Novel protein identification methods for biomarker discovery via a proteomic analysis of periodontally healthy and diseased gingival crevicular fluid samples

Journal of Clinical Periodontology

Volumn 39, Issue 3, 2012, Pages 203-212

  Baliban, Richard C ^a   Sakellari, Dimitra ^b   Li, Zukui ^a   Dimaggio, Peter A ^c   Garcia, Benjamin A ^c   Floudas, Christodoulos A ^a  

^a Princeton University   (United States)

^b ARISTOTLE UNIVERSITY OF THESSALONIKI   (Greece)

^c PRINCETON UNIVERSITY   (United States)

Author keywords

biomarkers; gingival crevicular fluid; periodontitis; proteomic analysis; tandem mass spectrometry

Indexed keywords

BACTERIAL PROTEIN; BIOLOGICAL MARKER; CARBONATE DEHYDRATASE; DEFENSIN; ELONGATION FACTOR 1; PROTEOME;

ARTICLE; CASE CONTROL STUDY; CHEMISTRY; CHRONIC PERIODONTITIS; COMPUTER PROGRAM; GINGIVITIS; HUMAN; METABOLISM; METHODOLOGY; PROTEOMICS; TANDEM MASS SPECTROMETRY;

BACTERIAL PROTEINS; BIOLOGICAL MARKERS; CARBONIC ANHYDRASES; CASE-CONTROL STUDIES; CHRONIC PERIODONTITIS; DEFENSINS; GINGIVAL CREVICULAR FLUID; HUMANS; PEPTIDE ELONGATION FACTOR 1; PROTEOME; PROTEOMICS; SOFTWARE; TANDEM MASS SPECTROMETRY;

EID: 84856597549     PISSN: 03036979     EISSN: 1600051X     Source Type: Journal    
DOI: 10.1111/j.1600-051X.2011.01805.x     Document Type: Article

References (38)

1. Armitage, G. C., (1999) Development of a classification system for periodontal diseases and conditions. Annals of Periodontology 4, 1-6.
2. Baliban, R. C., DiMaggio, P. A., Plazas-Mayorca, M. D., Young, N. L., Garcia, B. A., &, Floudas, C. A., (2010) A novel approach for untargeted post-translational modification identification using integer linear optimization and tandem mass spectrometry. Molecular & Cellular Proteomics 9, 764-779.
3. Bostanci, N., Heywood, W., Mills, K., Parkar, M., Nibali, L., &, Donos, N., (2010) Application of label-free absolute quantitative proteomics in human gingival crevicular fluid by LC/MS E (gingival exudatome). Journal of Proteome Research 9, 2191-2199.
4. Buduneli, N., &, Kinane, D. F., (2011) Host-derived diagnostic markers related to soft tissue destruction and bone degradation in periodontitis. Journal of Clinical Periodontology 38, 85-105.
5. Carr, S., Aebersold, R., Baldwin, M., Burlingame, A., Clauser, K., &, Nesvizhskii, A., (2004) The need for guidelines in publication of peptide and protein identification data. Molecular & Cellular Proteomics 3, 531-533.
6. Champagne, C. M., Buchanan, W., Reddy, M. S., Preisser, J. S., Beck, J. D., &, Offenbacher, S., (2003) Potential for gingival crevice fluid measures as predictors of risk for periodontal diseases. Periodontology 2000 31, 167-180. (Pubitemid 37487415)
7. Curtis, M. A., Sterne, J. A. C., Price, S. J., Griffiths, G. S., Coulthurst, S. K., Wilton, J. M. A., &, Johnson, N. W., (1990) The protein composition of gingival crevicular fluid sampled from male adolescents with no destructive periodontitis: baseline data of a longitudinal study. Journal of Periodontal Research 25, 6-16. (Pubitemid 20084459)
8. Delima, A. J., &, Van Dyke, T. E., (2003) Origin and function of the cellular components in gingival crevice fluid. Periodontology 2000 31, 55-76. (Pubitemid 37487410)
9. DiMaggio, P. A. Jr, &, Floudas, C. A., (2007a) De novo peptide identification via tandem mass spectrometry and integer linear optimization. Analytical Chemistry 79, 1433-1446.
10. DiMaggio, P. A. Jr, &, Floudas, C. A., (2007b) A mixed-integer optimization framework for de novo peptide identification. AIChE Journal 53, 160-173. (Pubitemid 46114027)
11. DiMaggio, P. A. Jr, Floudas, C. A., Lu, B., &, Yates, J. R. III, (2008) A hybrid method for peptide identification using integer linear optimization, local database search, and quadrupole time-of-flight or OrbiTrap tandem mass spectrometry. Journal of Proteome Research 7, 1584-1593.
12. Dommish, H., Acil, Y., Dunsche, A., Winter, J., &, Jepsen, S., (2005) Differential gene expression of human b-defensins (hBD-1-2-3) in inflammatory gingival diseases. Oral Microbiology and Immunology 20, 186-190. (Pubitemid 40559432)
13. Eley, B. M., &, Cox, S. W., (2003) Proteolytic and hydrolytic enzymes from putative periodontal pathogens: characterization, molecular genetics, effects on host defenses and tissues and detection in gingival crevice fluid. Periodontology 2000 31, 105-124. (Pubitemid 37487412)
14. Eng, J. K., McCormack, A. L., &, Yates, J. R. III, (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. Journal of the American Society for Mass Spectrometry 5, 976-989.
15. Frank, A., &, Pevzner, P., (2005) PepNovo: de novo peptide sequencing via probabilistic network modeling. Analytical Chemistry 77, 964-973. (Pubitemid 40261761)
16. Gorr, S.-U., (2009) Antimicrobial peptides of the oral cavity. Periodontology 2000 51, 152-180.
17. Gorr, S.-U., &, Abdolhosseini, M., (2011) Antimicrobial peptides and periodontal disease. Journal of Clinical Periodontology 38, 126-141.
18. Grant, M. M., Creese, A. J., Barr, G., Ling, M. R., Scott, A. E., Matthews, J. B., Griffiths, H. R., Cooper, H. J., &, Chapple, I. L. C., (2010) Proteomic analysis of a noninvasive human model of acute inflammation and its resolution: the twenty-one day gingivitis model. Journal of Proteome Research 9, 4732-4744.
19. Lamster, I. B., &, Ahlo, J. K., (2007) Analysis of gingival crevicular fluid as applied to the diagnosis of oral and systemic diseases. Annals of the New York Academy of Sciences 1098, 216-229. (Pubitemid 47092548)
20. Loo, J. A., Yan, W., Ramachandran, P., &, Wong, D. T., (2010) Comparative human salivary and plasma proteomes. Journal of Dental Research 89, 1016-1023.
21. Loos, B. G., &, Tjoa, S., (2005) Host-derived diagnosis markers for periodontitis: do they exist in gingival crevice fluid? Periodontology 2000 39, 53-72. (Pubitemid 43026179)
22. Lundy, F. T., Orr, D. F., Show, C., Lamey, P.-J., &, Linden, G. J., (2005) Detection of individual human neutrophil a-defensins (human neutrophil peptides 1, 2 and 3) in unfractionated gingival crevicular fluid: a MALDI-MS approach. Molecular Immunology 42, 575-579. (Pubitemid 39655935)
23. McLaughlin, W. S., Kirkham, J., Kowolik, M. J., &, Robinson, C., (1996) Human gingival crevicular fluid keratin at healthy, chronic gingivitis and chronic adult periodontitis sites. Journal of Clinical Periodontology 23, 331-335. (Pubitemid 126731958)
24. Moll, R., Divo, M., &, Langbein, L., (2008) The human keratins:biology and pathology. Histochemictry and Cell Biology 129, 705-733.
25. Nesvizhskii, A. I., (2010) A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. Journal of Proteomics 73, 2092-2123.
26. Nesvizhskii, A. I., Vitek, O., &, Aebersold, R., (2007) Analysis and validation of proteomic data generated by tandem mass spectrometry. Nature Methods 4, 787-797. (Pubitemid 350055575)
27. Ngo, L. H., Veith, P. D., Chen, Y.-Y., Chen, D., Cardy, I. B., &, Reynolds, E. C., (2010) Mass spectrometric analyses of peptides and proteins in human gingival crevicular fluid. Journal of Proteome Research 9, 1683-1693.
28. Nussbaum, G., &, Shapira, L., (2011) How has neutrophil research improved our understanding of periodontal pathogenesis? Journal of Clinical Periodontology 38 (Suppl. 11), 49-59.
29. Perkins, D. N., Pappin, D. J. C., Creasy, D. M., &, Cottrell, J. S., (1999) Probability-based protein identification by searching databases using mass spectrometry data. Electrophoresis 20, 3551-3567. (Pubitemid 30007252)
30. Pisano, E., Cabras, T., Montaldo, C., Piras, V., Inzitari, R., Olmi, C., Castagnola, M., &, Messana, I., (2005) Peptides of human gingival crevicular fluid determined by HPLC-ESI-MS. European Journal of Dental Education 113, 462-468. (Pubitemid 41784331)
31. Puklo, M., Guentsch, A., Hiemstra, P. S., Eick, S., &, Potempa, J., (2008) Analysis of neutrophilderived antimicrobial peptides in gingival crevicular fluid suggests importance of cathelicidin LL-37 in the innate immune response against periodontogenic bacteria. Oral Microbiology and Immunology 23, 328-335. (Pubitemid 351832179)
32. Sakellari, D., Menti, S., &, Konstantinidis, A., (2008) Free soluble receptor activator of nuclear factor-k b ligand in gingival crevicular fluid correlates with distinct pathogens in periodontitis patients. Journal of Clinical Periodontology 35, 938-943.
33. Sakiyama, Y., Kato, R., Inoue, S., Suzuki, K., Itabe, H., &, Yamamoto, M., (2010) Detection of oxidized low-density lipoproteins in gingival crevicular fluid from dental patients. Journal of Periodontal Research 45, 216-222.
34. Socransky, S. S., Haffajee, A. D., Cugini, M. A., Smith, C., &, Kent, R. L., (1998) Microbial complexes in subgingival plaque. Journal of Clinical Periodontology 25, 134-144. (Pubitemid 128705944)
35. Tanner, S., Shu, H., Frank, A., Wang, L. C., Zandi, E., Mumby, M., Pevzner, P. A., &, Bafna, V., (2005) InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Analytical Chemistry 77, 4626-4639. (Pubitemid 41542287)
36. Uitto, V. J., Overall, C. M., &, McCulloch, C., (2003) Proteolytic host cell enzymes in gingival crevice fluid. Periodontology 2000 31, 77-104. (Pubitemid 37487411)
37. Vitkov, L., Klappacher, M., Hannig, M., &, Krautgartner, D., (2009) Extracellular neutrophil traps in periodontitis. Journal of Periodontal Research 44, 664-672.
38. Witze, E. S., Old, W. M., Resing, K. A., &, Ahn, N. G., (2007) Mapping protein post-translational modifications with mass spectrometry. Nature Methods 4, 798-806. (Pubitemid 350055576)