Current Gel Electrophoresis Approaches to Low-Abundance Protein Marker Discovery

Proteomic and Metabolomic Approaches to Biomarker Discovery

Volumn , Issue , 2013, Pages 175-190

  Boschetti, Egisto ^a   Candiano, Giovanni ^b   Righetti, Pier Giorgio ^b  

^a EB Consult   (France)

^b G GASLINI INSTITUTE   (Italy)

Author keywords

Biological fluids; Biomarkers; Combinatorial peptide ligand libraries; Sera; Two dimensional maps

Indexed keywords

EID: 84880770747     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-0-12-394446-7.00011-X     Document Type: Chapter

References (59)

1. Westermeier R. Electrophoresis in Practice 2005, VCH. 4th ed.
2. Penque D. Two-dimensional gel electrophoresis and mass spectrometry for biomarker discovery. Proteomics Clin Appl 2009, 3:155-172.
3. Raymond S. Acrylamide gel electrophoresis. Ann NY Acad Sci 1964, 121:350-365.
4. Kaltschmidt E., Wittmarin H.G. Ribosomal proteins. VII: Two-dimensional polyacrylamide gel electrophoresis for fingerprinting of ribosomal proteins. Anal Biochem 1970, 36:401-412.
5. O'Farrell P.H. High resolution two-dimensional electrophoresis of proteins. J Biol Chem 1975, 250:400-4021.
6. Righetti P.G. Immobilized pH gradients: theory and methodology 1990, Elsevier, Amsterdam.
7. Righetti P.G., Bossi A. Isoelectric focusing in immobilized pH gradients: an update. J Chromatog B 1997, 699:777-789.
8. Luche S., Santoni V., Rabilloud T. Evaluation of nonionic and zwitterionic detergents as membrane protein solubilizers in two-dimensional electrophoresis. Proteomics 2003, 3:249-253.
9. Neuhoff V., Arold N., Taube D., et al. Improved staining of proteins in polyacrylamide gels including isoelectric focusing gels with clear background at nanogram sensitivity using Coomassie Brilliant Blue G-250 and R-250. Electrophoresis 1988, 9:255-262.
10. Hanash S.M., Tubergen D.G., Heyn R.M., et al. Two-dimensional gel electrophoresis of cell proteins in childhood leukemia, with silver staining: a preliminary report. Clin Chem 1982, 28:1026-1030.
11. Valdes I., Pitarch A., Gil C., et al. Novel procedure for the identification of proteins by mass fingerprinting combining two-dimensional electrophoresis with fluorescent SYPRO red staining. J Mass Spectrom 2000, 35:672-682.
12. Cong W.T., Hwang S.Y., Jin L.T., et al. Sensitive fluorescent staining for proteomic analysis of proteins in 1-D and 2-D SDS-PAGE and its comparison with SYPRO Ruby by PMF. Electrophoresis 2008, 29:4304-4315.
13. Lilley K.S., Friedman D.B. All about DIGE: quantification technology for differential-display 2D-gel proteomics. Expert Rev. Proteomics 2004, 1:401-409.
14. Unlu M., Morgan M.E., Minden J.S. Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 1997, 18:2071-2077.
15. Alban A., David S.O., Bjorkesten L., et al. A novel experimental design for comparative two-dimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics 2003, 3:36-44.
16. Westbrook J.A., Yan J.X., Wait R., et al. Zooming-in on the proteome: very narrow-range immobilised pH gradients reveal more protein species and isoforms. Electrophoresis 2001, 22:2865-2871.
17. Tirumalai R.S., Chan K.C., Prieto D.A., et al. Characterization of the low molecular weight human serum proteome. Mol Cell Proteomics 2003, 2:1096-1103.
18. Fountoulakis Takacs M.F., Takacs B. Enrichment of low-copy-number gene products by hydrophobic interaction chromatography. J Chromatogr A 1999, 833:57-168.
19. Dayarathna MK, Hancock WS, Hincapie M. A two steps fractionation approach for plasma proteomics using immunodepletion of abundant proteins and multi-lectin affinity chromatography: Application to the analysis of obesity, diabetes and hypertension diseases. J Sep Sci 200;831:1156-66.
20. Lei T., He Q.Y., Wang Y.L., et al. Heparin chromatography to deplete high-abundance proteins for serum proteomics. Clin Chim Acta 2008, 388:173-178.
21. Andersen J.N., Sathyanarayanan S., Di Bacco A., et al. Pathway-based identification of biomarkers for targeted therapeutics: personalized oncology with PI3K pathway inhibitors. Sci Transl Med 2010, 2:43-55.
22. Sykora C., Hoffmann R., Hoffmann P. Enrichment of multiphosphorylated peptides by immobilized metal affinity chromatography using Ga(III)- and Fe(III)-complexes. Protein Pept Lett 2007, 14:489-496.
23. Thingholm T.E., Jørgensen T.J., Jensen O.N., et al. Highly selective enrichment of phosphorylated peptides using titanium dioxide. Nat Protoc 2006, 1:1929-1935.
24. Shi Q., Gibson G.E. Oxidative stress and transcriptional regulation in Alzheimer disease. Alzheimer Dis Assoc Disord 2007, 21:276-291.
25. Ni R.J., Shen Z., Yang C.P., et al. Identification of low abundance polyA-binding proteins in Arabidopsis chloroplast using polyA-affinity column. Mol Biol Rep 2010, 37:637-641.
26. Xu Y., Wang B.C., Zhu Y.X. Identification of proteins expressed at extremely low level in Arabidopsis leaves. Biochem Biophys Res Commun 2007, 358:808-812.
27. Echan L.A., Tang H.Y., Ali-Khan N., et al. Depletion of multiple high-abundance proteins improves protein profiling capacities of human serum and plasma. Proteomics 2005, 5:3292-3303.
28. Hinerfeld D., Innamorati D., Pirro J., et al. Serum/Plasma depletion with chicken immunoglobulin Y antibodies for proteomic analysis from multiple mammalian species. J Biomol Tech 2004, 15:184-190.
29. Lin B., White J.T., Wu J., et al. Deep depletion of abundant serum proteins reveals low-abundant proteins as potential biomarkers for human ovarian cancer. Proteomics Clin Appl 2009, 3:853-861.
30. Stempfer R., Kubicek M., Lang I.M., et al. Quantitative assessment of human serum high-abundance protein depletion. Electrophoresis 2008, 29:4316-4323.
31. Shen Y., Kim J., Strittmatter E.F., et al. Characterization of the human blood plasma proteome. Proteomics 2005, 5:4034-4045.
32. Yadav A.K., Bhardwaj G., Basak T., et al. A systematic analysis of eluted fraction of plasma post immunoaffinity depletion: implications in biomarker discovery. PLoS ONE 2011, 6:e24442.
33. Tu C., Rudnick P.A., Martinez M.Y., et al. Depletion of abundant plasma proteins and limitations of plasma proteomics. J. Proteome Res 2010, 9:4982-4991.
34. Afkarian M., Bhasin M., Dillon S.T., et al. Optimizing a proteomics platform for urine biomarker discovery. Mol Cell Proteomics 2010, 9:2195-2204.
35. Righetti P.G., Boschetti E. The art of observing rare protein species with peptide libraries. Proteomics 2009, 9:1492-1510.
36. Righetti P.G., Boschetti E., Kravchuk A., et al. The proteome buccaneers: how to unearth your treasure chest via combinatorial peptide ligand libraries. Exp Rev Proteomics 2010, 7:373-385.
37. Li L., Sun C.J., Freeby S., Yee D., et al. Protein sample treatment with peptide ligand library: coverage and consistency. J Prot Bioinform 2009, 2:485-494.
38. Mouton-Barbosa E., Roux-Dalvai F., Bouyssié D., et al. In-depth exploration of cerebrospinal fluid by combining peptide ligand library treatment and label-free protein quantification. Mol Cell Proteomics 2010, 9:1006-1021.
39. Zhi W., Purohit S., Carey C., et al. Proteomic technologies for the discovery of type 1 diabetes biomarkers. J Diabetes Sci Technol 2010, 4:993-1002.
40. Matos J.M., Witzmann F.A., Cummings O.W., et al. A pilot study of proteomic profiles of human hepatocellular carcinoma in the United States. J Surg Res 2009, 155:237-243.
41. Bai S., Liu S., Guo X., et al. Proteome analysis of biomarkers in the cerebrospinal fluid of neuromyelitis optica patients. Mol Vi 2009, 15:1638-1648.
42. Nicholas B.L., Skipp P., Barton S., et al. Identification of lipocalin and apolipoprotein A1 as biomarkers of chronic obstructive pulmonary disease. Am J Respir Crit Care Med 2010, 181:1049-1060.
43. Byrne J.C., Downes M.R., O'Donoghue N., et al. 2D-DIGE as a strategy to identify serum markers for the progression of prostate cancer. J Proteome Res 2009, 8:942-957.
44. Taneja S., Sen S., Gupta V.K., et al. Plasma and urine biomarkers in acute viral hepatitis E. Proteome Sci 2009, 27:7-39.
45. Zhang L., Xiao H., Karlan S., et al. Discovery and preclinical validation of salivary transcriptomic and proteomic biomarkers for the non-invasive detection of breast cancer. PLoS One 2010, 5:e15573.
46. Sihlbom C., Kanmert I., Bahr H., et al. Evaluation of the combination of bead technology with SELDI-TOF-MS and 2-D DIGE for detection of plasma proteins. J Proteome Res 2008, 7:4191-4198.
47. Righetti P.G., Boschetti E., Zanella A., et al. Plucking, pillaging and plundering proteomes with combinatorial peptide ligand libraries. J Chromatogr A 2010, 1217:893-900.
48. Farinazzo A., Fasoli E., Kravchuk A.V., et al. En bloc elution of proteomes from combinatorial peptide ligand libraries. J Proteomics 2009, 72:725-730.
49. Leger T., Lavigne D., Lecaer J.P., et al. Solid-phase hexapeptide ligand libraries open up new perspectives in the discovery of biomarkers in human plasma. Clin Chim Acta 2011, 412:740-747.
50. D'Amato A., Bachi A., Fasoli E., et al. In-depth exploration of Hevea brasiliensis latex proteome and "hidden allergens" via combinatorial peptide ligand libraries. J Proteomics 2010, 73:1368-1380.
51. Shahali Y., Sutra J.P., Fasoli E., et al. Allergomic study of cypress pollen via combinatorial peptide ligand libraries. J Proteomics 2012, (in press).
52. Beseme O., Fertin M., Drobecq H., et al. Combinatorial peptide ligand library plasma treatment: advantages for accessing low-abundance proteins. Electrophoresis 2010, 31:2697-2704.
53. Fahiminiya S., Labas V., Dacheux J., et al. Improvement of 2D-PAGE resolution of human, porcine and equine follicular fluid by means of hexapeptide ligand library. Reprod Domest Anim 2011, 46:561-563.
54. Martinkova J., Jelinkova L., Jarkovska K., et al. Protein profiling of human follicular fluid: quest for biomarkers of ovarian hyperstimulation syndrome. Cancer Genom Proteom 2009, 6:58-65.
55. Marrocco C., Rinalducci S., Mohamadkhani A., et al. Plasma gelsolin protein: a candidate biomarker for hepatitis B-associated liver cirrhosis identified by proteomic approach. Blood Transfus 2010, 8:s105-s112.
56. Malaud E., Piquer D., Merle D., et al. Carotid atherosclerotic plaques: proteomics study after a low-abundance protein enrichment step. Electrophoresis 2012, 33:470-482.
57. Egidi M.G., Rinalducci S., Marrocco C., et al. Proteomic analysis of plasma derived from platelet buffy coats during storage at room temperature. An application of ProteoMiner technology. Platelets 2011, 22:252-269.
58. Candiano G., Santucci L., Bruschi M., et al. "Cheek-to-cheek" urinary proteome profiling via combinatorial peptide ligand libraries: A novel, unexpected elution system. J Proteomics 2012, 75:796-805.
59. Special issue on two dimensional gel electrophoresis. Clin Chem 1984, 30:1897-2108. L. Anderson, N.G. Anderson (Eds.).