Proteomics: Methodologies and applications to the study of human diseases

Revista da Associacao Medica Brasileira

Volumn 58, Issue 3, 2012, Pages 366-375

  Barbosa, Eduardo Buzolin ^a   Vidotto, Alessandra ^a   Polachini, Giovana Mussi ^a   Henrique, Tiago ^a   de Marqui, Alessandra Bernadete Trovó ^b   Tajara, Eloiza Helena ^a  

^a FACULDADE DE MEDICINA DE SÃO JOSÉ DO RIO PRETO   (Brazil)

^b FEDERAL UNIVERSITY OF TRIÂNGULO MINEIRO   (Brazil)

Author keywords

Diseases; Mass spectrometry; Neoplasms; Polyacrylamide gel electrophoresis; Proteomics

Indexed keywords

EID: 84864860127     PISSN: 01044230     EISSN: None     Source Type: Journal    
DOI: 10.1590/S0104-42302012000300019     Document Type: Review

References (154)

1. DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, et al. Use of a cDNA microarray to analyze gene expression patterns in human cancer. Nat Genet. 1996;14(4):457-60.
2. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW. Serial analysis of gene expression. Science. 1995;270(5235):484-7.
3. Fullwood MJ, Wei CL, Liu ET, Ruan Y. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009;19(4):521-32.
4. Gygi SP, Rochon Y, Franza BR, Aebersold R. Correlation between protein and mRNA abundance in yeast. Mol Cell Biol. 1999;19(3):1720-30.
5. Gstaiger M, Aebersold R. Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat Rev Genet. 2009;10(9):617-27.
6. Wilkins MR, Sanchez JC, Gooley AA, Appel RD, Humphery-Smith I, Hochstrasser DF, et al. Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol Genet Eng Rev. 1996;13:19-50.
7. Ahrens CH, Brunner E, Qeli E, Basler K, Aebersold R. Generating and navigating proteome maps using mass spectrometry. Nat Rev Mol Cell Biol. 2010;11(11):789-801.
8. Jensen ON. Modification-specific proteomics: characterization of post-translational modifications by mass spectrometry. Curr Opin Chem Biol. 2004;8(1):33-41.
9. Valledor L, Jorrin J. Back to the basics: maximizing the information obtained by quantitative two dimensional gel electrophoresis analyses by an appropriate experimental design and statistical analyses. J Proteomics. 2011;74(1):1-18.
10. Armirotti A, Damonte G. Achievements and perspectives of top-down proteomics. Proteomics. 2010;10(20):3566-76.
11. Kosako H, Nagano K. Quantitative phosphoproteomics strategies for understanding protein kinase-mediated signal transduction pathways. Expert Rev Proteomics. 2011;8(1):81-94.
12. Nirmalan NJ, Hughes C, Peng J, McKenna T, Langridge J, Cairns DA, et al. Initial development and validation of a novel extraction method for quantitative mining of the formalin-fixed, paraffin-embedded tissue proteome for biomarker investigations. J Proteome Res. 2011;10(2):896-906.
13. de Marqui AB, Vidotto A, Polachini GM, Bellato CM, Cabral H, Leopoldino AM, et al. Solubilization of proteins from human lymph node tissue and two-dimensional gel storage. J Biochem Mol Biol. 2006;39(2):216-22.
14. Bjellqvist B, Ek K, Righetti PG, Gianazza E, Gorg A, Westermeier R, et al. Isoelectric focusing in immobilized pH gradients: principle, methodology and some applications. J Biochem Biophys Methods. 1982;6(4):317-39.
15. OFarrell PH. High resolution two-dimensional electrophoresis of proteins. J Biol Chem. 1975;250(10):4007-21.
16. Dowsey AW, Dunn MJ, Yang GZ. The role of bioinformatics in two-dimensional gel electrophoresis. Proteomics. 2003;3(8):1567-96.
17. Rezaul K, Wu L, Mayya V, Hwang SI, Han D. A systematic characterization of mitochondrial proteome from human T leukemia cells. Mol Cell Proteomics. 2005;4(2):169-81.
18. Unlu M, Morgan ME, Minden JS. Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis. 1997;18(11):2071-7.
19. May C, Brosseron F, Chartowski P, Schumbrutzki C, Schoenebeck B, Marcus K. Instruments and methods in proteomics. Methods Mol Biol. 2011;696:3-26.
20. Schirmer EC, Yates JR, 3rd, Gerace L. MudPIT: A powerful proteomics tool for discovery. Discov Med. 2003;3(18):38-9.
21. Washburn MP, Wolters D, Yates JR, 3rd. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol. 2001;19(3):242-7.
22. Chen CH. Review of a current role of mass spectrometry for proteome research. Anal Chim Acta. 2008;624(1):16-36.
23. Zaluzec EJ, Gage DA, Watson JT. Matrix-assisted laser desorption ionization mass spectrometry: applications in peptide and protein characterization. Protein Expr Purif. 1995;6(2):109-23.
24. Tang N, Tornatore P, Weinberger SR. Current developments in SELDI affinity technology. Mass Spectrom Rev. 2004;23(1):34-44.
25. Gustafsson JO, Oehler MK, Ruszkiewicz A, McColl SR, Hoffmann P. MALDI imaging mass spectrometry (MALDI-IMS)-application of spatial proteomics for ovarian cancer classification and diagnosis. Int J Mol Sci. 2011;12(1):773-94.
26. Nguyen S, Fenn JB. Gas-phase ions of solute species from charged droplets of solutions. Proc Natl Acad Sci USA. 2007;104(4):1111-7.
27. Wollnik H. TOF-MS. Mass Spectrom Rev. 1993;12(1):89-114.
28. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis. 1999;20(18):3551-67.
29. Eng JK, McCormack AL, Yates JRI. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. Am Soc Mass Spectrom. 1994;5(976-989).
30. Chernushevich IV, Loboda AV, Thomson BA. An introduction to quadrupole-time-of-flight mass spectrometry. J Mass Spectrom. 2001;36(8):849-65.
31. Wang Y, Franzen J, Wanczek KP. The non-linear resonance ion trap. Part 2. A general theoretical analysis. Int J Mass Spectrom Ion Processes. 1993;124(1):125-44.
32. Hu Q, Noll RJ, Li H, Makarov A, Hardman M, Graham Cooks R. The Orbitrap: a new mass spectrometer. J Mass Spectrom. 2005;40(4):430-43.
33. Walther TC, Mann M. Mass spectrometry-based proteomics in cell biology. J Cell Biol. 2010;190(4):491-500.
34. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol. 1999;17(10):994-9.
35. Thompson A, Schafer J, Kuhn K, Kienle S, Schwarz J, Schmidt G, et al. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem. 2003;75(8):1895-904.
36. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics. 2002;1(5):376-86.
37. Piersma SR, Fiedler U, Span S, Lingnau A, Pham TV, Hoffmann S, et al. Workflow comparison for label-free, quantitative secretome proteomics for cancer biomarker discovery: method evaluation, differential analysis, and verification in serum. J Proteome Res. 2010;9(4):1913-22.
38. Old WM, Meyer-Arendt K, Aveline-Wolf L, Pierce KG, Mendoza A, Sevinsky JR, et al. Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics. 2005;4(10):1487-502.
39. Fey SJ, Larsen PM. 2D or not 2D. Two-dimensional gel electrophoresis. Curr Opin Chem Biol. 2001;5(1):26-33.
40. Walsh GM, Rogalski JC, Klockenbusch C, Kast J. Mass spectrometry-based proteomics in biomedical research: emerging technologies and future strategies. Expert Rev Mol Med. 2010;12:e30.
41. Sudhir PR, Hsu CL, Wang MJ, Wang YT, Chen YJ, Sung TY, et al. Phosphoproteomics identifies oncogenic Ras signaling targets and their involvement in lung adenocarcinomas. PLoS One. 2011;6(5):e20199.
42. Zeng X, Hood BL, Sun M, Conrads TP, Day RS, Weissfeld JL, et al. Lung cancer serum biomarker discovery using glycoprotein capture and liquid chromatography mass spectrometry. J Proteome Res. 2010;9(12):6440-9.
43. Matta A, Ralhan R, DeSouza LV, Siu KW. Mass spectrometry-based clinical proteomics: head-and-neck cancer biomarkers and drug-targets discovery. Mass Spectrom Rev. 2010;29(6):945-61.
44. Huijbers A, Velstra B, Dekker TJ, Mesker WE, van der Burgt YE, Mertens BJ, et al. Proteomic serum biomarkers and their potential application in cancer screening programs. Int J Mol Sci. 2010;11(11):4175-93.
45. Findeisen P, Neumaier M. Mass spectrometry based proteomics profiling as diagnostic tool in oncology: current status and future perspective. Clin Chem Lab Med. 2009;47(6):666-84.
46. Fung ET. A recipe for proteomics diagnostic test development: the OVA1 test, from biomarker discovery to FDA clearance. Clin Chem. 2010;56(2):327-9.
47. Zhang Z, Chan DW. The road from discovery to clinical diagnostics: lessons learned from the first FDA-cleared in vitro diagnostic multivariate index assay of proteomic biomarkers. Cancer Epidemiol Biomarkers Prev. 2010;19(12):2995-9.
48. Schiess R, Wollscheid B, Aebersold R. Targeted proteomic strategy for clinical biomarker discovery. Mol Oncol. 2009;3(1):33-44.
49. Vojtova L, Zima T, Tesar V, Michalova J, Prikryl P, Dostalova G, et al. Study of urinary proteomes in Anderson-Fabry disease. Ren Fail. 2010;32(10):1202-9.
50. Ottervald J, Franzen B, Nilsson K, Andersson LI, Khademi M, Eriksson B, et al. Multiple sclerosis: Identification and clinical evaluation of novel CSF biomarkers. J Proteomics. 2010;73(6):1117-32.
51. Zhou JY, Afjehi-Sadat L, Asress S, Duong DM, Cudkowicz M, Glass JD, et al. Galectin-3 is a candidate biomarker for amyotrophic lateral sclerosis: discovery by a proteomics approach. J Proteome Res. 2010;9(10):5133-41.
52. Blennow K, Hampel H, Weiner M, Zetterberg H. Cerebrospinal fluid and plasma biomarkers in Alzheimer disease. Nat Rev Neurol. 2010;6(3):131-44.
53. Steinacker P, Rist W, Swiatek-de-Lange M, Lehnert S, Jesse S, Pabst A, et al. Ubiquitin as potential cerebrospinal fluid marker of Creutzfeldt-Jakob disease. Proteomics. 2010;10(1):81-9.
54. van Dijk KD, Teunissen CE, Drukarch B, Jimenez CR, Groenewegen HJ, Berendse HW, et al. Diagnostic cerebrospinal fluid biomarkers for Parkinsons disease: a pathogenetically based approach. Neurobiol Dis. 2010;39(3):229-41.
55. Merkel D, Rist W, Seither P, Weith A, Lenter MC. Proteomic study of human bronchoalveolar lavage fluids from smokers with chronic obstructive pulmonary disease by combining surface-enhanced laser desorption/ionization-mass spectrometry profiling with mass spectrometric protein identification. Proteomics. 2005;5(11):2972-80.
56. Gobezie R, Kho A, Krastins B, Sarracino DA, Thornhill TS, Chase M, et al. High abundance synovial fluid proteome: distinct profiles in health and osteoarthritis. Arthritis Res Ther. 2007;9(2):R36.
57. Lema I, Brea D, Rodriguez-Gonzalez R, Diez-Feijoo E, Sobrino T. Proteomic analysis of the tear film in patients with keratoconus. Mol Vis 2010;16:2055-61.
58. Pawlik TM, Fritsche H, Coombes KR, Xiao L, Krishnamurthy S, Hunt KK, et al. Significant differences in nipple aspirate fluid protein expression between healthy women and those with breast cancer demonstrated by time-of-flight mass spectrometry. Breast Cancer Res Treat. 2005;89(2):149-57.
59. Dawes C. Salivary flow patterns and the health of hard and soft oral tissues. J Am Dent Assoc. 2008;139(Suppl):18S-24S.
60. Amaechi BT, Higham SM. In vitro remineralization of eroded enamel lesions by saliva. J Dent. 2001;29(5):371-6.
61. Tabak LA. In defense of the oral cavity: the protective role of the salivary secretions. Pediatr Dent. 2006;28(2):110-7; discussion 92-8.
62. Suh KI, Lee JY, Chung JW, Kim YK, Kho HS. Relationship between salivary flow rate and clinical symptoms and behaviours in patients with dry mouth. J Oral Rehabil. 2007;34(10):739-44.
63. Musumeci V, Cherubini P, Zuppi C, Zappacosta B, Ghirlanda G, Di Salvo S. Aminotransferases and lactate dehydrogenase in saliva of diabetic patients. J Oral Pathol Med. 1993;22(2):73-6.
64. Hirtz C, Chevalier F, Centeno D, Egea JC, Rossignol M, Sommerer N, et al. Complexity of the human whole saliva proteome. J Physiol Biochem. 2005;61(3):469-80.
65. Beeley JA, Sweeney D, Lindsay JC, Buchanan ML, Sarna L, Khoo KS. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis of human parotid salivary proteins. Electrophoresis. 1991;12(12):1032-41.
66. Beeley JA, Khoo KS. Salivary proteins in rheumatoid arthritis and Sjogrens syndrome: one-dimensional and two-dimensional electrophoretic studies. Electrophoresis. 1999;20(7):1652-60.
67. Denny P, Hagen FK, Hardt M, Liao L, Yan W, Arellanno M, et al. The proteomes of human parotid and submandibular/sublingual gland salivas collected as the ductal secretions. J Proteome Res. 2008;7(5):1994-2006.
68. Fábián TK, Gáspár J, Fejérdy L, Kaán B, Bálint M, Csermely P, et al. HSP-70 is present in human saliva. Med Sci Monit. 2003;9(1):62-5.
69. Fang X, Yang L, Wang W, Song T, Lee CS, DeVoe DL, et al. Comparison of electrokinetics-based multidimensional separations coupled with electrospray ionization-tandem mass spectrometry for characterization of human salivary proteins. Anal Chem. 2007;79(15):5785-92.
70. Ghafouri B, Tagesson C, Lindahl M. Mapping of proteins in human saliva using two-dimensional gel electrophoresis and peptide mass fingerprinting. Proteomics. 2003;3(6):1003-15.
71. Guo T, Rudnick PA, Wang W, Lee CS, Devoe DL, Balgley BM. Characterization of the human salivary proteome by capillary isoelectric focusing/nanoreversed-phase liquid chromatography coupled with ESI-tandem MS. J Proteome Res. 2006;5(6):1469-78.
72. Hardt M, Thomas LR, Dixon SE, Newport G, Agabian N, Prakobphol A, et al. Toward defining the human parotid gland salivary proteome and peptidome: identification and characterization using 2D SDS-PAGE, ultrafiltration, HPLC, and mass spectrometry. Biochemistry. 2005;44(8):2885-99.
73. Hu S, Yu T, Xie Y, Yang Y, Li Y, Zhou X, et al. Discovery of oral fluid biomarkers for human oral cancer by mass spectrometry. Cancer Genomics Proteomics. 2007;4(2):55-64.
74. Hu S, Arellano M, Boontheung P, Wang J, Zhou H, Jiang J, et al. Salivary proteomics for oral cancer biomarker discovery. Clin Cancer Res. 2008;14(19):6246-52.
75. Hu S, Denny P, Xie Y, Loo JA, Wolinsky LE, Li Y, et al. Differentially expressed protein markers in human submandibular and sublingual secretions. Int J Oncol. 2004;25(5):1423-30.
76. Hu S, Xie Y, Ramachandran P, Ogorzalek Loo RR, Li Y, Loo JA, 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(6):1714-28.
77. Huang CM. Comparative proteomic analysis of human whole saliva. Arch Oral Biol. 2004;49(12):951-62.
78. Messana I, Cabras T, Inzitari R, Lupi A, Zuppi C, Olmi C, et al. Characterization of the human salivary basic proline-rich protein complex by a proteomic approach. J Proteome Res. 2004;3(4):792-800.
79. Papale M, Pedicillo MC, Di Paolo S, Thatcher BJ, Lo Muzio L, Bufo P, et al. Saliva analysis by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF/MS): from sample collection to data analysis. Clin Chem Lab Med. 2008;46(1):89-99.
80. Ramachandran P, Boontheung P, Xie Y, Sondej M, Wong DT, Loo JA. Identification of N-linked glycoproteins in human saliva by glycoprotein capture and mass spectrometry. J Proteome Res. 2006;5(6):1493-503.
81. Schipper R, Loof A, de Groot J, Harthoorn L, van Heerde W, Dransfield E. Salivary protein/peptide profiling with SELDI-TOF-MS. Ann NY Acad Sci. 2007;1098:498-503.
82. Todd AL, Ng WY, Lee YS, Loke KY, Thai AC. Evidence of autoantibodies to glutamic acid decarboxylase in oral fluid of type 1 diabetic patients. Diabetes Res Clin Pract. 2002;57(3):171-7.
83. Vitorino R, Lobo MJ, Ferrer-Correira AJ, Dubin JR, Tomer KB, Domingues PM, et al. Identification of human whole saliva protein components using proteomics. Proteomics. 2004;4(4):1109-15.
84. Walz A, Stuhler K, Wattenberg A, Hawranke E, Meyer HE, Schmalz G, et al. Proteome analysis of glandular parotid and submandibular-sublingual saliva in comparison to whole human saliva by two-dimensional gel electrophoresis. Proteomics. 2006;6(5):1631-9.
85. Wilmarth PA, Riviere MA, Rustvold DL, Lauten JD, Madden TE, David LL. Two-dimensional liquid chromatography study of the human whole saliva proteome. J Proteome Res. 2004;3(5):1017-23.
86. Xie H, Rhodus NL, Griffin RJ, Carlis JV, Griffin TJ. A catalogue of human saliva proteins identified by free flow electrophoresis-based peptide separation and tandem mass spectrometry. Mol Cell Proteomics. 2005;4(11):1826-30.
87. Yao Y, Berg EA, Costello CE, Troxler RF, Oppenheim FG. Identification of protein components in human acquired enamel pellicle and whole saliva using novel proteomics approaches. J Biol Chem. 2003;278(7):5300-8.
88. Salivary Proteome Knowledge Base. Available from: http://hspp.dent.ucla.edu/cgi-bin/hspmscgi-bin/search_pro_c.cgi.
89. Sys-BodyFluid Database. Available from: www.biosino.org/bodyfluid/fluid.jsp?bf=Saliva.
90. Navazesh M. Methods for collecting saliva. Ann NY Acad Sci. 1993;694:72-7.
91. Hardt M, Witkowska HE, Webb S, Thomas LR, Dixon SE, Hall SC, et al. Assessing the effects of diurnal variation on the composition of human parotid saliva: quantitative analysis of native peptides using iTRAQ reagents. Anal Chem. 2005;77(15):4947-54.
92. Aps JK, Martens LC. Review: The physiology of saliva and transfer of drugs into saliva. Forensic Sci Int. 2005;150(2-3):119-31.
93. Lu Y, Bentley GR, Gann PH, Hodges KR, Chatterton RT. Salivary estradiol and progesterone levels in conception and nonconception cycles in women: evaluation of a new assay for salivary estradiol. Fertil Steril. 1999;71(5):863-8.
94. Maseda C, Hama K, Fukui Y, Matsubara K, Takahashi S, Akane A. Detection of delta 9-THC in saliva by capillary GC/ECD after marihuana smoking. Forensic Sci Int. 1986;32(4):259-66.
95. Gonzalez M, Banderas JA, Baez A, Belmont R. Salivary lead and cadmium in a young population residing in Mexico city. Toxicol Lett. 1997;93(1):55-64.
96. Li C, Ha T, Ferguson DA, Jr., Chi DS, Zhao R, Patel NR, et al. A newly developed PCR assay of H. pylori in gastric biopsy, saliva, and feces. Evidence of high prevalence of H. pylori in saliva supports oral transmission. Dig Dis Sci. 1996;41(11):2142-9.
97. Henskens YM, Veerman EC, Mantel MS, van der Velden U, Nieuw Amerongen AV. Cystatins S and C in human whole saliva and in glandular salivas in periodontal health and disease. J Dent Res. 1994;73(10):1606-14.
98. Anil S, Remani P, Beena VT, Nair RG, Vijayakumar T. Immunoglobulins in the saliva of diabetic patients with periodontitis. Ann Dent. 1995;54(1-2):30-3.
99. Mandel ID, Kutscher A, Denning CR, Thompson RH, Jr., Zegarelli EV. Salivary studies in cystic fibrosis. Am J Dis Child. 1967;113(4):431-8.
100. Ben-Aryeh H, Spielman A, Szargel R, Gutman D, Scharf J, Nahir M, et al. Sialochemistry for diagnosis of Sjogrens syndrome in xerostomic patients. Oral Surg Oral Med Oral Pathol. 1981;52(5):487-90.
101. Armstrong D, Van Wormer D, Dimmitt S. Tissue peroxidase in the normal and neoplastic salivary gland. J Clin Lab Anal. 1991;5(4):293-8.
102. Jenzano JW, Courts NF, Timko DA, Lundblad RL. Levels of glandular kallikrein in whole saliva obtained from patients with solid tumors remote from the oral cavity. J Dent Res. 1986;65(1):67-70.
103. Streckfus C, Bigler L, Dellinger T, Dai X, Kingman A, Thigpen JT. The presence of soluble c-erbB-2 in saliva and serum among women with breast carcinoma: a preliminary study. Clin Cancer Res. 2000;6(6):2363-70.
104. Chen DX, Schwartz PE, Li FQ. Saliva and serum CA 125 assays for detecting malignant ovarian tumors. Obstet Gynecol. 1990;75(4):701-4.
105. Ohshiro K, Rosenthal DI, Koomen JM, Streckfus CF, Chambers M, Kobayashi R, et al. Pre-analytic saliva processing affect proteomic results and biomarker screening of head and neck squamous carcinoma. Int J Oncol. 2007;30(3):743-9.
106. Dowling P, Wormald R, Meleady P, Henry M, Curran A, Clynes M. Analysis of the saliva proteome from patients with head and neck squamous cell carcinoma reveals differences in abundance levels of proteins associated with tumour progression and metastasis. J Proteomics. 2008;71(2):168-75.
107. de Jong EP, Xie H, Onsongo G, Stone MD, Chen XB, Kooren JA, et al. Quantitative proteomics reveals myosin and actin as promising saliva biomarkers for distinguishing pre-malignant and malignant oral lesions. PLoS One. 2010;5(6):e11148.
108. Wu JY, Yi C, Chung HR, Wang DJ, Chang WC, Lee SY, et al. Potential biomarkers in saliva for oral squamous cell carcinoma. Oral Oncol. 2010;46(4):226-31.
109. Castagnola M, Cabras T, Vitali A, Sanna MT, Messana I. Biotechnological implications of the salivary proteome. Trends Biotechnol. 2011; 29(8):409-18.
110. Jou YJ, Lin CD, Lai CH, Chen CH, Kao JY, Chen SY, et al. Proteomic identification of salivary transferrin as a biomarker for early detection of oral cancer. Anal Chim Acta. 2010;681(1-2):41-8.
111. Daniels TR, Delgado T, Rodriguez JA, Helguera G, Penichet ML. The transferrin receptor part I: biology and targeting with cytotoxic antibodies for the treatment of cancer. Clin Immunol. 2006;121(2):144-58.
112. Vidotto A, Henrique T, Raposo LS, Maniglia JV, Tajara EH. Salivary and serum proteomics in head and neck carcinomas: before and after surgery and radiotherapy. Cancer Biomark. 2010; 8(2):95-107.
113. Omenn GS, States DJ, Adamski M, Blackwell TW, Menon R, Hermjakob H, et al. Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics. 2005;5(13):3226-45.
114. Surinova S, Schiess R, Huttenhain R, Cerciello F, Wollscheid B, Aebersold R. On the development of plasma protein biomarkers. J Proteome Res. 2011;10(1):5-16.
115. Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics. 2002;1(11):845-67.
116. Tirumalai RS, Chan KC, Prieto DA, Issaq HJ, Conrads TP, Veenstra TD. Characterization of the low molecular weight human serum proteome. Mol Cell Proteomics. 2003;2(10):1096-103.
117. 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(4):1694-705.
118. Wolf-Yadlin A, Hautaniemi S, Lauffenburger DA, White FM. Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc Natl Acad Sci USA. 2007;104(14):5860-5.
119. Picotti P, Bodenmiller B, Mueller LN, Domon B, Aebersold R. Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell. 2009;138(4):795-806.
120. Keshishian H, Addona T, Burgess M, Kuhn E, Carr SA. Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol Cell Proteomics. 2007;6(12):2212-29.
121. Riaz S, Alam SS, Akhtar MW. Proteomic identification of human serum biomarkers in diabetes mellitus type 2. J Pharm Biomed Anal. 2010;51(5):1103-7.
122. Liu X, Feng Q, Chen Y, Zuo J, Gupta N, Chang Y, et al. Proteomics-based identification of differentially-expressed proteins including galectin-1 in the blood plasma of type 2 diabetic patients. J Proteome Res. 2009;8(3):1255-62.
123. de Seny D, Fillet M, Ribbens C, Maree R, Meuwis MA, Lutteri L, et al. Monomeric calgranulins measured by SELDI-TOF mass spectrometry and calprotectin measured by ELISA as biomarkers in arthritis. Clin Chem. 2008;54(6):1066-75.
124. Kiernan UA, Nedelkov D, Nelson RW. Multiplexed mass spectrometric immunoassay in biomarker research: a novel approach to the determination of a myocardial infarct. J Proteome Res. 2006;5(11):2928-34.
125. He QY, Lau GK, Zhou Y, Yuen ST, Lin MC, Kung HF, et al. Serum biomarkers of hepatitis B virus infected liver inflammation: a proteomic study. Proteomics. 2003;3(5):666-74.
126. Zhao X, Xiao WZ, Pu XP, Zhong LJ. Proteome analysis of the sera from Chinese Parkinson's disease patients. Neurosci Lett. 2010;479(2):175-9.
127. Seeber B, Sammel MD, Fan X, Gerton GL, Shaunik A, Chittams J, et al. Proteomic analysis of serum yields six candidate proteins that are differentially regulated in a subset of women with endometriosis. Fertil Steril. 2010;93(7):2137-44.
128. Minami S, Sato Y, Matsumoto T, Kageyama T, Kawashima Y, Yoshio K, et al. Proteomic study of sera from patients with bladder cancer: usefulness of S100A8 and S100A9 proteins. Cancer Genomics Proteomics. 2010;7(4):181-9.
129. Freed GL, Cazares LH, Fichandler CE, Fuller TW, Sawyer CA, Stack BC, Jr., et al. Differential capture of serum proteins for expression profiling and biomarker discovery in pre-and posttreatment head and neck cancer samples. Laryngoscope. 2008;118(1):61-8.
130. Lai CH, Chang NW, Lin CF, Lin CD, Lin YJ, Wan L, et al. Proteomics-based identification of haptoglobin as a novel plasma biomarker in oral squamous cell carcinoma. Clin Chim Acta. 2010;411(13-14):984-91.
131. Wei YS, Zheng YH, Liang WB, Zhang JZ, Yang ZH, Lv ML, et al. Identification of serum biomarkers for nasopharyngeal carcinoma by proteomic analysis. Cancer. 2008;112(3):544-51.
132. Cheng AJ, Chen LC, Chien KY, Chen YJ, Chang JT, Wang HM, et al. Oral cancer plasma tumor marker identified with bead-based affinity-fractionated proteomic technology. Clin Chem. 2005;51(12):2236-44.
133. Ransohoff DF, Martin C, Wiggins WS, Hitt BA, Keku TO, Galanko JA, et al. Assessment of serum proteomics to detect large colon adenomas. Cancer Epidemiol Biomarkers Prev. 2008;17(8):2188-93.
134. Gemoll T, Roblick UJ, Auer G, Jornvall H, Habermann JK. SELDI-TOF serum proteomics and colorectal cancer: a current overview. Arch Physiol Biochem. 2010;116(4-5):188-96.
135. Liu WL, Zhang G, Wang JY, Cao JY, Guo XZ, Xu LH, et al. Proteomics-based identification of autoantibody against CDC25B as a novel serum marker in esophageal squamous cell carcinoma. Biochem Biophys Res Commun. 2008;375(3):440-5.
136. Chong PK, Lee H, Loh MC, Choong LY, Lin Q, So JB, et al. Upregulation of plasma C9 protein in gastric cancer patients. Proteomics. 2010;10(18):3210-21.
137. Sun Y, Zang Z, Xu X, Zhang Z, Zhong L, Zan W, et al. Differential proteomics identification of HSP90 as potential serum biomarker in hepatocellular carcinoma by two-dimensional electrophoresis and mass spectrometry. Int J Mol Sci. 2010;11(4):1423-33.
138. Feng JT, Liu YK, Song HY, Dai Z, Qin LX, Almofti MR, et al. Heat-shock protein 27: a potential biomarker for hepatocellular carcinoma identified by serum proteome analysis. Proteomics. 2005;5(17):4581-8.
139. Hamrita B, Chahed K, Trimeche M, Guillier CL, Hammann P, Chaieb A, et al. Proteomics-based identification of alpha1-antitrypsin and haptoglobin precursors as novel serum markers in infiltrating ductal breast carcinomas. Clin Chim Acta. 2009;404(2):111-8.
140. Goncalves A, Esterni B, Bertucci F, Sauvan R, Chabannon C, Cubizolles M, et al. Postoperative serum proteomic profiles may predict metastatic relapse in high-risk primary breast cancer patients receiving adjuvant chemotherapy. Oncogene. 2006;25(7):981-9.
141. Rong Y, Jin D, Hou C, Hu J, Wu W, Ni X, et al. Proteomics analysis of serum protein profiling in pancreatic cancer patients by DIGE: up-regulation of mannose-binding lectin 2 and myosin light chain kinase 2. BMC Gastroenterol. 2010;10:68.
142. Xue A, Scarlett CJ, Chung L, Butturini G, Scarpa A, Gandy R, et al. Discovery of serum biomarkers for pancreatic adenocarcinoma using proteomic analysis. Br J Cancer. 2010;103(3):391-400.
143. Al-Ruwaili JA, Larkin SE, Zeidan BA, Taylor MG, Adra CN, Aukim-Hastie CL, et al. Discovery of serum protein biomarkers for prostate cancer progression by proteomic analysis. Cancer Genomics Proteomics. 2010;7(2):93-103.
144. Byrne JC, Downes MR, ODonoghue N, OKeane C, ONeill A, Fan Y, et al. 2D-DIGE as a strategy to identify serum markers for the progression of prostate cancer. J Proteome Res. 2009;8(2):942-57.
145. Bharti A, Ma PC, Maulik G, Singh R, Khan E, Skarin AT, et al. Haptoglobin alpha-subunit and hepatocyte growth factor can potentially serve as serum tumor biomarkers in small cell lung cancer. Anticancer Res. 2004;24(2C):1031-8.
146. Shevchenko VE, Arnotskaya NE, Zaridze DG. Detection of lung cancer using plasma protein profiling by matrix-assisted laser desorption/ionization mass spectrometry. Eur J Mass Spectrom. 2010;16(4):539-49.
147. Hara T, Honda K, Ono M, Naito K, Hirohashi S, Yamada T. Identification of 2 serum biomarkers of renal cell carcinoma by surface enhanced laser desorption/ionization mass spectrometry. J Urol. 2005;174(4 Pt 1):1213-7.
148. Sarkissian G, Fergelot P, Lamy PJ, Patard JJ, Culine S, Jouin P, et al. Identification of pro-MMP-7 as a serum marker for renal cell carcinoma by use of proteomic analysis. Clin Chem. 2008;54(3):574-81.
149. Vermaat JS, van der Tweel I, Mehra N, Sleijfer S, Haanen JB, Roodhart JM, et al. Two-protein signature of novel serological markers apolipoprotein-A2 and serum amyloid alpha predicts prognosis in patients with metastatic renal cell cancer and improves the currently used prognostic survival models Ann Oncol. 2010;21(7):1472-81.
150. Kolla V, Jeno P, Moes S, Tercanli S, Lapaire O, Choolani M, et al. Quantitative proteomics analysis of maternal plasma in Down syndrome pregnancies using isobaric tagging reagent (iTRAQ). J Biomed Biotechnol. 2010;2010:952047.
151. Hawkridge AM, Muddiman DC. Mass spectrometry-based biomarker discovery: toward a global proteome index of individuality. Annu Rev Anal Chem. 2009;2:265-77.
152. Apweiler R, Aslanidis C, Deufel T, Gerstner A, Hansen J, Hochstrasser D, et al. Approaching clinical proteomics: current state and future fields of application in fluid proteomics. Clin Chem Lab Med. 2009;47(6):724-44.
153. Zhang Z, Bast RC Jr, Yu Y, Li J, Sokoll LJ, Rai AJ, et al. Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer. Cancer Res. 2004;64(16):5882-90.
154. Ye B, Skates S, Mok SC, Horick NK, Rosenberg HF, Vitonis A, et al. Proteomic-based discovery and characterization of glycosylated eosinophil-derived neurotoxin and COOH-terminal osteopontin fragments for ovarian cancer in urine. Clin Cancer Res. 2006;12(2):432-41.