Ocular Proteomics with Emphasis on Two-Dimensional Gel Electrophoresis and Mass Spectrometry

Biological Procedures Online

Henrik Vorum¹  Bent Honoré²  Jan Ulrik Prause³  Steffen Heegaard³  Nakul Mandal² 

[1]Department of Ophthalmology, Aalborg Hospital, Aarhus University Hospital, Aalborg, Denmark

[2]Department of Medical Biochemistry, Aarhus University, Aarhus, Denmark

[3]Eye Pathology Section, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark

关键词: mass spectrometry;    2D-DIGE;    2D-PAGE;    sample preparation;    ocular proteomics;   

Others  :  797139
DOI  :  10.1007/s12575-009-9019-7

 received in 2009-08-19, accepted in 2009-09-28,  发布年份 2009

【 摘 要 】

The intention of this review is to provide an overview of current methodologies employed in the rapidly developing field of ocular proteomics with emphasis on sample preparation, two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Appropriate sample preparation for the diverse range of cells and tissues of the eye is essential to ensure reliable results. Current methods of protein staining for 2D-PAGE, protein labelling for two-dimensional difference gel electrophoresis, gel-based expression analysis and protein identification by MS are summarised. The uses of gel-free MS-based strategies (MuDPIT, iTRAQ, ICAT and SILAC) are also discussed. Proteomic technologies promise to shed new light onto ocular disease processes that could lead to the discovery of strong novel biomarkers and therapeutic targets useful in many ophthalmic conditions.

【 授权许可】

   
2010 Mandal et al; licensee Springer

【 图 表 】

Figure 1.

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Figure 4.

【 参考文献 】

• [1]Resnikoff S, Pascolini D, Etya'ale D, Kocur I, Pararajasegaram R, Pokharel GP, Mariotti SP: Global data on visual impairment in the year 2002. Bull World Health Organ 2004, 82(11):844-851.
• [2]Sommer A: Global health, global vision. Arch Ophthalmol 2004, 122:911-912.
• [3]Frick KD, Foster A: The magnitude and cost of global blindness: an increasing problem that can be alleviated. Am J Ophthalmol 2003, 135:471-476.
• [4]Steely HT Jr, Clark AF: The use of proteomics in ophthalmic research. Pharmacogenomics 2000, 1:267-280.
• [5]Lam TC, Chun RK, Li KK, To CH: Application of proteomic technology in eye research: a mini review. Clin Exp Optom 2008, 91:23-33.
• [6]Collins FS, Green ED, Guttmacher AE, Guyer MS: A vision for the future of genomics research. Nature 2003, 422:835-847.
• [7]International Human Genome Sequencing Consortium: Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
• [8]Celera Genomics: The sequence of the human genome. Science 2001, 291:1304-1351.
• [9]Pandey A, Mann M: Proteomics to study genes and genomes. Nature 2000, 405:837-846.
• [10]Anderson NG, Matheson A, Anderson NL: Back to the future: the human protein index (HPI) and the agenda for post-proteomic biology. Proteomics 2001, 1:3-12.
• [11]Honoré B, Ostergaard M, Vorum H: Functional genomics studied by proteomics. Bioessays 2004, 26:901-915.
• [12]de Godoy LM, Olsen JV, Cox J, Nielsen ML, Hubner NC, Fröhlich F, Walther TC, Mann M: Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 2008, 455(7217):1251-1254.
• [13]Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L: Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 2001, 292(5518):929-934.
• [14]Graves PR, Haystead TA: Molecular biologist's guide to proteomics. Microbiol Mol Biol Rev 2002, 66:39-63.
• [15]O'Farrell PH: High resolution two-dimensional electrophoresis of proteins. J Biol Chem 1975, 250:4007-4021.
• [16]Rabilloud T: Two-dimensional gel electrophoresis in proteomics: old, old fashioned, but it still climbs up the mountains. Proteomics 2002, 2:3-10.
• [17]Wittmann-Liebold B, Graack HR, Pohl T: Two-dimensional gel electrophoresis as tool for proteomics studies in combination with protein identification by mass spectrometry. Proteomics 2006, 6:4688-4703.
• [18]Blackstock WP, Weir MP: Proteomics: quantitative and physical mapping of cellular proteins. Trends Biotechnol 1999, 17:121-127.
• [19]Jackson D, Rowlinson RA, Eaton CK, Nickson JA, Wilson ID, Mills JD, Wilkinson RW: Prostatic tissue protein alterations due to delayed time to freezing. Proteomics 2006, 6(13):3901-3908.
• [20]Sarto C, Valsecchi C, Mocarelli P: Renal cell carcinoma: handling and treatment. Proteomics 2002, 2:1627-1629.
• [21]Cañas B, Piñeiro C, Calvo E, López-Ferrer D, Gallardo JM: Trends in sample preparation for classical and second generation proteomics. J Chromatogr A 2007, 1153(1–2):235-258.
• [22]Tannu NS, Hemby SE: Methods for proteomics in neuroscience. Prog Brain Res 2006, 158:41-82.
• [23]López JL: Two-dimensional electrophoresis in proteome expression analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2007, 849(1–2):190-202.
• [24]Hopkinson A, McIntosh RS, Layfield R, Keyte J, Dua HS, Tighe PJ: Optimised two-dimensional electrophoresis procedures for the protein characterisation of structural tissues. Proteomics 2005, 5:1967-1979.
• [25]Braun RJ, Kinkl N, Beer M, Ueffing M: Two-dimensional electrophoresis of membrane proteins. Anal Bioanal Chem 2007, 389:1033-1045.
• [26]Distler AM, Kerner J, Hoppel CL: Proteomics of mitochondrial inner and outer membranes. Proteomics 2008, 8:4066-4082.
• [27]Rabilloud T, Chevallet M, Luche S, Lelong C: Fully denaturing two-dimensional electrophoresis of membrane proteins: a critical update. Proteomics 2008, 8:3965-3973.
• [28]Thompson LJ, Wang F, Proia AD, Peters KG, Jarrold B, Greis KD: Proteome analysis of the rat cornea during angiogenesis. Proteomics 2003, 3:2258-2266.
• [29]Scroggs MW, Proia AD, Smith CF, Halperin EC, Klintworth GK: The effect of total-body irradiation on corneal neovascularization in the Fischer 344 rat after chemical cauterization. Invest Ophthalmol Vis Sci 1991, 32:2105-2111.
• [30]Nielsen K, Vorum H, Fagerholm P, Birkenkamp-Demtröder K, Honoré B, Ehlers N, Orntoft TF: Proteome profiling of corneal epithelium and identification of marker proteins for keratoconus, a pilot study. Exp Eye Res 2006, 82(2):201-209.
• [31]Nielsen K, Birkenkamp-Demtroder K, Ehlers N, Orntoft TF: Identification of differentially expressed genes in keratoconus epithelium analyzed on microarrays. Invest Ophthalmol Vis Sci 2003, 44:2466-2476.
• [32]Jurkunas UV, Bitar MS, Rawe I, Harris DL, Colby K, Joyce NC: Increased clusterin expression in Fuchs' endothelial dystrophy. Invest Ophthalmol Vis Sci 2008, 49:2946-2955.
• [33]Karring H, Thogersen IB, Klintworth GK, Moller-Pedersen T, Enghild JJ: A dataset of human cornea proteins identified by Peptide mass fingerprinting and tandem mass spectrometry. Mol Cell Proteomics 2005, 4:1406-1408.
• [34]Shimmura S, Miyashita H, Higa K, Yoshida S, Shimazaki J, Tsubota K: Proteomic analysis of soluble factors secreted by limbal fibroblasts. Mol Vis 2006, 12:478-484.
• [35]Patel N, Solanki E, Picciani R, Cavett V, Caldwell-Busby JA, Bhattacharya SK: Strategies to recover proteins from ocular tissues for proteomics. Proteomics 2008, 8:1055-1070.
• [36]Lu F, Zhou X, Xie R, Wu Y, Hu Y, Zhang L, Li H, Mao X, Hu D, Qu J: Feasibility of two-dimensional gel electrophoresis used for proteomic analysis of human scleral fibroblasts. Curr Eye Res 2007, 32(4):319-329.
• [37]Zhang Y, Gao Q, Duan S, He Y, Sun X, Jiang R, Duan J, Zhong X, Ge J: Upregulation of Copine1 in trabecular meshwork cells of POAG patients: a membrane proteomics approach. Mol Vis 2008, 14:1028-1036.
• [38]Shinzato M, Yamashiro Y, Miyara N, Iwamatsu A, Takeuchi K, Umikawa M, Bayarjargal M, Kariya K, Sawaguchi S: Proteomic analysis of the trabecular meshwork of rats in a steroid-induced ocular hypertension model: downregulation of type I collagen C-propeptides. Ophthalmic Res 2007, 39(6):330-337.
• [39]Steely HT, Dillow GW, Bian L, Grundstad J, Braun TA, Casavant TL, McCartney MD, Clark AF: Protein expression in a transformed trabecular meshwork cell line: proteome analysis. Mol Vis 2006, 12:372-383.
• [40]Picciani R, Junk AK, Bhattacharya SK: Technical Brief: a novel strategy for enrichment of trabecular meshwork protease proteome. Mol Vis 2008, 14:871-877.
• [41]Zhao X, Ramsey KE, Stephan DA, Russell P: Gene and protein expression changes in human trabecular meshwork cells treated with transforming growth factor-beta. Invest Ophthalmol Vis Sci 2004, 45:4023-4034.
• [42]Funding M, Vorum H, Honoré B, Nexo E, Ehlers N: Proteomic analysis of aqueous humour from patients with acute corneal rejection. Acta Ophthalmol Scand 2005, 83:31-39.
• [43]Duan X, Lu Q, Xue P, Zhang H, Dong Z, Yang F, Wang N: Proteomic analysis of aqueous humor from patients with myopia. Mol Vis 2008, 14:370-377.
• [44]Grus FH, Joachim SC, Sandmann S, Thiel U, Bruns K, Lackner KJ, Pfeiffer N: Transthyretin and complex protein pattern in aqueous humor of patients with primary open-angle glaucoma. Mol Vis 2008, 14:1437-1445.
• [45]Herber S, Grus FH, Sabuncuo P, Augustin AJ: Two-dimensional analysis of tear protein patterns of diabetic patients. Electrophoresis 2001, 22:1838-1844.
• [46]Bergman L, Seregard S, Nilsson B, Ringborg U, Lundell G, Ragnarsson-Olding B: Incidence of uveal melanoma in Sweden from 1960 to 1998. Invest Ophthalmol Vis Sci 2002, 43:2579-2583.
• [47]Damato B: Treatment of primary intraocular melanoma. Expert Rev Anticancer Ther 2006, 6:493-506.
• [48]Pardo M, Garcia A, Thomas B, Piñeiro A, Akoulitchev A, Dwek RA, Zitzmann N: Proteome analysis of a human uveal melanoma primary cell culture by 2-DE and MS. Proteomics 2005, 5(18):4980-4993.
• [49]Zuidervaart W, Hensbergen PJ, Wong MC: Proteomic analysis of uveal melanoma reveals novel potential markers involved in tumor progression. Invest Ophthalmol Vis Sci 2006, 47:786-793.
• [50]Coupland SE, Vorum H, Mandal N, Kalirai H, Honoré B, Urbak SF, Lake SL, Dopierala J, Damato BE: Proteomics of uveal melanomas suggests HSP-27 as a possible surrogate marker of chromosome 3 loss. Invest Ophthalmol Vis Sci 2010, 51(1):12-20.
• [51]Andley UP: Crystallins in the eye: function and pathology. Prog Retin Eye Res 2007, 26:78-98.
• [52]Hoehenwarter W, Klose J, Jungblut PR: Eye lens proteomics. Amino Acids 2006, 30:369-389.
• [53]Bhat SP: Transparency and non-refractive functions of crystallins—a proposal. Exp Eye Res 2004, 79:809-816.
• [54]Wilmarth PA, Taube JR, Riviere MA, Duncan MK, David LL: Proteomic and sequence analysis of chicken lens crystallins reveals alternate splicing and translational forms of beta B2 and beta A2 crystallins. Invest Ophthalmol Vis Sci 2004, 45:2705-2715.
• [55]Harrington V, Srivastava OP, Kirk M: Proteomic analysis of water insoluble proteins from normal and cataractous human lenses. Mol Vis 2007, 13:1680-1694.
• [56]Posner M, Hawke M, Lacava C, Prince CJ, Bellanco NR, Corbin RW: A proteome map of the zebrafish (Danio rerio) lens reveals similarities between zebrafish and mammalian crystallin expression. Mol Vis 2008, 14:806-814.
• [57]Bahk SC, Lee SH, Jang JU, Choi CU, Lee BS, Chae SC, Song HJ, Park ZY, Yang YS, Chung HT: Identification of crystallin family proteins in vitreous body in rat endotoxin-induced uveitis: involvement of crystallin truncation in uveitis pathogenesis. Proteomics 2006, 6(11):3436-3444.
• [58]Deeg CA, Altmann F, Hauck SM, Schoeffmann S, Amann B, Stangassinger M, Ueffing M: Down-regulation of pigment epithelium-derived factor in uveitic lesion associates with focal vascular endothelial growth factor expression and breakdown of the blood-retinal barrier. Proteomics 2007, 7(9):1540-1548.
• [59]Nakanishi T, Koyama R, Ikeda T, Shimizu A: Catalogue of soluble proteins in the human vitreous humor: comparison between diabetic retinopathy and macular hole. J Chromatogr B Analyt Technol Biomed Life Sci 2002, 776:89-100.
• [60]Yamane K, Minamoto A, Yamashita H, Takamura H, Miyamoto-Myoken Y, Yoshizato K, Nabetani T, Tsugita A, Mishima HK: Proteome analysis of human vitreous proteins. Mol Cell Proteomics 2003, 2(11):1177-1187.
• [61]Ouchi M, West K, Crabb JW, Kinoshita S, Kamei M: Proteomic analysis of vitreous from diabetic macular edema. Exp Eye Res 2005, 81:176-182.
• [62]Kim T, Kim SJ, Kim K, Kang UB, Lee C, Park KS, Yu HG, Kim Y: Profiling of vitreous proteomes from proliferative diabetic retinopathy and nondiabetic patients. Proteomics 2007, 7(22):4203-4215.
• [63]Ulrich JN, Spannagl M, Kampik A, Gandorfer A: Components of the fibrinolytic system in the vitreous body in patients with vitreoretinal disorders. Clin Experiment Ophthalmol 2008, 36:431-436.
• [64]Neal RE, Bettelheim FA, Lin C, Winn KC, Garland DL, Zigler JS Jr: Alterations in human vitreous humour following cataract extraction. Exp Eye Res 2005, 80:337-347.
• [65]Liu T, Qian WJ, Mottaz HM, Gritsenko MA, Norbeck AD, Moore RJ, Purvine PO, Camp DG, Smith RD: Evaluation of multiprotein immunoaffinity subtraction for plasma proteomics and candidate biomarker discovery using mass spectrometry. Mol Cell Proteomics 2006, 5(11):2167-2174.
• [66]Quin GG, Len AC, Billson FA, Gillies MC: Proteome map of normal rat retina and comparison with the proteome of diabetic rat retina: new insight in the pathogenesis of diabetic retinopathy. Proteomics 2007, 7:2636-2650.
• [67]Wang YD, Wu JD, Jiang ZL, Wang YB, Wang XH, Liu C, Tong MQ: Comparative proteome analysis of neural retinas from type 2 diabetic rats by two-dimensional electrophoresis. Curr Eye Res 2007, 32(10):891-901.
• [68]Fort PE, Freeman WM, Losiewicz MK, Singh RS, Gardner TW: The retinal proteome in experimental diabetic retinopathy: up-regulation of crystallins and reversal by systemic and periocular insulin. Mol Cell Proteomics 2009, 8:767-779.
• [69]Ethen CM, Reilly C, Feng X, Olsen TW, Ferrington DA: The proteome of central and peripheral retina with progression of age-related macular degeneration. Invest Ophthalmol Vis Sci 2006, 47:2280-2290.
• [70]Vorum H, Ostergaard M, Rice GE, Honore B, Bek T: Identification of differentially regulated proteins in a patient with Leber's Congenital Amaurosis—a proteomic study. Proteome Sci 2007, 5:5. BioMed Central Full Text
• [71]Nordgaard CL, Berg KM, Kapphahn RJ, Reilly C, Feng X, Olsen TW, Ferrington DA: Proteomics of the retinal pigment epithelium reveals altered protein expression at progressive stages of age-related macular degeneration. Invest Ophthalmol Vis Sci 2006, 47(3):815-822.
• [72]Nordgaard CL, Karunadharma PP, Feng X, Olsen TW, Ferrington DA: Mitochondrial proteomics of the retinal pigment epithelium at progressive stages of age-related macular degeneration. Invest Ophthalmol Vis Sci 2008, 49:2848-2855.
• [73]Shibuya M, Okamoto H, Nozawa T, Utsumi J, Reddy VN, Echizen H, Tanaka Y, Iwata T: Proteomic and transcriptomic analyses of retinal pigment epithelial cells exposed to REF-1/TFPI-2. Invest Ophthalmol Vis Sci 2007, 48:516-521.
• [74]Schacke W, Beck KF, Pfeilschifter J, Hattenbach LO: Expression of ubiquitin carboxy-terminal hydrolase-l1 in photocoagulated human retinal pigment epithelial cells. Curr Eye Res 2007, 32:367-372.
• [75]Alge CS, Hauck SM, Priglinger SG, Kampik A, Ueffing M: Differential protein profiling of primary versus immortalized human RPE cells identifies expression patterns associated with cytoskeletal remodeling and cell survival. J Proteome Res 2006, 5:862-878.
• [76]West KA, Yan L, Shadrach K, Sun J, Hasan A, Miyagi M, Crabb JS, Hollyfield JG, Marmorstein AD, Crabb JW: Protein database, human retinal pigment epithelium. Mol Cell Proteomics 2003, 2(1):37-49.
• [77]Crabb JW, Miyagi M, Gu X, Shadrach K, West KA, Sakaguchi H, Kamei M, Hasan A, Yan L, Rayborn ME, Salomon RG, Hollyfield JG: Drusen proteome analysis: an approach to the etiology of age-related macular degeneration. Proc Natl Acad Sci U S A 2002, 99(23):14682-14687.
• [78]Umeda S, Suzuki MT, Okamoto H, Ono F, Mizota A, Terao K, Yoshikawa Y, Tanaka Y, Iwata T: Molecular composition of drusen and possible involvement of anti-retinal autoimmunity in two different forms of macular degeneration in cynomolgus monkey (Macaca fascicularis). FASEB J 2005, 19(12):1683-1685.
• [79]Chevalier F, Rofidal V, Vanova P, Bergoin A, Rossignol M: Proteomic capacity of recent fluorescent dyes for protein staining. Phytochemistry 2004, 65:1499-1506.
• [80]Harris LR, Churchward MA, Butt RH, Coorssen JR: Assessing detection methods for gel-based proteomic analyses. J Proteome Res 2007, 6:1418-1425.
• [81]Smejkal GB: The Coomassie chronicles: past, present and future perspectives in polyacrylamide gel staining. Expert Rev Proteomics 2004, 1:381-387.
• [82]Neuhoff V, Arold N, Taube D, Ehrhardt W: 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.
• [83]Chevallet M, Luche S, Rabilloud T: Silver staining of proteins in polyacrylamide gels. Nat Protoc 2006, 1:1852-1858.
• [84]Miller I, Crawford J, Gianazza E: Protein stains for proteomic applications: which, when, why? Proteomics 2006, 6:5385-5408.
• [85]Luo S, Wehr NB, Levine RL: Quantitation of protein on gels and blots by infrared fluorescence of Coomassie blue and Fast Green. Anal Biochem 2006, 350:233-238.
• [86]Lopez MF, Berggren K, Chernokalskaya E, Lazarev A, Robinson M, Patton WF: A comparison of silver stain and SYPRO Ruby Protein Gel Stain with respect to protein detection in two-dimensional gels and identification by peptide mass profiling. Electrophoresis 2000, 21:3673-3683.
• [87]Shevchenko A, Wilm M, Vorm O, Mann M: Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal Chem 1996, 68:850-858.
• [88]Lopez MF: Better approaches to finding the needle in a haystack: optimizing proteome analysis through automation. Electrophoresis 2000, 21:1082-1093.
• [89]Mortz E, Krogh TN, Vorum H, Görg A: Improved silver staining protocols for high sensitivity protein identification using matrix-assisted laser desorption/ionization-time of flight analysis. Proteomics 2001, 1(11):1359-1363.
• [90]Winkler C, Denker K, Wortelkamp S, Sickmann A: Silver- and Coomassie-staining protocols: detection limits and compatibility with ESI MS. Electrophoresis 2007, 28:2095-2099.
• [91]Lin JF, Chen QX, Tian HY, Gao X, Yu ML, Xu GJ, Zhao FK: Stain efficiency and MALDI-TOF MS compatibility of seven visible staining procedures. Anal Bioanal Chem 2008, 390(7):1765-1773.
• [92]Chevallet M, Diemer H, Luche S, van Dorsselaer A, Rabilloud T, Leize-Wagner E: Improved mass spectrometry compatibility is afforded by ammoniacal silver staining. Proteomics 2006, 6:2350-2354.
• [93]Dutt MJ, Lee KH: Proteomic analysis. Curr Opin Biotechnol 2000, 11:176-179.
• [94]Chevallet M, Luche S, Diemer H, Strub JM, Van Dorsselaer A, Rabilloud T: Sweet silver: a formaldehyde-free silver staining using aldoses as developing agents, with enhanced compatibility with mass spectrometry. Proteomics 2008, 8:4853-4861.
• [95]Candiano G, Bruschi M, Musante L, Santucci L, Ghiggeri GM, Carnemolla B, Orecchia P, Zardi L, Righetti PG: Blue silver: a very sensitive colloidal Coomassie G-250 staining for proteome analysis. Electrophoresis 2004, 25(9):1327-1333.
• [96]Nishihara JC, Champion KM: Quantitative evaluation of proteins in one- and two-dimensional polyacrylamide gels using a fluorescent stain. Electrophoresis 2002, 23:2203-2215.
• [97]Berggren K, Chernokalskaya E, Steinberg TH, Kemper C, Lopez MF, Diwu Z, Haugland RP, Patton WF: Background-free, high sensitivity staining of proteins in one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gels using a luminescent ruthenium complex. Electrophoresis 2000, 21(12):2509-2521.
• [98]Mackintosh JA, Choi HY, Bae SH, Veal DA, Bell PJ, Ferrari BC, Van Dyk DD, Verrills NM, Paik YK, Karuso P: A fluorescent natural product for ultra sensitive detection of proteins in one-dimensional and two-dimensional gel electrophoresis. Proteomics 2003, 3(12):2273-2288.
• [99]Smejkal GB, Robinson MH, Lazarev A: Comparison of fluorescent stains: relative photostability and differential staining of proteins in two-dimensional gels. Electrophoresis 2004, 25:2511-2519.
• [100]Unlü M, Morgan ME, Minden JS: Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 1997, 18(11):2071-2077.
• [101]Viswanathan S, Unlü M, Minden JS: Two-dimensional difference gel electrophoresis. Nat Protoc 2006, 1(3):1351-1358.
• [102]Timms JF, Cramer R: Difference gel electrophoresis. Proteomics 2008, 8:4886-4897.
• [103]Marouga R, David S, Hawkins E: The development of the DIGE system: 2D fluorescence difference gel analysis technology. Anal Bioanal Chem 2005, 382:669-678.
• [104]Hannigan A, Burchmore R, Wilson JB: The optimization of protocols for proteome difference gel electrophoresis (DiGE) analysis of preneoplastic skin. J Proteome Res 2007, 6:3422-3432.
• [105]Wheelock AM, Goto S: Effects of post-electrophoretic analysis on variance in gel-based proteomics. Expert Rev Proteomics 2006, 3:129-142.
• [106]Minden JS, Dowd SR, Meyer HE, Stuhler K: Difference gel electrophoresis. Electrophoresis 2009, 30(Suppl 1):S156-161.
• [107]Tannu NS, Hemby SE: Two-dimensional fluorescence difference gel electrophoresis for comparative proteomics profiling. Nat Protoc 2006, 1:1732-1742.
• [108]García-Ramírez M, Canals F, Hernández C, Colomé N, Ferrer C, Carrasco E, García-Arumí J, Simó R: Proteomic analysis of human vitreous fluid by fluorescence-based difference gel electrophoresis (DIGE): a new strategy for identifying potential candidates in the pathogenesis of proliferative diabetic retinopathy. Diabetologia 2007, 50(6):1294-1303.
• [109]Lam TC, Li KK, Lo SC, Guggenheim JA, To CH: Application of fluorescence difference gel electrophoresis technology in searching for protein biomarkers in chick myopia. J Proteome Res 2007, 6:4135-4149.
• [110]Zamora DO, Riviere M, Choi D, Pan Y, Planck SR, Rosenbaum JT, David LL, Smith JR: Proteomic profiling of human retinal and choroidal endothelial cells reveals molecular heterogeneity related to tissue of origin. Mol Vis 2007, 13:2058-2065.
• [111]Zipplies JK, Hauck SM, Schoeffmann S, Amann B, Stangassinger M, Ueffing M, Deeg CA: Serum PEDF levels are decreased in a spontaneous animal model for human autoimmune uveitis. J Proteome Res 2009, 8(2):992-998.
• [112]Raman B, Cheung A, Marten MR: Quantitative comparison and evaluation of two commercially available, two-dimensional electrophoresis image analysis software packages, Z3 and Melanie. Electrophoresis 2002, 23:2194-2202.
• [113]Rosengren AT, Salmi JM, Aittokallio T, Westerholm J, Lahesmaa R, Nyman TA, Nevalainen OS: Comparison of PDQuest and Progenesis software packages in the analysis of two-dimensional electrophoresis gels. Proteomics 2003, 3(10):1936-1946.
• [114]Arora PS, Yamagiwa H, Srivastava A, Bolander ME, Sarkar G: Comparative evaluation of two two-dimensional gel electrophoresis image analysis software applications using synovial fluids from patients with joint disease. J Orthop Sci 2005, 10:160-166.
• [115]Wheelock AM, Buckpitt AR: Software-induced variance in two-dimensional gel electrophoresis image analysis. Electrophoresis 2005, 26:4508-4520.
• [116]Shively JE: The chemistry of protein sequence analysis. EXS 2000, 88:99-117.
• [117]Aebersold R, Mann M: Mass spectrometry-based proteomics. Nature 2003, 422:198-207.
• [118]Reinders J, Lewandrowski U, Moebius J, Wagner Y, Sickmann A: Challenges in mass spectrometry-based proteomics. Proteomics 2004, 4:3686-3703.
• [119]Cravatt BF, Simon GM, Yates JR: The biological impact of mass-spectrometry-based proteomics. Nature 2007, 450:991-1000.
• [120]Cañas B, López-Ferrer D, Ramos-Fernández A, Camafeita E, Calvo E: Mass spectrometry technologies for proteomics. Brief Funct Genomic Proteomic 2006, 4(4):295-320.
• [121]Chait BT: Chemistry. Mass spectrometry: bottom-up or top-down? Science 2006, 314:65-66.
• [122]Washburn MP, Wolters D, Yates JR: Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001, 19:242-247.
• [123]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, 17:994-999.
• [124]Allison WT, Veldhoen KM, Hawryshyn CW: Proteomic analysis of opsins and thyroid hormone-induced retinal development using isotope-coded affinity tags (ICAT) and mass spectrometry. Mol Vis 2006, 12:655-672.
• [125]Unwin RD, Pierce A, Watson RB, Sternberg DW, Whetton AD: Quantitative proteomic analysis using isobaric protein tags enables rapid comparison of changes in transcript and protein levels in transformed cells. Mol Cell Proteomics 2005, 4:924-935.
• [126]Zhou L, Beuerman RW, Huang L, Barathi A, Foo YH, Li SF, Chew FT, Tan D: Proteomic analysis of rabbit tear fluid: Defensin levels after an experimental corneal wound are correlated to wound closure. Proteomics 2007, 7(17):3194-3206.
• [127]Zhou L, Beuerman RW, Chan CM, Zhao SZ, Li XR, Yang H, Tong L, Liu S, Stern ME, Tan D: Identification of tear fluid biomarkers in dry eye syndrome using iTRAQ quantitative proteomics. J Proteome Res 2009, 8(11):4889-4905.
• [128]Mann M: Functional and quantitative proteomics using SILAC. Nat Rev Mol Cell Biol 2006, 7:952-958.
• [129]An E, Lu X, Flippin J, Devaney JM, Halligan B, Hoffman EP, Strunnikova N, Csaky K, Hathout Y: Secreted proteome profiling in human RPE cell cultures derived from donors with age related macular degeneration and age matched healthy donors. J Proteome Res 2006, 5(10):2599-2610.
• [130]Choe LH, Aggarwal K, Franck Z, Lee KH: A comparison of the consistency of proteome quantitation using two-dimensional electrophoresis and shotgun isobaric tagging in Escherichia coli cells. Electrophoresis 2005, 26:2437-2449.
• [131]Gagné JP, Mercier G, Bonicalzi ME, Mes-Masson AM, Droit A, Winstall E, Isabelle M, Poirier GG: Comparative proteome analysis of human epithelial ovarian cancer. Proteome Sci 2007, 5:16. BioMed Central Full Text
• [132]Wu WW, Wang G, Baek SJ, Shen RF: Comparative study of three proteomic quantitative methods, DIGE, cICAT, and iTRAQ, using 2D gel- or LC-MALDI TOF/TOF. J Proteome Res 2006, 5:651-658.
• [133]Bindschedler LV, Palmblad M, Cramer R: Hydroponic isotope labelling of entire plants (HILEP) for quantitative plant proteomics; an oxidative stress case study. Phytochemistry 2008, 69:1962-1972.
• [134]Honoré B: Genome- and proteome-based technologies: status and applications in the postgenomic era. Expert Rev Mol Diagn 2001, 1(3):265-274.