Application of proteomic technology in eye research: a mini review

REFERENCES

• Wilkins MR, Sanchez JC, Gooley AA, Appel RD, Humphery‐smith I, Hochstrasser DF, Williams KL. 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.
   PubMed Web of Science ®Google Scholar
• Celis JE, Gromov P. 2D protein electrophoresis: can it be perfected? Curr Opin Biotechnol 1999; 10: 16–21.
   PubMed Web of Science ®Google Scholar
• Celis JE, Rasmussen HH, Leffers H, Madsen P, Honore B, Gesser B, Dejgaard K, Vandekerckhove J. Human cellular protein patterns and their link to genome DNA sequence data: usefulness of two‐dimensional gel electrophoresis and microsequencing. Faseb J 1991; 5: 2200–2208.
   PubMed Web of Science ®Google Scholar
• Laub MT, Mcadams HH, Feldblyum T, Fraser CM, Shapiro L. Global analysis of the genetic network controlling a bacterial cell cycle. Science 2000; 290: 2144–2148.
   PubMed Web of Science ®Google Scholar
• Haynes PA, Gygi SP, Figeys D, Aebersold R. Proteome analysis: biological assay or data archive? Electrophoresis 1998; 19: 1862–1871.
   Web of Science ®Google Scholar
• Tanito M, Haniu H, Elliott MH, Singh AK, Matsumoto H, Anderson RE. Identification of 4‐hydroxynonenal‐modified retinal proteins induced by photooxidative stress prior to retinal degeneration. Free Radic Biol Med 2006; 41: 1847–1859.
   PubMed Web of Science ®Google Scholar
• Tew KD, Monks A, Barone L, Rosser D, Akerman G, Montali JA, Wheatley JB, Schmidt DE Jr. Glutathione‐associated enzymes in the human cell lines of the National Cancer Institute Drug Screening Program. Mol Pharmacol 1996; 50: 149–159.
   PubMed Web of Science ®Google Scholar
• O’farrell PH. High resolution two‐dimensional electrophoresis of proteins. J Biol Chem 1975; 250: 4007–4021.
   PubMed Web of Science ®Google Scholar
• Klose J. Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik 1975; 26: 231–243.
   PubMedGoogle Scholar
• Gorg A, Obermaier C, Boguth G, Harder A, Scheibe B, Wildgruber R, Weiss W. The current state of two‐dimensional electrophoresis with immobilized pH gradients. Electrophoresis 2000; 21: 1037–1053.
   PubMed Web of Science ®Google Scholar
• Choe LH, Lee KH. A comparison of three commercially available isoelectric focusing units for proteome analysis: the multiphor, the IPGphor and the protean IEF cell. Electrophoresis 2000; 21: 993–1000.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Lauber WM, Carroll JA, Dufield DR, Kiesel JR, Radabaugh MR, Malone JP. Mass spectrometry compatibility of two‐dimensional gel protein stains. Electrophoresis 2001; 22: 906–918.
   PubMed Web of Science ®Google Scholar
• Tonge R, Shaw J, Middleton B, Rowlinson R, Rayner S, Young J, Pognan F, Hawkins E, Currie I, Davison M. Validation and development of fluorescence two‐dimensional differential gel electrophoresis proteomics technology. Proteomics 2001; 1: 377–396.
   PubMed Web of Science ®Google Scholar
• Unlu M, Morgan ME, Minden JS. Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 1997; 18: 2071–2077.
   PubMed Web of Science ®Google Scholar
• Steinberg TH, Pretty on top K, Berggren KN, Kemper C, Jones L, Diwu Z, Haugland RP, Patton WF. Rapid and simple single nanogram detection of glycoproteins in polyacrylamide gels and on electroblots. Proteomics 2001; 1: 841–855.
   PubMed Web of Science ®Google Scholar
• Wu J, Lenchik NJ, Pabst MJ, Solomon SS, Shull J, Gerling IC. Functional characterization of two‐dimensional gel‐separated proteins using sequential staining. Electrophoresis 2005; 26: 225–237.
   PubMed Web of Science ®Google Scholar
• Hart C, Schulenberg B, Patton WF. Selective proteome‐wide detection of hydrophobic integral membrane proteins using a novel fluorescence‐based staining technology. Electrophoresis 2004; 25: 2486–2493.
   Web of Science ®Google Scholar
• Irvine GB. High‐performance size‐exclusion chromatography of peptides. J Biochem Biophys Methods 2003; 56: 233–242.
   PubMedGoogle Scholar
• Rahbar S, Lee TD, Baker JA, Rabinowitz LT, Asmerom Y, Legesse K, Ranney HM. Reverse phase high‐performance liquid chromatography and secondary ion mass spectrometry. A strategy for identification of ten human hemoglobin variants. Hemoglobin 1986; 10: 379–400.
   PubMed Web of Science ®Google Scholar
• Maruska A, Kornysova O. Continuous beds (monoliths): stationary phases for liquid chromatography formed using the hydrophobic interaction‐based phase separation mechanism. J Biochem Biophys Methods 2004; 59: 1–48.
   Google Scholar
• Fritz JS. Early milestones in the development of ion‐exchange chromatography: a personal account. J Chromatogr A 2004; 1039: 3–12.
   Web of Science ®Google Scholar
• Bollag DM. Gel‐filtration chromatography. Methods Mol Biol 1994; 36: 1–9.
   PubMedGoogle Scholar
• Lee WC, Lee KH. Applications of affinity chromatography in proteomics. Anal Biochem 2004; 324: 1–10.
   PubMed Web of Science ®Google Scholar
• Kobayashi N. Recent progress of free‐flow electrophoresis method and its application for proteomics. Tanpakushitsu Kakusan Koso 2004; 49: 1333–1340.
   Google Scholar
• Dolnik V. Recent developments in capillary zone electrophoresis of proteins. Electrophoresis 1999; 20: 3106–3115.
   Web of Science ®Google Scholar
• Karas M, Hillenkamp F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal Chem 1988; 60: 2299–2301.
   PubMed Web of Science ®Google Scholar
• Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM. Electrospray ionization for mass spectrometry of large biomolecules. Science 1989; 246: 64–71.
   PubMed Web of Science ®Google Scholar
• Veenstra TD. Electrospray ionization mass spectrometry: a promising new technique in the study of protein/DNA noncovalent complexes. Biochem Biophys Res Commun 1999; 257: 1–5.
   PubMed Web of Science ®Google Scholar
• Watanabe K, Harayama S. SWISS‐PROT: the curated protein sequence database on Internet. Tanpakushitsu Kakusan Koso 2001; 46: 80–86.
   Google Scholar
• Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O’donovan C, Phan I, Pilbout S, Schneider M. The SWISS‐PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 2003; 31: 365–370.
   PubMed Web of Science ®Google Scholar
• Wu CH, Yeh LS, Huang H, Arminski L, Castro‐alvear J, Chen Y, Hu Z, Kourtesis P, Ledley RS, Suzek BE, Vinayaka CR, Zhang J, Barker WC. The Protein Information Resource. Nucleic Acids Res 2003; 31: 345–347.
   PubMed Web of Science ®Google Scholar
• Cottrell JS. Protein identification by peptide mass fingerprinting. Pept Res 1994; 7: 115–124.
   PubMedGoogle Scholar
• Pappin DJ, Hojrup P, Bleasby AJ. Rapid identification of proteins by peptide‐mass fingerprinting. Curr Biol 1993; 3: 327–332.
   PubMed Web of Science ®Google Scholar
• Medzihradszky KF, Campbell JM, Baldwin MA, Falick AM, Juhasz P, Vestal ML, Burlingame AL. The characteristics of peptide collision‐induced dissociation using a high‐performance MALDI‐TOF/TOF tandem mass spectrometer. Anal Chem 2000; 72: 552–558.
   PubMed Web of Science ®Google Scholar
• Laiko VV, Moyer SC, Cotter RJ. Atmospheric pressure MALDI/ion trap mass spectrometry. Anal Chem 2000; 72: 5239–5243.
   PubMed Web of Science ®Google Scholar
• Hendrickson CL, Emmett MR. Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Annu Rev Phys Chem 1999; 50: 517–536.
   Web of Science ®Google Scholar
• Loboda AV, Krutchinsky AN, Bromirski M, Ens W, Standing KG. A tandem quadrupole/time‐of‐flight mass spectrometer with a matrix‐assisted laser desorption/ionization source: design and performance. Rapid Commun Mass Spectrom 2000; 14: 1047–1057.
   PubMed Web of Science ®Google Scholar
• Han DK, Eng J, Zhou H, Aebersold R. Quantitative profiling of differentiation‐induced microsomal proteins using isotope‐coded affinity tags and mass spectrometry. Nat Biotechnol 2001; 19: 946–951.
   PubMed Web of Science ®Google Scholar
• Patterson SD. Proteomics: the industrialization of protein chemistry. Curr Opin Biotechnol 2000; 11: 413–418.
   PubMed Web of Science ®Google Scholar
• Shadforth IP, Dunkley TP, Lilley KS, Bessant C. i‐Tracker: for quantitative proteomics using iTRAQ. BMC Genomics 2005; 6: 145.
   PubMed Web of Science ®Google Scholar
• Hanash S, Celis JE. The Human Proteome Organization: a mission to advance proteome knowledge. Mol Cell Proteomics 2002; 1: 413–414.
   PubMed Web of Science ®Google Scholar
• Kavallaris M, Marshall GM. Proteomics and disease: opportunities and challenges. Med J Aust 2005; 182: 575–579.
   PubMed Web of Science ®Google Scholar
• Stults JT, Arnott D. Proteomics. Methods Enzymol 2005; 402: 245–289.
   PubMed Web of Science ®Google Scholar
• Buhimschi CS, Weiner CP, Buhimschi IA. Clinical proteomics: a novel diagnostic tool for the new biology of preterm labor, part I: proteomics tools. Obstet Gynecol Surv 2006; 61: 481–486.
   PubMed Web of Science ®Google Scholar
• Smith JC, Figeys D. Proteomics technology in systems biology. Mol Biosyst 2006; 2: 364–370.
   Google Scholar
• Pierce JD, Fakhari M, Works KV, Pierce JT, Clancy RL. Understanding proteomics. Nurs Health Sci 2007; 9: 54–60.
   Web of Science ®Google Scholar
• Reeh S, Pedersen S, Neidhardt FC. Transient rates of synthesis of five amionacyl‐transfer ribonucleic acid synthetases during a shift‐up of Escherichia coli. J Bacteriol 1977; 129: 702–706.
   Web of Science ®Google Scholar
• Linn T, Losick R. The program of protein synthesis during sporulation in Bacillus subtilis. Cell 1976; 8: 103–114.
   Web of Science ®Google Scholar
• Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM et al. Whole‐genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995; 269: 496–512.
   PubMed Web of Science ®Google Scholar
• Visintin M, Meli GA, Cannistraci I, Cattaneo A. Intracellular antibodies for proteomics. J Immunol Methods 2004; 290: 135–153.
   Web of Science ®Google Scholar
• Senderowicz AM. Targeting cell cycle and apoptosis for the treatment of human malignancies. Curr Opin Cell Biol 2004; 16: 670–678.
   PubMed Web of Science ®Google Scholar
• Graves PR, Haystead TA. A functional proteomics approach to signal transduction. Recent Prog Horm Res 2003; 58: 1–24.
   PubMedGoogle Scholar
• Purcell AW, Gorman JJ. Immunoproteomics: Mass spectrometry‐based methods to study the targets of the immune response. Mol Cell Proteomics 2004; 3: 193–208.
   PubMed Web of Science ®Google Scholar
• Wilson KE, Ryan MM, Prime JE, Pashby DP, Orange PR, O’beirne G, Whateley JG, Bahn S, Morris CM. Functional genomics and proteomics: application in neurosciences. J Neurol Neurosurg Psychiatry 2004; 75: 529–538.
   Web of Science ®Google Scholar
• Kersten B, Burkle L, Kuhn EJ, Giavalisco P, Konthur Z, Lueking A, Walter G, Eickhoff H, Schneider U. Large‐scale plant proteomics. Plant Mol Biol 2002; 48: 133–141.
   PubMed Web of Science ®Google Scholar
• Pineiro C, Barros‐velazquez J, Vazquez J, Figueras A, Gallardo JM. Proteomics as a tool for the investigation of seafood and other marine products. J Proteome Res 2003; 2: 127–135.
   Web of Science ®Google Scholar
• Kennedy S. The role of proteomics in toxicology: identification of biomarkers of toxicity by protein expression analysis. Biomarkers 2002; 7: 269–290.
   PubMed Web of Science ®Google Scholar
• Sellers TA, Yates JR. Review of proteomics with applications to genetic epidemiology. Genet Epidemiol 2003; 24: 83–98.
   PubMed Web of Science ®Google Scholar
• Navas A, Albar JP. Application of proteomics in phylogenetic and evolutionary studies. Proteomics 2004; 4: 299–302.
   PubMed Web of Science ®Google Scholar
• Hoehenwarter W, Klose J, Jungblut PR. Eye lens proteomics. Amino Acids 2006; 30: 369–389.
   PubMed Web of Science ®Google Scholar
• Dixon DW, Gill AF, Giribabu L, Vzorov AN, Alam AB, Compans RW. Sulfonated naphthyl porphyrins as agents against HIV‐1. J Inorg Biochem 2005; 99: 813–821.
   PubMed Web of Science ®Google Scholar
• Johnson JR, Florens L, Carucci DJ, Yates JR 3rd. Proteomics in malaria. J Proteome Res 2004; 3: 296–306.
   PubMed Web of Science ®Google Scholar
• Butterfield DA. Proteomics: a new approach to investigate oxidative stress in Alzheimer’s disease brain. Brain Res 2004; 1000: 1–7.
   PubMed Web of Science ®Google Scholar
• Sparre T, Bergholdt R, Nerup J, Pociot F. Application of genomics and proteomics in type 1 diabetes pathogenesis research. Expert Rev Mol Diagn 2003; 3: 743–757.
   PubMed Web of Science ®Google Scholar
• Hammack BN, Fung KY, Hunsucker SW, Duncan MW, Burgoon MP, Owens GP, Gilden DH. Proteomic analysis of multiple sclerosis cerebrospinal fluid. Mult Scler 2004; 10: 245–260.
   PubMed Web of Science ®Google Scholar
• Macri J, Rapundalo ST. Application of proteomics to the study of cardiovascular biology. Trends Cardiovasc Med 2001; 11: 66–75.
   Web of Science ®Google Scholar
• Iwaki H, Kageyama S, Isono T, Wakabayashi Y, Okada Y, Yoshimura K, Terai A, Arai Y, Iwamura H, Kawakita M, Yoshiki T. Diagnostic potential in bladder cancer of a panel of tumor markers (calreticulin, gamma‐synuclein, and catechol‐o‐methyltransferase) identified by proteomic analysis. Cancer Sci 2004; 95: 955–961.
   PubMed Web of Science ®Google Scholar
• Rogers MA, Clarke P, Noble J, Munro NP, Paul A, Selby PJ, Banks RE. Proteomic profiling of urinary proteins in renal cancer by surface enhanced laser desorption ionization and neural‐network analysis: identification of key issues affecting potential clinical utility. Cancer Res 2003; 63: 6971–6983.
   PubMed Web of Science ®Google Scholar
• Somiari RI, Somiari S, Russell S, Shriver CD. Proteomics of breast carcinoma. J Chromatogr B Analyt Technol Biomed Life Sci 2005; 815: 215–225.
   PubMed Web of Science ®Google Scholar
• Posadas EM, Davidson B, Kohn EC. Proteomics and ovarian cancer: implications for diagnosis and treatment: a critical review of the recent literature. Curr Opin Oncol 2004; 16: 478–484.
   PubMed Web of Science ®Google Scholar
• Granville CA, Dennis PA. An overview of lung cancer genomics and proteomics. Am J Respir Cell Mol Biol 2005; 32: 169–176.
   PubMed Web of Science ®Google Scholar
• Steinert R, Buschmann T, Van der linden M, Fels LM, Lippert H, Reymond MA. The role of proteomics in the diagnosis and outcome prediction in colorectal cancer. Technol Cancer Res Treat 2002; 1: 297–304.
   Web of Science ®Google Scholar
• Li N, Wang N, Zheng J, Liu XM, Lever OW, Erickson PM, Li L. Characterization of human tear proteome using multiple proteomic analysis techniques. J Proteome Res 2005; 4: 2052–2061.
   PubMed Web of Science ®Google Scholar
• Yip TT, Chan JW, Cho WC, Yip TT, Wang Z, Kwan TL, Law SC, Tsang DN, Chan JK, Lee KC, Cheng WW, Ma VW, Yip C, Lim CK, Ngan RK, Au JS, Chan A, Lim WW. Protein chip array profiling analysis in patients with severe acute respiratory syndrome identified serum amyloid a protein as a biomarker potentially useful in monitoring the extent of pneumonia. Clin Chem 2005; 51: 47–55.
   PubMed Web of Science ®Google Scholar
• Ren Y, He QY, Fan J, Jones B, Zhou Y, Xie Y, Cheung CY, Wu A, Chiu JF, Peiris JS, Tam PK. The use of proteomics in the discovery of serum biomarkers from patients with severe acute respiratory syndrome. Proteomics 2004; 4: 3477–3484.
   PubMed Web of Science ®Google Scholar
• Hale JE, Gelfanova V, Ludwig JR, Knierman MD. Application of proteomics for discovery of protein biomarkers. Brief Funct Genomic Proteomic 2003; 2: 185–193.
   Google Scholar
• Jeffery DA, Bogyo M. Chemical proteomics and its application to drug discovery. Curr Opin Biotechnol 2003; 14: 87–95.
   PubMed Web of Science ®Google Scholar
• Zhou L, Beuerman RW, Barathi A, Tan D. Analysis of rabbit tear proteins by high‐pressure liquid chromatography/electrospray ionization mass spectrometry. Rapid Commun Mass Spectrom 2003; 17: 401–412.
   Google Scholar
• Fung KY, Morris C, Sathe S, Sack R, Duncan MW. Characterization of the in vivo forms of lacrimal‐specific proline‐rich proteins in human tear fluid. Proteomics 2004; 4: 3953–3959.
   Web of Science ®Google Scholar
• Tsai PS, Evans JE, Green KM, Sullivan RM, Schaumberg DA, Richards SM, Dana MR, Sullivan DA. Proteomic analysis of human meibomian gland secretions. Br J Ophthalmol 2006; 90: 372–377.
   PubMed Web of Science ®Google Scholar
• Nichols KK, Ham BM, Nichols JJ, Ziegler C, Green‐church KB. Identification of fatty acids and fatty acid amides in human meibomian gland secretions. Invest Ophthalmol Vis Sci 2007; 48: 34–39.
   Web of Science ®Google Scholar
• De souza GA, Godoy LM, Mann M. Identification of 491 proteins in the tear fluid proteome reveals a large number of proteases and protease inhibitors. Genome Biol 2006; 7: R72.
   PubMed Web of Science ®Google Scholar
• Ham BM, Cole RB, Jacob JT. Identification and comparison of the polar phospholipids in normal and dry eye rabbit tears by MALDI‐TOF mass spectrometry. Invest Ophthalmol Vis Sci 2006; 47: 3330–3338.
   PubMed Web of Science ®Google Scholar
• Ham BM, Jacob JT, Cole RB. Single eye analysis and contralateral eye comparison of tear proteins in normal and dry eye model rabbits by MALDI‐ToF mass spectrometry using wax‐coated target plates. Anal Bioanal Chem 2007; 387: 889–900.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Kathiresan T, Krishnan K, Krishnakumar V, Agrawal R, Anand A, Muralidhar D, Mishra AK, Dhople VM, Aggrawal RK, Sharma Y. Triose phosphate isomerase, a novel enzyme‐crystallin, and tau‐crystallin in crocodile cornea. High accumulation of both proteins during late embryonic development. Febs J 2006; 273: 3370–3380.
   Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Zanello SB, Nayak R, Zanello LP, Farthing‐nayak P. Identification and distribution of 14.3.3sigma (stratifin) in the human cornea. Curr Eye Res 2006; 31: 825–833.
   PubMed Web of Science ®Google Scholar
• Han J, Schey KL. MALDI tissue imaging of ocular lens alpha‐crystallin. Invest Ophthalmol Vis Sci 2006; 47: 2990–2996.
   Web of Science ®Google Scholar
• Robinson NE, Lampi KJ, Mciver RT, Williams RH, Muster WC, Kruppa G, Robinson AB. Quantitative measurement of deamidation in lens betaB2‐crystallin and peptides by direct electrospray injection and fragmentation in a Fourier transform mass spectrometer. Mol Vis 2005; 11: 1211–1219.
   PubMed Web of Science ®Google Scholar
• Robinson NE, Lampi KJ, Speir JP, Kruppa G, Easterling M, Robinson AB. Quantitative measurement of young human eye lens crystallins by direct injection Fourier transform ion cyclotron resonance mass spectrometry. Mol Vis 2006; 12: 704–711.
   Web of Science ®Google Scholar
• Schaefer H, Chamrad DC, Herrmann M, Stuwe J, Becker G, Klose J, Blueggel M, Meyer HE, Marcus K. Study of posttranslational modifications in lenticular alpha A‐crystallin of mice using proteomic analysis techniques. Biochim Biophys Acta 2006; 1764: 1948–1962.
   Web of Science ®Google Scholar
• Wu Y, Pan S, Li S, Huang Q, Fu SC. Distribution of human lens crystallins and their sulphydryl contents of different age in two‐dimension electrophoresis. Yan Ke Xue Bao 1999; 15: 32–35.
   Google Scholar
• Russell P. Two‐dimensional gel electrophoresis of human lens epithelium: a study of spatial protein patterns and aging. Exp Eye Res 1991; 52: 613–618.
   Web of Science ®Google Scholar
• Datiles MB, Schumer DJ, Zigler JS Jr, Russell P, Anderson L, Garland D. Two‐dimensional gel electrophoretic analysis of human lens proteins. Curr Eye Res 1992; 11: 669–677.
   PubMed Web of Science ®Google Scholar
• Ball LE, Garland DL, Crouch RK, Schey KL. Post‐translational modifications of aquaporin 0 (AQP0) in the normal human lens: spatial and temporal occurrence. Biochemistry 2004; 43: 9856–9865.
   Web of Science ®Google Scholar
• 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: 3436–3444.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Laicine EM, Haddad A. Transferrin, one of the major vitreous proteins, is produced within the eye. Exp Eye Res 1994; 59: 441–445.
   PubMed Web of Science ®Google Scholar
• Shimizu A, Nakanishi T, Koyama R, Ikeda T. Proteomics in clinical research: new approach of mass spectrometry. Rinsho Byori 2002; 50: 169–172.
   PubMedGoogle Scholar
• 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: 1177–1187.
   PubMed Web of Science ®Google Scholar
• Wu CW, Sauter JL, Johnson PK, Chen CD, Olsen TW. Identification and localization of major soluble vitreous proteins in human ocular tissue. Am J Ophthalmol 2004; 137: 655–661.
   PubMed Web of Science ®Google Scholar
• Gao BB, Clermont A, Rook S, Fonda SJ, Srinivasan VJ, Wojtkowski M, Fujimoto JG, Avery RL, Arrigg PG, Bursell SE, Aiello LP, Feener EP. Extracellular carbonic anhydrase mediates hemorrhagic retinal and cerebral vascular permeability through prekallikrein activation. Nat Med 2007; 13: 181–188.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Alge CS, SuppmannS, Priglinger SG, Neubauer AS, May CA, Hauck S, Welge‐lussen U, Ueffing M, Kampik A. Comparative proteome analysis of native differentiated and cultured dedifferentiated human RPE cells. Invest Ophthalmol Vis Sci 2003; 44: 3629–3641.
   PubMed Web of Science ®Google Scholar
• Schutt F, Ueberle B, Schnolzer M, Holz FG, Kopitz J. Proteome analysis of lipofuscin in human retinal pigment epithelial cells. FEBS Lett 2002; 528: 217–221.
   Web of Science ®Google Scholar
• Azarian SM, Mcleod I, Lillo C, Gibbs D, Yates JR, Williams DS. Proteomic analysis of mature melanosomes from the retinal pigmented epithelium. J Proteome Res 2006; 5: 521–529.
   Web of Science ®Google Scholar
• Bonilha VL, Bhattacharya SK, West KA, Sun J, Crabb JW, Rayborn ME, Hollyfield JG. Proteomic characterization of isolated retinal pigment epithelium microvilli. Mol Cell Proteomics 2004; 3: 1119–1127.
   Web of Science ®Google Scholar
• Nawrot M, West K, Huang J, Possin DE, Bretscher A, Crabb JW, Saari JC. Cellular retinaldehyde‐binding protein interacts with ERM‐binding phosphoprotein 50 in retinal pigment epithelium. Invest Ophthalmol Vis Sci 2004; 45: 393–401.
   Web of Science ®Google Scholar
• Hathout Y, Flippin J, Fan C, Liu P, Csaky K. Metabolic labeling of human primary retinal pigment epithelial cells for accurate comparative proteomics. J Proteome Res 2005; 4: 620–627.
   PubMed Web of Science ®Google Scholar
• Schlosshauer B. Membrane proteins and glycoproteins specific to central nervous system axons and growth cones. Brain Res 1985; 351: 237–244.
   Google Scholar
• Hildebrandt JD, Codina J, Rosenthal W, Birnbaumer L, Neer EJ, Yamazaki A, Bitensky MW. Characterization by two‐dimensional peptide mapping of the gamma subunits of Ns and Ni, the regulatory proteins of adenylyl cyclase, and of transducin, the guanine nucleotide‐binding protein of rod outer segments of the eye. J Biol Chem 1985; 260: 14867–14872.
   PubMed Web of Science ®Google Scholar
• Balsamo J, Pratt RS, Emmerling MR, Grunwald GB, Lilien J. Identification of the chick neural retina cell surface N‐acetylgalactosaminyltransferase using monoclonal antibodies. J Cell Biochem 1986; 32: 125–141.
   Web of Science ®Google Scholar
• Banga JP, Kasp E, Suleyman S, Brown E, Ellis BA, Sanders MD, Dumonde DC. Comparative biochemical analysis of purified S‐antigen from human, bovine, porcine and rat retina. Exp Eye Res 1987; 44: 199–207.
   PubMed Web of Science ®Google Scholar
• Jones PS, Schechter N. Distribution of specific intermediate‐filament proteins in the goldfish retina. J Comp Neurol 1987; 266: 112–121.
   Web of Science ®Google Scholar
• Lewis SE, Nixon RA. Multiple phosphorylated variants of the high molecular mass subunit of neurofilaments in axons of retinal cell neurons: characterization and evidence for their differential association with stationary and moving neurofilaments. J Cell Biol 1988; 107: 2689–2701.
   PubMed Web of Science ®Google Scholar
• Janssen‐bienhold U, Nagel H, Weiler R. In vitro phosphorylation in isolated horizontal cells of the fish retina: effects of the state of light adaptation. Eur J Neurosci 1993; 5: 584–593.
   Web of Science ®Google Scholar
• Wodarczyk L, Merrill VK, Perry GW. Differential regulation of fast axonally transported proteins during the early response of rat retinal ganglion cells to axotomy. J Neurochem 1997; 68: 1114–1123.
   Web of Science ®Google Scholar
• Deretic D, Aebersold RH, Morrison HD, Papermaster DS. Alpha A‐ and alpha B‐crystallin in the retina. Association with the post‐Golgi compartment of frog retinal photoreceptors. J Biol Chem 1994; 269: 16853–16861.
   Web of Science ®Google Scholar
• Sakaguchi H, Miyagi M, Darrow RM, Crabb JS, Hollyfield JG, Organisciak DT, Crabb JW. Intense light exposure changes the crystallin content in retina. Exp Eye Res 2003; 76: 131–133.
   Web of Science ®Google Scholar
• Organisciak D, Darrow R, Gu X, Barsalou L, Crabb JW. Genetic, age and light mediated effects on crystallin protein expression in the retina. Photochem Photobiol 2006; 82: 1088–1096.
   Web of Science ®Google Scholar
• Semple‐rowland SL, Adamus G, Cohen RJ, Ulshafer RJ. A reliable two‐dimensional gel electrophoresis procedure for separating neural proteins. Electrophoresis 1991; 12: 307–312.
   Web of Science ®Google Scholar
• Morel V, Poschet R, Traverso V, Deretic D. Towards the proteome of the rhodopsin‐bearing post‐Golgi compartment of retinal photoreceptor cells. Electrophoresis 2000; 21: 3460–3469.
   PubMed Web of Science ®Google Scholar
• Konig S, Schmidt O, Rose K, Thanos S, Besselmann M, Zeller M. Sodium dodecyl sulfate versus acid‐labile surfactant gel electrophoresis: comparative proteomic studies on rat retina and mouse brain. Electrophoresis 2003; 24: 751–756.
   Web of Science ®Google Scholar
• Wohabrebbi A, Umstot ES, Iannaccone A, Desiderio DM, Jablonski MM. Downregulation of a unique photoreceptor protein correlates with improper outer segment assembly. J Neurosci Res 2002; 67: 298–308.
   Web of Science ®Google Scholar
• Martin RE, Elliott MH, Brush RS, Anderson RE. Detailed characterization of the lipid composition of detergent‐resistant membranes from photoreceptor rod outer segment membranes. Invest Ophthalmol Vis Sci 2005; 46: 1147–1154.
   Web of Science ®Google Scholar
• Clack JW, Juhl M, Rice CA, Li J, Witzmann FA. Proteomic analysis of transducin beta‐subunit structural heterogeneity. Electrophoresis 2003; 24: 3493–3499.
   Web of Science ®Google Scholar
• Sineshchekova OO, Cardasis HL, Severance EG, Smith WC, Battelle BA. Sequential phosphorylation of visual arrestin in intact Limulus photoreceptors: identification of a highly light‐regulated site. Vis Neurosci 2004; 21: 715–724.
   Web of Science ®Google Scholar
• Wiechmann AF, Komori N, Matsumoto H. Melatonin induces alterations in protein expression in the Xenopus laevis retina. J Pineal Res 2002; 32: 270–274.
   Web of Science ®Google Scholar
• Hauck SM, Suppmann S, Ueffing M. Proteomic profiling of primary retinal Muller glia cells reveals a shift in expression patterns upon adaptation to in vitro conditions. Glia 2003; 44: 251–263.
   PubMed Web of Science ®Google Scholar
• Lund LM, Mcquarrie IG. Calcium/calmodulin‐dependent protein kinase II alpha in optic axons moves with slow axonal transport and undergoes posttranslational modification. Biochem Biophys Res Commun 2001; 289: 1157–1161.
   Web of Science ®Google Scholar
• Mulugeta S, Ciavarra RP, Maney RK, Tedeschi B. Three subpopulations of fast axonally transported retinal ganglion cell proteins are differentially trafficked in the rat optic pathway. J Neurosci Res 2000; 59: 247–258.
   Web of Science ®Google Scholar
• Mcfarlane I, Breen KC, Di giamberardino L, Moya KL. Inhibition of N‐glycan processing alters axonal transport of synaptic glycoproteins in vivo. Neuroreport 2000; 11: 1543–1547.
   Web of Science ®Google Scholar
• 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: 815–822.
   PubMed Web of Science ®Google Scholar
• 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.
   Web of Science ®Google Scholar
• Koo BS, Lee DY, Ha HS, Kim JC, Kim CW. Comparative analysis of the tear protein expression in blepharitis patients using two‐dimensional electrophoresis. J Proteome Res 2005; 4: 719–724.
   PubMed Web of Science ®Google Scholar
• Okumura N, Fukushima A, Igarashi A, Sumi T, Yamagishi T, Ueno H. Pharmacokinetic analysis of platelet‐activating factor in the tears of guinea pigs with allergic conjunctivitis. J Ocul Pharmacol Ther 2006; 22: 347–352.
   PubMed Web of Science ®Google Scholar
• Grus FH, Podust VN, Bruns K, Lackner K, Fu S, Dalmasso EA, Wirthlin A, Pfeiffer N. SELDI‐TOF‐MS ProteinChip array profiling of tears from patients with dry eye. Invest Ophthalmol Vis Sci 2005; 46: 863–876.
   PubMed Web of Science ®Google Scholar
• Baker GR, Morton M, Rajapaska RS, Bullock M, Gullu S, Mazzi B, Ludgate M. Altered tear composition in smokers and patients with Graves’ ophthalmopathy. Arch Ophthalmol 2006; 124: 1451–1456.
   PubMedGoogle Scholar
• Nielsen K, Vorum H, Fagerholm P, Birkenkamp‐demtroder K, Honore 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: 201–209.
   PubMed Web of Science ®Google Scholar
• Srivastava OP, Chandrasekaran D, Pfister RR. Molecular changes in selected epithelial proteins in human keratoconus corneas compared to normal corneas. Mol Vis 2006; 12: 1615–1625.
   Web of Science ®Google Scholar
• Lampi KJ, Ma Z, Hanson SR, Azuma M, Shih M, Shearer TR, Smith DL, Smith JB, David LL. Age‐related changes in human lens crystallins identified by two‐dimensional electrophoresis and mass spectrometry. Exp Eye Res 1998; 67: 31–43.
   PubMed Web of Science ®Google Scholar
• Kliffen M, Mooy CM, Luider TM, Huijmans JG, Kerkvliet S, De jong PT. Identification of glycosaminoglycans in age‐related macular deposits. Arch Ophthalmol 1996; 114: 1009–1014.
   Google Scholar
• Kliffen M, De jong PT, Luider TM. Protein analysis of human maculae in relation to age‐related maculopathy. Lab Invest 1995; 73: 267–272.
   Web of Science ®Google Scholar
• 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: 14682–14687.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Bresgen M, Baum U, Esser P, Wiedemann P, Heimann K. Protein composition of the vitreous body in proliferative diabetic retinopathy. An analysis with 2‐D‐electrophoresis. Ophthalmologe 1994; 91: 758–762.
   Google Scholar
• Kim SJ, Kim S, Park J, Lee HK, Park KS, Yu HG, Kim Y. Differential expression of vitreous proteins in proliferative diabetic retinopathy. Curr Eye Res 2006; 31: 231–240.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Bhattacharya SK, Rockwood EJ, Smith SD, Bonilha VL, Crabb JS, Kuchtey RW, Robertson NG, Peachey NS, Morton CC, Crabb JW. Proteomics reveal Cochlin deposits associated with glaucomatous trabecular meshwork. J Biol Chem 2005; 280: 6080–6084.
   PubMed Web of Science ®Google Scholar
• Maruyama I, Ohguro H, Ikeda Y. Retinal ganglion cells recognized by serum autoantibody against gamma‐enolase found in glaucoma patients. Invest Ophthalmol Vis Sci 2000; 41: 1657–1665.
   PubMed Web of Science ®Google Scholar
• Steely HT Jr, Clark AF. The use of proteomics in ophthalmic research. Pharmacogenomics 2000; 1: 267–280.
   PubMedGoogle Scholar
• Tezel G, Yang X, Cai J. Proteomic identification of oxidatively modified retinal proteins in a chronic pressure‐induced rat model of glaucoma. Invest Ophthalmol Vis Sci 2005; 46: 3177–3187.
   PubMed Web of Science ®Google Scholar
• Hollo G, Whitson JT, Faulkner R, Mccue B, Curtis M, Wieland H, Chastain J, Sanders M, Desantis L, Przydryga J, Dahlin DC. Concentrations of betaxolol in ocular tissues of patients with glaucoma and normal monkeys after 1 month of topical ocular administration. Invest Ophthalmol Vis Sci 2006; 47: 235–240.
   PubMed Web of Science ®Google Scholar
• 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: 1540–1548.
   Web of Science ®Google Scholar
• Missotten GS, Beijnen JH, Keunen JE, Bonfrer JM. Proteomics in uveal melanoma. Melanoma Res 2003; 13: 627–629.
   PubMed Web of Science ®Google Scholar
• Lewis GP, Matsumoto B, Fisher SK. Changes in the organization and expression of cytoskeletal proteins during retinal degeneration induced by retinal detachment. Invest Ophthalmol Vis Sci 1995; 36: 2404–2416.
   PubMed Web of Science ®Google Scholar
• Lewis GP, Guerin CJ, Anderson DH, Matsumoto B, Fisher SK. Rapid changes in the expression of glial cell proteins caused by experimental retinal detachment. Am J Ophthalmol 1994; 118: 368–376.
   PubMed Web of Science ®Google Scholar
• Maeda A, Ohguro H, Maeda T, Nakagawa T, Kuroki Y. Low expression of alpha A‐crystallins and rhodopsin kinase of photoreceptors in retinal dystrophy rat. Invest Ophthalmol Vis Sci 1999; 40: 2788–2794.
   Web of Science ®Google Scholar
• 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: 1683–1685.
   PubMed Web of Science ®Google Scholar
• Lim R, Mitchell P, Cumming RG. Refractive associations with cataract: the Blue Mountains Eye Study. Invest Ophthalmol Vis Sci 1999; 40: 3021–3026.
   PubMed Web of Science ®Google Scholar
• Akiba J. Prevalence of posterior vitreous detachment in high myopia. Ophthalmology 1993; 100: 1384–1388.
   PubMed Web of Science ®Google Scholar
• Coppe AM, Ripandelli G, Parisi V, Varano M, Stirpe M. Prevalence of asymptomatic macular holes in highly myopic eyes. Ophthalmology 2005; 112: 2103–2109.
   PubMed Web of Science ®Google Scholar
• Pierro L, Camesasca FI, Mischi M, Brancato R. Peripheral retinal changes and axial myopia. Retina 1992; 12: 12–17.
   PubMed Web of Science ®Google Scholar
• Secretan M, Kuhn D, Soubrane G, Coscas G. Long‐term visual outcome of choroidal neovascularization in pathologic myopia: natural history and laser treatment. Eur J Ophthalmol 1997; 7: 307–316.
   PubMedGoogle Scholar
• Lam TC, Li KK, Lo SC, Guggenheim JA, To CH. A chick retinal proteome database and differential retinal protein expressions during early ocular development. J Proteome Res 2006; 5: 771–784.
   Web of Science ®Google Scholar
• Lam TC, Li KK, Lo SC, Guggenheim JA, To CH. Differential protein expressions in the emmetropization of chick retina by a proteomic approach. In: The Association for Research in Vision and Ophthalmology (ARVO) annual meeting. Fort Lauderdale, Florida, United States, 2005.
   Google Scholar
• Lam TC, Chun KM, Li KK, Do CW, Lo SC, Guggenheim JA, To CH. A global retinal proteins expressions involving compensated myopia by proteomic approach. In: Eleventh International Myopia Conference, Singapore, 2006.
   Google Scholar
• Bertrand E, Fritsch C, Diether S, Lambrou G, Mueller D, Schaeffel F, Schindler P, Schmid KL, Van oostrum J, Voshol H. Identification of Apolipoprotein A1 as a ‘STOP’ signal for myopia. Mol Cell Proteomics 2006; 5: 2158–2166.
   PubMed Web of Science ®Google Scholar