateral quadrant (control site) in the same jaw</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Periopaper strips (Oraflow, Plainview, NY, USA)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">One dimensional LC-MS and Two dimensional (2D) LC-MS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">2789 proteins in control group and 2421 proteins in root resorption group</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Mass spectrometry is useful tool for analyzing external root resorption</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B73-ijms-17-00728" ref-type="bibr">73</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Kinney <italic>et al.</italic></td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Collection from the mesio-buccal aspect of each site (tooth) for up-to 28 teeth per patient</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Methylcellulose strip (Pro Flow, Inc., Amityville, NY, USA)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">ELISA and Quantibody Human Cytokine Array (HCA)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"></td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">This method offer improved patient monitoring and disease control</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B74-ijms-17-00728" ref-type="bibr">74</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Huynh <italic>et al.</italic></td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Collection were chosen based on how well they represented the healthy, gingivitis and chronic periodontitis inclusion criteria</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Glass-microcapillary tube (Drummond Scientific, Brookmall, PA, USA)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">One dimensional Gel-Electrophoresis and Nano-LC-ESI-MS</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">121 proteins identified</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Concluded various biomarkers which differentiate between healthy periodontium, gingivitis and chronic periodontitis</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B35-ijms-17-00728" ref-type="bibr">35</xref>]</td></tr></tbody></table></table-wrap><table-wrap id="ijms-17-00728-t003" position="float"><object-id pub-id-type="pii">ijms-17-00728-t003_Table 3</object-id><label>Table 3</label><caption><p>Use of proteomics techniques for dental materials analysis.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Author Name</th><th align="left" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Title of Study</th><th align="left" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Outcomes</th><th align="left" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">References</th></tr></thead><tbody><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Boyan <italic>et al.</italic></td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Porcine fetal enamel matrix derivative enhances bone formation induced by demineralized freeze dried bone allograft <italic>in vivo</italic></td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Emdogain contains a number of low-molecular-weight proteins (mainly amelogenins), associated with cementogenesis and osteogenesis during tooth development</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B109-ijms-17-00728" ref-type="bibr">109</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Derhami <italic>et al.</italic></td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Proteomic analysis of human skin fibroblasts grown on titanium: Novel approach to study molecular biocompatibility</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Gain a better understanding of the molecular basis of biocompatibility of human skin fibroblast on titanium</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B110-ijms-17-00728" ref-type="bibr">110</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Koin <italic>et al.</italic></td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Analysis of the degradation of a model dental composite</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Liquid chromatography mass spectrometry (LC-MS) found leaching of intact BisGMA and several degradation products that contained the bisphenol A moiety from the overlayer into distilled water after 2 weeks of aging</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B111-ijms-17-00728" ref-type="bibr">111</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Jung <italic>et al.</italic></td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Proteomic analysis in cyclosporin A (CsA)-induced overgrowth of human gingival fibroblast (HGF)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">The CsA-treated HGF demonstrated that Prx 1 may play a crucial role in the HGF proliferation induced by CsA and proteomic analysis data provide an efficient approach in understanding the mechanisms of HGF proliferation by CsA</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B112-ijms-17-00728" ref-type="bibr">112</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Taiyoji <italic>et al.</italic></td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Identification of proteinaceous inhibitors of a cysteine proteinase (an Arg-specific gingipain) from Porphyromonas gingivalis in rice grain, using targeted-proteomics approaches</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">These results suggest that these rice proteins may be useful as nutraceutical ingredients for the prevention and management of periodontal diseases</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B113-ijms-17-00728" ref-type="bibr">113</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Haigh <italic>et al.</italic></td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Alterations in the salivary proteome associated with periodontitis</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Results highlight the predominant involvement of S100 proteins in the host response during periodontitis</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B113-ijms-17-00728" ref-type="bibr">113</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Zilm and Bartold <italic>et al.</italic></td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Proteomic identification of proteinase inhibitors in the porcine enamel matrix derivative, EMD<sup>®</sup></td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Enamel matrix derivatives (EMD) contains a number of high-molecular-weight compounds which include the proteinase inhibitors, fetuin A and α1-antichymotrypsin</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B114-ijms-17-00728" ref-type="bibr">114</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Dorkhan <italic>et al.</italic></td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Effects of saliva or serum coating on adherence of Streptococcus oralis strains to titanium</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">The adherence of LA11 and 89C strain to the moderately rough surfaces coated with saliva was more than twice that seen on the smooth saliva coated surfaces. This clearly demonstrates that surface topography is, at least to some degree, maintained in the presence of a saliva coating</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B115-ijms-17-00728" ref-type="bibr">115</xref>]</td></tr><tr><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Zhao <italic>et al.</italic></td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Quantitative proteomic analysis of human osteoblast-like MG-63 cells in response to bio-inert implant material titanium and polyetheretherketone (PEEK)</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Titanium and polyetheretherketone (PEEK) induces similar response in osteoblast proteome and PEEK causing worse proliferation was related to mRNA processing</td><td align="left" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">[<xref rid="B116-ijms-17-00728" ref-type="bibr">116</xref>]</td></tr></tbody></table></table-wrap></floats-group></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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