10 years of SELDI: What have we learnt?

Current Proteomics

Volumn 7, Issue 1, 2010, Pages 15-25

  Wei, Wenbin ^a   Martin, Ashley ^a   Johnson, Philip J ^a   Ward, Douglas G ^a  

^a UNIVERSITY OF BIRMINGHAM   (United Kingdom)

Author keywords

Biomarker; Cancer; Peptidome; Proteome; SELDI; Serum

Indexed keywords

EID: 77953724736     PISSN: 15701646     EISSN: None     Source Type: Journal    
DOI: 10.2174/157016410790979617     Document Type: Article

References (90)

1. Hutchens, T.W. and Yip, T.T. New desorption strategies for the mass spectrometric analysis of macromolecules. Rapid Commun. Mass Spectrom., 1993, 7, 576-580.
2. Poon, T.C.W.; Yip, T-T; Chan, A.T.C.; Yip, C.; Yip, V.; Mok, T.S.K.; Lee, C.C.Y.; Leung, T.W.T.; Ho, S.K.W. and Johnson, P.J. Comprehensive proteomic profiling identifies serum proteomic signatures for detection of hepatocellular carcinoma and its subtypes. Clin. Chem., 2003, 49, 752-760.
3. Roche, S.; Tiers, L.; Provansal, M.; Piva, M.T. and Lehmann, S. Interest of major serum protein removal for surface-enhanced Laser desorption/ionization - time of flight (SELDI-TOF) proteomic blood profiling. Proteome Sci., 2006, 4, 20.
4. Thulasiraman, V.; Lin, S.; Gheorghiu, L.; Lathrop, J.; Lomas, L.; Hammond, D. and Boschetti, E. Reduction of the concentration difference of proteins in biological liquids using a library of combinatorial ligands. Electrophoresis, 2005, 26, 3561-3571.
5. Emanuele, V.A. and Gurbaxani, B.M. Benchmarking currently available SELDI-TOF MS preprocessing techniques. Proteomics, 2009, 9, 1754-1762.
6. Paweletz, C.P.; Trock, B.; Pennanen, M.; Tsangaris, T.; Magnant, C.; Liotta, L.A. and Petricoin, E.F. Proteomic patterns of nipple aspirate fluids obtained by SELDI-TOF: potential for new biomarkers to aid in the diagnosis of breast cancer. Dis. Markers, 2001, 17, 301-307.
7. Petricoin, E.F.; Ardekani, A.M.; Hitt, B.A.; Levine, P.; Fusaro, V.; Steinberg, S.; Mills, G.; Simone, C.; Fishman, D.; Kohn, E. and Liotta, L.A. Use of proteomic patterns in serum to identiy ovarian cancer. Lancet, 2002, 359, 572-575.
8. Baggerly, K.A.; Morris, J.S. and Coombes, K.R. Reproducibility of SELDI-TOF protein patterns in serum: comparing data sets from different experiments. Bioinformatics, 2004, 20, 777-785.
9. Sorace, J.M. and Zhan, M. A data review and re-assessment of ovarian cancer serum proteomic profiling. BMC Bioinformatics, 2003, 4, 24.
10. Liotta. L.A; Lowenthal, M.; Mehta, A.; Conrads, T.P.; Veenstra, T.D.; Fishman, D.A. and Petricoin, E.F. Importance of communication between producers and consumers of publicly available experimental data. J. Natl. Cancer Inst., 2005, 97, 310-314.
11. Wagner, L. A test before its time? FDA stalls distribution process of proteomic test. J. Natl. Cancer Inst., 2004, 96, 500-501.
12. Pepe, M.S.; Etzioni, R.; Feng, Z.; Potter, J.D.; Thompson, M.L.; Thornquist, M.; Winget, M. and Yasui, Y. Phases of biomarker development for early detection of cancer. J. Natl. Cancer Inst., 2001, 93, 1054-1061.
13. Peng, J.; Stanley, A.J.; Cairns, D.; Selby, P.J. and Banks, R.E. Using the protein chip interface with quadrupole time-of-flight mass spectrometry to directly identify peaks in SELDI profiles: initial evaluation using low molecular weight serum peaks. Proteomics, 2009, 9, 492-498.
14. Ward, D.G.; Suggett, N.; Cheng, Y.; Wei, W.; Johnson, H.; Billingham, L.J.; Ismail, T.; Wakelam, M.J.O.; Johnson, P.J. and Martin, A. Identification of serum biomarkers for colon cancer by proteomic analysis. Br. J. Cancer, 2006, 94,1898-1905.
15. Kozak, K.R.; Su, F.; Whitelegge, J.P.; Faull, K.; Reddy, S. and Farias-Eisner, R. Characterization of serum biomarkers for detection of early stage ovarian cancer. Proteomics, 2005, 5, 4589-4596.
16. Tomosugi, N.; Kawabata, H.; Wakatabe, R.; Higuchi, M.; Yamaya, H.; Umehara, H. and Ishikawa, I. Detection of serum hepcidin in renal failure and inflammation by using proteinchip system. Blood, 2006, 15, 1381-1387.
17. Ward. D.; Nyangoma, S.; Joy, H.; Hamilton, E.; Wei, W.; Tselepis, C.; Steven, N.; Wakelam, M.J.O.; Johnson, P.J.; Ismail, T. and Martin, A. Proteomic profiling of urine for the detection of colon cancer. Proteome Sci., 2008, 6, 19.
18. Ward, D.; Roberts, K.; Stonelake, P.; Goon, P.; Zampronio, C.G.; Martin, A.; Johnson, P.J.; Iqbal, T. and Tselepis, C. SELDI-TOFMS determination of hepcidin in clinical samples using stable isotope labelled hepcidin as an internal standard. Proteome Sci., 2008, 6, 28.
19. Banks, RE.; Stanley, A.; Cairns, D.E.; Barrett, J.H.; Clarke, P.; Thompson, D. and Selby, P.J. Influences of blood sample processing on low-molecular-weight proteome identified by surfaceenhanced laser desorption/ionization mass spectrometry. Clin. Chem., 2005, 51, 1637-1649.
20. Rai, A.J.; Gelfand, C.A.; Haywood, B.C.; Warunek, D.J.; Yi, J.; Schuchard, M.D.; Mehigh, R.J.; Cockrill, S.L.; Scott, G.B.; Tammen, H.; Schulz-Knappe, P.; Speicher, D.W.; Vitzthum, F.; Haab, B.B.; Siest, G. and Chan, D.W. HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples. Proteomics, 2005, 5, 3262-3277.
21. Benjamini, Y. and Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. Series B (methodological), 1995, 57, 289-300.
22. Hastie, T.; Tibshirani, R. and Friedman, J. The Elements of Statistical Learning; Data Mining, Inference and Prediction. Springer Verlag: New York 2001.
23. Varma, S. and Simon, R. Bias in error estimation when using crossvalidation for model selection. BMC Bioinformatics, 2006, 7, 91.
24. Villanueva, J.; Shaffer, D.R.; Philip, J.; Chaparro, C.A.; Erdjument-Bromage, H.; Olshen, A.B.; Fleisher, M.; Lilja, H.; Brogi, E.; Boyd, J.; Sanchez-Carbayo, M.; Holland, E.C.; Cordon-Cardo, C.; Scher, H.I. and Tempst, P. Differential exoprotease activities confer tumor-specific serum peptidome patterns. J. Clin. Invest., 2006, 116, 271-284.
25. Taguchi, F.; Solomon, B.; Gregorc, V.; Roder, H.; Gray, R.; Kasahara, K.; Nishio, M.; Brahmer, J.; Spreafico, A.; Ludovini, V.; Massion, P.P.; Dziadziuszko, R.; Schiller, J.; Grigorieva, J.; Tsypin, M.; Hunsucker, S.W.; Caprioli, R.; Duncan, M.W.; Hirsch, F.R.; Bunn, P.A. and Carbone, D.P. Mass spectrometry to classify non-small-cell lung cancer patients for clinical outcome after treatment with epidermal growth factor receptor tyrosine kinase inhibitors: a multicohort cross-institutional study. J. Natl. Cancer Inst., 2007, 99, 838-846.
26. Yildiz, P.B.; Shyr, Y.; Rahman, J.S.; Wardwell, N.R.; Zimmerman, L.J.; Shakhtour, B.; Gray, W.H.; Chen. S.; Li, M.; Roder, H.; Liebler, D.C.; Bigbee, W.L.; Siegfried, J.M.; Weissfeld, J.L.; Gonzalez, A.L.; Ninan, M.; Johnson, D.H.; Carbone, D.P.; Caprioli, R.M. and Massion, P.P. Diagnostic accuracy of MALDI mass spectrometric analysis of unfractionated serum in lung cancer. J. Thorac. Oncol., 2007, 2, 893-901.
27. Melle, C.; Ernst, G.; Schimmel, B.; Bleul, A. and Von Eggeling, F. Colon-derived liver metastasis, colorectal carcinoma, and hepatocellular carcinoma can be discriminated by the Ca(2+)-binding proteins S100A6 and S100A11. PLoS ONE, 2008, 3, e3767.
28. Albrethsen, J.; Bogebo, R.; Gammeltoft, S.; Olsen, J.; Winther, B. and Raskov, H. Upregulated expression of human neutrophil peptides 1, 2 and 3 (HNP 1-3) in colon cancer serum and tumours: a biomarker study. BMC Cancer, 2005, 19, 8.
29. Escher, N.; Spies-Weisshart, B.; Kaatz, M.; Melle, C.; Bleul, A.; Driesch, D.; Wollina, U. and Von Eggeling, F. Identification of HNP3 as a tumour marker in CD4+ and CD4- lymphocytes of patients with cutaneous T-cell lymphoma. Eur. J. Cancer, 2006, 42, 249-255.
30. Gonçalves, A.; Charafe-Jauffret, E.; Bertucci, F.; Audebert, S.; Toiron, Y.; Esterni, B.; Monville, F.; Tarpin, C.; Jacquemier, J.; Houvenaeghel, G.; Chabannon, C.; Extra, J.M.; Viens, P.; Borg, J.P. and Birnbaum, D. Protein profiling of human breast tumor cells identifies novel biomarkers associated with molecular subtypes. Mol. Cell. Proteom., 2008, 7, 1420-1433.
31. Guo, J.; Yang, E.; Desouza, L.; Diehl, G.; Rodrigues, M.J.; Romaschin, A.D.; Colgan, T.J. and Siu, K.W. A strategy for highresolution protein identification in surface-enhanced laser desorption/ionization mass spectrometry: calgranulin A and chaperonin 10 as protein markers for endometrial carcinoma. Proteomics, 2005, 5, 1953-1966.
32. Melle, C.; Ernst, G.; Schimmel, B.; Bleul, A.; Mothes, H.; Kaufmann, R.; Settmacher, U. and Von Eggeling, F. Different expression of calgizzarin (S100A11) in normal colonic epithelium, adenoma and colorectal carcinoma. Int. J. Oncol., 2006, 28, 195-200.
33. Melle, C.; Ernst, G.; Schimmel, B.; Bleul, A.; Thieme, H.; Kaufmann, R.; Mothes, H.; Settmacher, U.; Claussen, U.; Halbhuber, K.J. and Von Eggeling, F. Discovery and identification of alphadefensins as low abundant, tumor-derived serum markers in colorectal cancer. Gastroenterology, 2005, 129, 66-73.
34. Roesch-Ely, M.; Nees, M.; Karsai, S.; Ruess, A.; Bogumil, R.; Warnken, U.; Schnölzer, M.; Dietz, A.; Plinkert, P.K.; Hofele, C. and Bosch, F.X. Proteomic analysis reveals successive aberrations in protein expression from healthy mucosa to invasive head and neck cancer. Oncogene, 2007, 26, 54-64.
35. Akashi, T. and Yamori, T. A novel method for analyzing phosphoproteins using SELDI-TOF MS in combination with a series of recombinant proteins. Proteomics, 2007, 7, 2350-2354.
36. Ueda, K.; Fukase, Y.; Katagiri, T.; Ishikawa, N.; Irie, S.; Sato, T.; Ito, H.; Nakayama, H.; Miyagi, Y.; Tsuchiya, E.; Kohno, N.; Shiwa, M.; Nakamura, Y. and Daigo, Y. Targeted serum glycoproteomics for the discovery of lung cancer-associated glycosylation disorders using lectin-coupled ProteinChip arrays. Proteomics, 2009, 9, 2182-2192.
37. Ueda, M.; Misumi, Y.; Mizuguchi, M.; Nakamura, M.; Yamashita, T.; Sekijima, Y.; Ota, K.; Shinriki, S.; Jono, H.; Ikeda, S.; Suhr, O.B. and Ando, Y. SELDI-TOF mass spectrometry evaluation of variant transthyretins for diagnosis and pathogenesis of familial amyloidotic polyneuropathy. Clin. Chem., 2009, 55, 1223-1227.
38. Krause, A.; Neitz, S.; Mägert, H.J.; Schulz, A.; Forssmann, W.G.; Schulz-Knappe, P. and Adermann, K. LEAP-1, a novel highly disulfide-bonded human peptide, exhibits antimicrobial activity. FEBS Lett., 2000, 480, 147-150.
39. Pigeon, C.; Ilyin, G.; Courselaud, B.; Leroyer, P.; Turlin, B.; Brissot, P. and Loréal, O. A new mouse liver-specific gene, encoding a protein homologous to human antimicrobial peptide hepcidin, is overexpressed during iron overload. J. Biol. Chem., 2001, 276, 7811-7819.
40. Kemna, E.H.; Tjalsma, H.; Laarakkers, C.; Nemeth, E.; Willems, H. and Swinkels, D.W. Novel urine hepcidin assay by mass spectrometry. Blood, 2005, 106, 3268-3270.
41. Swinkels, D.W.; Girelli, D.; Laarakkers, C.; Kroot, J.; Campostrini, N.; Kemna, E.H. and Tjalsma, H. Advances in quantitative hepcidin measurements by time-of-flight mass spectrometry. PLoS ONE, 2008, 3, e2706.
42. Lewczuk, P.; Esselmann, H.; Meyer, M.; Wollscheid, V.; Neumann, M.; Otto, M.; Maler, J.M.; Rüther, E.; Kornhuber, J. and Wiltfang, J. The amyloid-beta (Abeta) peptide pattern in cerebrospinal fluid in Alzheimer's disease: evidence of a novel carboxyterminally elongated Abeta peptide. Rapid Commun. Mass Spectrom., 2003, 17, 1291-1296.
43. Austen, B.M.; Frears, E.R. and Davies, H. The use of SELDI proteinchip arrays to monitor production of Alzheimer's betaamyloid in transfected cells. J. Pept. Sci., 2000, 6, 459-469.
44. Vehmas, A.K.; Borchelt, D.R.; Price, D.L.; McCarthy, D.; Wills-Karp, M.; Peper, M.J.; Rudow, G.; Luyinbazi, J.; Siew, L.T. and Troncoso, J.C. Beta-Amyloid peptide vaccination results in marked changes in serum and brain Abeta levels in APPswe/PS1DeltaE9 mice, as detected by SELDI-TOF-based ProteinChip technology. DNA Cell Biol., 2001, 20, 713-721.
45. Beher, D.; Wrigley, J.D.; Owens, A.P. and Shearman, M.S. Generation of C-terminally truncated amyloid-beta peptides is dependent on gamma-secretase activity. J. Neurochem., 2002, 82, 563-575.
46. Frears, E.R.; Stephens, D.J.; Walters, C.E.; Davies, H. and Austen, B.M. The role of cholesterol in the biosynthesis of beta-amyloid. Neuroreport., 1999, 10, 1699-1705.
47. Esh, C.; Patton, L.; Kalback, W.; Kokjohn, T.A.; Lopez, J.; Brune, D.; Newell, A.J.; Beach, T.; Schenk, D.; Games, D.; Paul, S.; Bales, K.; Ghetti, B.; Castaño, E.M. and Roher, A.E. Altered APP processing in PDAPP (Val717 -> Phe) transgenic mice yields extended-length Abeta peptides. Biochemistry, 2005, 44, 13807-13819.
48. Lewis, H.D.; Beher, D.; Smith, D.; Hewson, L.; Cookson, N.; Reynolds, D.S.; Dawson, G.R.; Jiang, M.; Van der Ploeg, L.H.; Qian, S.; Rosahl, T.W.; Kalaria, R.N. and Shearman, M.S. Novel aspects of accumulation dynamics and A beta composition in transgenic models of AD. Neurobiol. Aging, 2004, 25, 1175-1185.
49. Peronnet, E.; Becquart, L.; Poirier, F.; Cubizolles, M.; Choquet-Kastylevsky, G. and Jolivet-Reynaud, C. SELDI-TOF MS analysis of the Cardiac Troponin I forms present in plasma from patients with myocardial infarction. Proteomics, 2006, 6, 6288-6289.
50. Bovenkamp, D.E.; Stanley, B.A. and Van Eyk, J.E. Optimization of cardiac troponin I pull-down by IDM affinity beads and SELDI. Methods Mol. Biol., 2007, 357, 91-102.
51. Hou, Y.; Le Bihan, M.C.; Vega-Avelaira, D. and Coulton, G.R. Proteomic changes in hearts of kyphoscoliosis (ky) mutant mice in the absence of structural pathology: implication for the analysis of early human heart disease. Proteomics, 2006, 6, 3096-3108.
52. Le Bihan, M.C.; Hou, Y.; Harris, N.; Tarelli, E. and Coulton, G.R. Proteomic analysis of fast and slow muscles from normal and kyphoscoliotic mice using protein arrays, 2-DE and MS. Proteomics, 2006, 6, 4646-4661.
53. Dyer, E.C.; Jacques, A.M.; Hoskins, A.C.; Ward, D.G.; Gallon, C.E.; Messer, A.E.; Kaski, J.; Burch, M.; Kentish, J.C.; Marston, S.B. Functional analysis of a unique troponin C mutation, Gly159Asp that causes familial dilated cardiomyopathy, studied in explanted heart muscle. Circ. Heart Fail., 2009, 2, 456-464.
54. Song, J.; Patel, M.; Rosenzweig, C.N.; Chan-Li, Y.; Sokoll, L.J.; Fung, E.T.; Choi-Miura, N.H.; Goggins, M.; Chan, D.W. and Zhang, Z. Quantification of fragments of human serum inter-alphatrypsin inhibitor heavy chain 4 by surface-enhanced laser desorption/ ionization-based immunoassay. Clin. Chem., 2006, 52, 1045-1053.
55. Li, J.; Rosenzweig, J.M.; Wang, Y.Y. and Chan, D.W. Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin. Chem., 2002, 48, 1296-1304.
56. Li, J.; Orlandi, R.; White, C.N.; Rosenzweig, J.; Zhao, J.; Seregni, E.; Morelli, D.; Yu, Y.; Meng, X.Y.; Zhang, Z.; Davidson, N.E.; Fung, E.T. and Chan, D.W. Independent validation of candidate breast cancer serum biomarkers identified by mass spectrometry. Clin. Chem., 2005, 51, 2229-2235.
57. Mathelin, C.; Cromer, A.; Wendling, C.; Tomasetto, C. and Rio, M.C. Serum biomarkers for detection of breast cancers: a prospective study. Breast Cancer Res. Treat., 2006, 96, 83-90.
58. Van Winden, A.W.; Gast, M.C.; Beijnen, J.H.; Rutgers, E.J.; Grobbee, D.E.; Peeters, P.H. and Van Gils, C.H. Validation of previously identified serum biomarkers for breast cancer with SELDITOF MS: a case control study. BMC Med. Genomics, 2009, 2, 4.
59. Belluco, C.; Petricoin, E.F.; Mammano, E.; Facchiano, F.; Ross-Rucker, S.; Nitti, D.; Di Maggio, C.; Liu, C.; Lise, M.; Liotta, L.A. and Whiteley, G. Serum proteomic analysis identifies a highly sensitive and specific discriminatory pattern in stage 1 breast cancer. Ann. Surg. Oncol., 2007, 14, 2470-2476.
60. Munro, N.P.; Cairns, D.A.; Clarke, P.; Rogers, M.; Stanley, AJ.; Barrett, J.H.; Harnden, P.; Thompson, D.; Eardley, I.; Banks, R.E. and Knowles, M.A. Urinary biomarker profiling in transitional cell carcinoma. Int. J. Cancer, 2006, 119, 2642-2650.
61. Rai, A.J.; Stemmer, P.M.; Zhang, Z.; Adam, B.L.; Morgan, W.T.; Caffrey, R.E.; Podust, VN.; Patel, M.; Lim, LY.; Shipulina, N.V.; Chan, D.W.; Semmes, O.J. and Leung, H.C. Analysis of Human Proteome Organization Plasma Proteome Project (HUPO PPP) reference specimens using surface enhanced laser desorption/ionization-time of flight (SELDI-TOF) mass spectrometry: multi-institution correlation of spectra and identification of biomarkers. Proteomics, 2005, 5, 3467-3474.
62. Semmes, O.J.; Feng, Z.; Adam, B.L.; Banez, L.L.; Bigbee, W.L.; Campos, D.; Cazares, L.H.; Chan, D.W.; Grizzle; W.E.; Izbicka, E.; Kagan, J.; Malik, G.; McLerran, D.; Moul, J.W.; Partin, A.; Prasanna, P.; Rosenzweig, J.; Sokoll, L.J.; Srivastava, S.; Srivastava, S.; Thompson, I.; Welsh, M.J.; White, N.; Winget, M.; Yasui, Y.; Zhang, Z. and Zhu, L. Evaluation of serum protein profiling by surface-enhanced laser desorption/ionization time-offlight mass spectrometry for the detection of prostate cancer: I. Assessment of platform reproducibility. Clin. Chem., 2005, 51, 102-112.
63. Zhang, Z.; Bast, R.C.; Yu, Y.; Li, J.; Sokoll, L.J.; Rai, A.J.; Rosenzweig, J.M.; Cameron, B.; Wang, Y.Y.; Meng, X.; Berchuck, A.; Van Haaften-Day, C.; Hacker, N.F.; de Bruijn, H.W.; Van der Zee, A.G.; Jacobs, I.J.; Fung, E.T. and Chan, D.W. Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer. Cancer Res., 2004, 64, 5882-5890.
64. McLerran, D.; Grizzle, W.E.; Feng, Z.; Thompson, I.M.; Bigbee, W.L.; Cazares, L.H.; Chan, D.W.; Dahlgren, J.; Diaz, J.; Kagan, J.; Lin, D.W.; Malik, G.; Oelschlager, D.; Partin, A.; Randolph, T.W.; Sokoll, L.; Srivastava, S.; Srivastava, S.; Thornquist, M.; Troyer, D.; Wright, G.L.; Zhang, Z.; Zhu, L. and Semmes, O.J. SELDITOF MS whole serum proteomic profiling with IMAC surface does not reliably detect prostate cancer. Clin. Chem., 2008, 54, 53-60.
65. Adam, B.L.; Qu, Y.Q.; Davis, J.W.; Ward, M.D.; Clements, M.A.; Cazares, L.H.; Semmes, O.J.; Schellhammer, P.F.; Yasui, Y.; Feng, Z. and Wright, G.L. Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men. Cancer Res., 2002, 62, 3609-3614.
66. Qu, Y.; Adam, B.L.; Yasui, Y.; Ward, M.D.; Cazares, L.H.; Schellhammer, P.F.; Feng, Z.; Semmes, O.J. and Wright, G.L. Boosted decision tree analysis of surface-enhanced laser desorption/ionization mass spectral serum profiles discriminates prostate cancer from non-cancer patients. Clin. Chem., 2002, 48, 1835-1843.
67. Ward, D.G.; Chen, Y.C.; N'Kontchou, G.; Thar, T.T.; Barget, N.; Wei, W.; Billingham, L.J.; Martin, A.; Beaugrand, M.; Johnson, P. J. HCC induced changes in the serum proteome of hepatitis C infected chronic liver disease patients. Br. J. Cancer, 2006, 94, 287-292.
68. Mohri, Y.; Mohri, T.; Wei, W.; Qi, Y.; Martin, A.; Miki, C.; Kusunoki, M.; Ward, D.G. and Johnson, P.J. Identification of macrophage migration inhibitory factor and human neutrophil peptides 1-3 as potential biomarkers for gastric cancer. Br. J. Cancer, 2009, 101, 295-302.
69. Lustgarten, J.L.; Kimmel, C.; Ryberg, H. and Hogan, W. EPO-KB: a searchable knowledge base of biomarker to protein links. Bioinformatics, 2008, 24, 1418-1419.
70. Lee, I.N.; Chen, C.; Sheu, J.C.; Lee, H.; Huang, G.T.; Chen, D.S.; Yu, C.Y.; Wen, C.L.; Lu, F.J. and Chow, L.P. Identification of complement C3a as a candidate biomarker in human chronic hepatitis C and HCV-related hepatocellular carcinoma using a proteomics approach. Proteomics, 2006, 6, 2856-2873.
71. Miguet, L.; Bogumil, R.; Decloquement, P.; Herbrecht, R.; Potier, N.; Mauvieux, L. and Van Dorsselaer, A. Discovery and identification of potential biomarkers in a prospective study of chronic lymphoid malignancies using SELDI-TOF-MS. J. Proteome Res., 2006, 5, 2258-2269.
72. Gao, W.M.; Kuick, R.; Orchekowski, R.P.; Misek, D.E.; Qiu, J.; Greenberg, A.K.; Rom, W.N.; Brenner, D.E.; Omenn, G.S.; Haab, B.B. and Hanash, S.M. Distinctive serum protein profiles involving abundant proteins in lung cancer patients based upon antibody microarray analysis. BMC Cancer, 2005, 5, 110.
73. Poon, T.C.W.; Chan, A.T.C.; Zee, B.; Ho, S.K.W.; Mok, T.S.K.; Leung, T.W.T. and Johnson, P.J. Application of classification tree and neural network algorithms to the identification of serological liver marker profiles for the diagnosis of hepatocellular carcinoma. Oncology, 2001, 61, 275-283.
74. Gaspari, M.; Ming-Cheng Cheng, M.; Terracciano, R.; Liu, X.; Nijdam, A.J.; Vaccari, L.; di Fabrizio, E.; Petricoin, E.F.; Liotta, L.A.; Cuda, G.; Venuta, S. and Ferrari, M. Nanoporous surfaces as harvesting agents for mass spectrometric analysis of peptides in human plasma. J. Proteome Res., 2006, 5, 1261-1266.
75. Lowenthal, M.S.; Mehta, A.I.; Frogale, K.; Bandle, R.W.; Araujo, R.P.; Hood, B.L.; Veenstra, T.D.; Conrads, T.P.; Goldsmith, P.; Fishman, D.; Petricoin, E.F. and Liotta, L.A. Analysis of albuminassociated peptides and proteins from ovarian cancer patients. Clin. Chem., 2005, 51, 1933-1945.
76. Tammen, H.; Schulte, I.; Hess, R.; Menzel, C.; Kellmann, M.; Mohring, T. and Schulz-Knappe, P. Peptidomic analysis of human blood specimens: comparison between plasma specimens and serum by differential peptide display. Proteomics, 2005, 5, 3414-3422.
77. Tirumalai, R.S.; Chan, K.C.; Prieto, D.A.; Issaq, H.J.; Conrads, T.P. and Veenstra, T.D. Characterization of the low molecular weight human serum proteome. Mol. Cell. Proteom., 2003, 2, 1096-1103.
78. Vallant, R.M.; Szabo, Z.; Trojer, L.; Najam-ul-Haq, M.; Rainer, M.; Huck, C.W., Bakry, R. and Bonn, G.K. A new analytical material- enhanced laser desorption ionization (MELDI) based approach for the determination of low-mass serum constituents using fullerene derivatives for selective enrichment. J. Proteome Res., 2007, 6, 44-53.
79. Graumann, J.; Hubner, N.C.; Kim, J.B.; Ko, K.; Moser, M.; Kumar, C.; Cox, J.; Schöler, H. and Mann, M. Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5,111 proteins. Mol. Cell. Proteom., 2008, 7, 672-683.
80. Zhou, L.; Beuerman R.W.; Ang, L.P.; Chan, C.M.; Li, S.F.; Chew, F.T. and Tan D.T. Elevation of human alpha-defensins and S100 calcium binding protein A8 and A9 in tear fluid of pterygium patients. Invest. Ophthalmol. Vis. Sci., 2009, 50, 2077-2086.
81. Luciano-Montalvo, C.; Ciborowski, P.; Duan, F.; Gendelman, H.E. and Meléndez, L. Proteomic analyses associate cystatin B with restricted HIV-1 replication in placental macrophages. Placenta, 2008, 29, 1016-1023.
82. Le, Q.T.; Shi, G.; Cao, H.; Nelson, D.W.; Wang, Y., Chen, E.Y., Zhao, S., Kong, C., Richardson, D.; O'Byrne, K.J.; Giaccia, A.J. and Koong, A.C. Galectin-1: a link between tumor hypoxia and tumor immune privilege. J. Clin. Oncol., 2005, 23, 8932-8941.
83. Mazzatti, D.J.; Pawelec, G.; Longdin, R.; Powell, J.R. and Forsey, R.J. SELDI-TOF-MS ProteinChip array profiling of T-cell clones propagated in long-term culture identifies human profilin-1 as a potential bio-marker of immunosenescence. Proteome Sci., 2007, 5, 7.
84. Melle, C.; Ernst, G.; Schimmel, B.; Bleul, A.; Kaufmann, R.; Hommann, M.; Richter, K.K.; Daffner, W.; Settmacher, U.; Claussen, U. A and Von Eggeling, F. Characterization of pepsinogen C as a potential biomarker for gastric cancer using a histoproteomic approach. J. Proteome Res., 2005, 4, 1799-1804.
85. Shiwa, M.; Nishimura, Y.; Wakatabe, R.; Fukawa, A.; Arikuni, H.; Ota, H.; Kato, Y. and Yamori, T. Rapid discovery and identification of a tissue-specific tumor biomarker from 39 human cancer cell lines using the SELDI ProteinChip platform. Biochem. Biophys. Res. Commun., 2003, 309, 18-25.
86. Furuta, M.; Shiraishi, T.; Okamoto, H.; Mineta, T.; Tabuchi, K. and Shiwa, M. Identification of pleiotrophin in conditioned medium secreted from neural stem cells by SELDI-TOF and SELDI-tandem mass spectrometry. Brain Res. Dev. Brain Res., 2004, 152, 189-197.
87. Akashi, T.; Nishimura, Y.; Wakatabe, R.; Shiwa, M. and Yamori, T. Proteomics-based identification of biomarkers for predicting sensitivity to a PI3-kinase inhibitor in cancer. Biochem. Biophys. Res. Commun., 2007, 352, 514-521.
88. Diamond, D.L.; Zhang, Y.; Gaiger, A.; Smithgall, M.; Vedvick, T.S. and Carter, D. Use of ProteinChip array surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDITOF MS) to identify thymosin beta-4, a differentially secreted protein from lymphoblastoid cell lines. J. Am. Soc. Mass Spectrom., 2003, 14, 760-765.
89. Melle, C.; Camacho, J.A; Surber, R.; Betge, S.; Von Eggeling, F. and Zimmer, T. Region-specific alterations of global protein expression in the remodelled rat myocardium. Int. J. Mol. Med., 2006, 18, 1207-1215.
90. Ricolleau, G.; Charbonnel, C.; Lodé, L.; Loussouarn, D.; Joalland, M.P.; Bogumil, R.; Jourdain, S.; Minvielle, S.; Campone, M.; Déporte-Fety, R.; Campion, L. and Jézéquel, P. Surface-enhanced laser desorption/ionization time of flight mass spectrometry protein profiling identifies ubiquitin and ferritin light chain as prognostic biomarkers in node-negative breast cancer tumors. Proteomics, 2006, 6, 1963-1975.