Toward a standardized saliva proteome analysis methodology

Journal of Proteomics

Volumn 75, Issue 17, 2012, Pages 5140-5165

  Vitorino, Rui ^a   Guedes, Sofia ^a   Manadas, Bruno ^b,c   Ferreira, Rita ^a   Amado, Francisco ^a  

^a UNIVERSITY OF AVEIRO   (Portugal)

^b Biocant ^*  (Portugal)

^c UNIVERSITY OF COIMBRA   (Portugal)

Author keywords

LC MS MS; Peptidomic; Proteomics; PTM; Whole saliva

Indexed keywords

PROTEOME;

ADULT; ARTICLE; FEMALE; GEL ELECTROPHORESIS; HUMAN; HUMAN EXPERIMENT; MALE; NORMAL HUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; SALIVA ANALYSIS; ULTRACENTRIFUGATION; ULTRASOUND; WESTERN BLOTTING;

ADULT; CLUSTER ANALYSIS; ELECTROPHORESIS, POLYACRYLAMIDE GEL; HUMANS; MALE; MODELS, BIOLOGICAL; PROTEOME; PROTEOMICS; REFERENCE STANDARDS; SALIVA; SALIVARY PROTEINS AND PEPTIDES; SEQUENCE ANALYSIS, PROTEIN; YOUNG ADULT;

EID: 84865548707     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2012.05.045     Document Type: Article

References (44)

1. Amado F.M., Vitorino R.M., Domingues P.M., Lobo M.J., Duarte J.A. Analysis of the human saliva proteome. Expert Rev Proteomics 2005, 2:521-539.
2. Kawas S.A., Rahim Z.H., Ferguson D.B. Potential uses of human salivary protein and peptide analysis in the diagnosis of disease. Arch Oral Biol 2012, 57:1-9.
3. Stone M.D., Chen X., McGowan T., Bandhakavi S., Cheng B., Rhodus N.L., et al. Large-scale phosphoproteomics analysis of whole saliva reveals a distinct phosphorylation pattern. J Proteome Res 2011, 10:1728-1736.
4. Messana I., Inzitari R., Fanali C., Cabras T., Castagnola M. Facts and artifacts in proteomics of body fluids. What proteomics of saliva is telling us?. J Sep Sci 2008, 31:1948-1963.
5. Schipper R., Silletti E., Vingerhoeds M. Saliva as research material: biochemical, physicochemical and practical aspects. Arch Oral Biol 2007, 52:1114-1135.
6. Oppenheim F.G., Salih E., Siqueira W.L., Zhang W., Helmerhorst E.J. Salivary proteome and its genetic polymorphisms. Ann N Y Acad Sci 2007, 1098:22-50.
7. Chevalier F., Hirtz C., Chay S., Cuisinier F., Sommerer N., Rossignol M., et al. Proteomic studies of saliva: a proposal for a standardized handling of clinical samples. Clin Proteomics 2007, 3:13-21.
8. Yan W., Apweiler R., Balgley B.M., Boontheung P., Bundy J.L., Cargile B.J., et al. Systematic comparison of the human saliva and plasma proteomes. Proteomics Clin Appl 2009, 3:116-134.
9. Xie H., Rhodus N.L., Griffin R.J., Carlis J.V., Griffin T.J. A catalogue of human saliva proteins identified by free flow electrophoresis-based peptide separation and tandem mass spectrometry. Mol Cell Proteomics 2005, 4:1826-1830.
10. Hu S., Xie Y., Ramachandran P., Ogorzalek Loo R.R., Li Y., Loo J.A., et al. Large-scale identification of proteins in human salivary proteome by liquid chromatography/mass spectrometry and two-dimensional gel electrophoresis-mass spectrometry. Proteomics 2005, 5:1714-1728.
11. Wilmarth P.A., Riviere M.A., Rustvold D.L., Lauten J.D., Madden T.E., David L.L. Two-dimensional liquid chromatography study of the human whole saliva proteome. J Proteome Res 2004, 3:1017-1023.
12. Messana I., Cabras T., Pisano E., Sanna M.T., Olianas A., Manconi B., et al. Trafficking and postsecretory events responsible for the formation of secreted human salivary peptides: a proteomics approach. Mol Cell Proteomics 2008, 7:911-926.
13. Vitorino R., Barros A., Caseiro A., Domingues P., Duarte J., Amado F. Towards defining the whole salivary peptidome. Proteom Clin Appl. 2009, 3:528-540.
14. Vitorino R., Lobo M.J., Duarte J.A., Ferrer-Correia A.J., Domingues P.M., Amado F.M. Analysis of salivary peptides using HPLC-electrospray mass spectrometry. Biomed Chromatogr 2004, 18:570-575.
15. de Jong E.P., van Riper S.K., Koopmeiners J.S., Carlis J.V., Griffin T.J. Sample collection and handling considerations for peptidomic studies in whole saliva; implications for biomarker discovery. Clin Chim Acta 2011, 412:2284-2288.
16. Snyder S.L., Sobocinski P.Z. An improved 2,4,6-trinitrobenzenesulfonic acid method for the determination of amines. Anal Biochem 1975, 64:284-288.
17. Vitorino R., Lobo M.J., Ferrer-Correira A.J., Dubin J.R., Tomer K.B., Domingues P.M., et al. Identification of human whole saliva protein components using proteomics. Proteomics 2004, 4:1109-1115.
18. Vitorino R., de Morais Guedes S., Ferreira R., Lobo M.J., Duarte J., Ferrer-Correia A.J., et al. Two-dimensional electrophoresis study of in vitro pellicle formation and dental caries susceptibility. Eur J Oral Sci 2006, 114:147-153.
19. Tastet C., Lescuyer P., Diemer H., Luche S., van Dorsselaer A., Rabilloud T. A versatile electrophoresis system for the analysis of high- and low-molecular-weight proteins. Electrophoresis 2003, 24:1787-1794.
20. Manadas B., English J.A., Wynne K.J., Cotter D.R., Dunn M.J. Comparative analysis of OFFGel, strong cation exchange with pH gradient, and RP at high pH for first-dimensional separation of peptides from a membrane-enriched protein fraction. Proteomics 2009, 9:5194-5198.
21. Gan C.S., Chong P.K., Pham T.K., Wright P.C. Technical, experimental, and biological variations in isobaric tags for relative and absolute quantitation (iTRAQ). J Proteome Res 2007, 6:821-827.
22. Topkas E., Keith P., Dimeski G., Cooper-White J., Punyadeera C. Evaluation of saliva collection devices for the analysis of proteins. Clin Chim Acta 2012.
23. Rudney J.D., Xie H., Rhodus N.L., Ondrey F.G., Griffin T.J. A metaproteomic analysis of the human salivary microbiota by three-dimensional peptide fractionation and tandem mass spectrometry. Mol Oral Microbiol 2010, 25:38-49.
24. White M.R., Helmerhorst E.J., Ligtenberg A., Karpel M., Tecle T., Siqueira W.L., et al. Multiple components contribute to ability of saliva to inhibit influenza viruses. Oral Microbiol Immunol 2009, 24:18-24.
25. Denny P.C., Denny P.A., Klauser D.K., Hong S.H., Navazesh M., Tabak L.A. Age-related changes in mucins from human whole saliva. J Dent Res 1991, 70:1320-1327.
26. Quintana M., Palicki O., Lucchi G., Ducoroy P., Chambon C., Salles C., et al. Inter-individual variability of protein patterns in saliva of healthy adults. J Proteomics 2009, 72:822-830.
27. Duan X., Young R., Straubinger R.M., Page B., Cao J., Wang H., et al. A straightforward and highly efficient precipitation/on-pellet digestion procedure coupled with a long gradient nano-LC separation and Orbitrap mass spectrometry for label-free expression profiling of the swine heart mitochondrial proteome. J Proteome Res 2009, 8:2838-2850.
28. Martins D., Menezes de Oliveira B., dos Santos Farias A., Oka Horiuchi R.S., Crepaldi Domingues C., de Paula E., et al. The use of ASB-14 in combination with CHAPS is the best for solubilization of human brain proteins for two-dimensional gel electrophoresis. Briefings in Functional Genomics and Proteomics 2007, 6:70-75.
29. Chen E.I., Cociorva D., Norris J.L., Yates J.R. Optimization of mass spectrometry-compatible surfactants for shotgun proteomics. J Proteome Res 2007, 6:2529-2538.
30. Gorg A., Weiss W., Dunn M.J. Current two-dimensional electrophoresis technology for proteomics. Proteomics 2004, 4:3665-3685.
31. Gundry R.L., White M.Y., Murray C.I., Kane L.A., Fu Q., Stanley B.A., et al. Preparation of proteins and peptides for mass spectrometry analysis in a bottom-up proteomics workflow. Current Protocols in Molecular Biology 2009, Chapter 10:Unit10 25. F.M. Ausubel (Ed.).
32. Graham D.R.M., Garnham C.P., Fu Q., Robbins J., Van Eyk J.E. Improvements in two-dimensional gel electrophoresis by utilizing a low cost "in-house" neutral pH sodium dodecyl sulfate-polyacrylamide gel electrophoresis system. Proteomics 2005, 5:2309-2314.
33. Amado F., Lobo M.J., Domingues P., Duarte J.A., Vitorino R. Salivary peptidomics. Expert Rev Proteomics 2010, 7:709-721.
34. Iontcheva I., Oppenheim F.G., Troxler R.F. Human salivary mucin MG1 selectively forms heterotypic complexes with amylase, proline-rich proteins, statherin, and histatins. J Dent Res 1997, 76:734-743.
35. Fleissig Y., Deutsch O., Reichenberg E., Redlich M., Zaks B., Palmon A., et al. Different proteomic protein patterns in saliva of Sjogren's syndrome patients. Oral Dis 2009, 15:61-68.
36. Neyraud E., Sayd T., Morzel M., Dransfield E. Proteomic analysis of human whole and parotid salivas following stimulation by different tastes. J Proteome Res 2006, 5:2474-2480.
37. Haigh B.J., Stewart K.W., Whelan J.R., Barnett M.P., Smolenski G.A., Wheeler T.T. Alterations in the salivary proteome associated with periodontitis. J Clin Periodontol 2010, 37:241-247.
38. Hu S., Loo J.A., Wong D.T. Human saliva proteome analysis. Ann N Y Acad Sci 2007, 1098:323-329.
39. Sondej M., Denny P., Xie Y., Ramachandran P., Si Y., Takashima J., et al. Glycoprofiling of the human salivary proteome. Clin Proteomics 2009, 5:52-68.
40. Hu S., Loo J.A., Wong D.T. Human body fluid proteome analysis. Proteomics 2006, 6:6326-6353.
41. Besson D., Pavageau A.H., Valo I., Bourreau A., Belanger A., Eymerit-Morin C., et al. A quantitative proteomic approach of the different stages of colorectal cancer establishes OLFM4 as a new nonmetastatic tumor marker. Mol Cell Proteomics 2011, 10. (M111 009712).
42. Levine M. Susceptibility to dental caries and the salivary proline-rich proteins. Int J dentistry 2011, 2011:953412.
43. Vitorino R., Barros A.S., Caseiro A., Ferreira R., Amado F. Evaluation of different extraction procedures for salivary peptide analysis. Talanta. 2012 May 30, 94:209-215.
44. Kawashima Y., Fukutomi T., Tomonaga T., Takahashi H., Nomura F., Maeda T., et al. High-yield peptide-extraction method for the discovery of subnanomolar biomarkers from small serum samples. J Proteome Res 2010, 9:1694-1705.