The Human Eye Proteome Project: Perspectives on an emerging proteome

Proteomics

Volumn 13, Issue 16, 2013, Pages 2500-2511

  Semba, Richard D ^a   Enghild, Jan J ^b   Venkatraman, Vidya ^c   Dyrlund, Thomas F ^b   Van Eyk, Jennifer E ^c  

^a JOHNS HOPKINS UNIVERSITY   (United States)

^b AARHUS UNIVERSITY   (Denmark)

^c JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Biomedicine; Cornea; Eye; Retina; Vision

Indexed keywords

BIOLOGICAL MARKER; EYE PROTEIN;

AQUEOUS HUMOR; BODY FLUID; CHOROID; CILIARY BODY; CORNEA; DIABETIC RETINOPATHY; EYE; EYE DISEASE; HUMAN; IRIS; LACRIMAL FLUID; LENS; MOLECULAR BIOLOGY; OPEN ANGLE GLAUCOMA; OPHTHALMOLOGY; OPTIC NERVE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; RETINA; RETINA MACULA AGE RELATED DEGENERATION; REVIEW; SCLERA; TEAR FILM; TISSUES; VISION; VITREOUS BODY;

EID: 84881508088     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201300075     Document Type: Review

References (143)

1. Pascolini, D., Mariotti, S. P., Global estimates of visual impairment. Br. J. Ophthalmol. 2012, 96, 614-618.
2. Gordois, A., Cutler, H., Pezzullo, L., Gordon, K. et al., An estimation of the worldwide economic and health burden of visual impairment. Glob. Public. Health. 2012, 7, 465-481.
3. Aebersold, R., Bader, G. D., Edwards, A. M., van Eyk, J. E. et al., The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community. J. Proteome Res. 2013, 12, 23-27.
4. Li, N., Wang, N., Zheng, J., Liu, X. M. et al., Characterization of human tear proteome using multiple proteomic analysis techniques. J. Proteome Res. 2005, 4, 2051-2061.
5. De Souza, G. A., de Godoy, L. M. F., 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.
6. Green-Church, K. B., Nichols, K. K., Kleinholz, N. M., Zhang, L., Nichols, J. J., Investigation of the human tear film proteome using multiple proteomic approaches. Mol. Vis. 2008, 14, 456-470.
7. Zhou, L., Zhao, S. Z., Koh, S. W., Chen, L. et al., In-depth analysis of the human tear proteome. J. Proteomics 2012, 75, 3877-3885.
8. González, N., Iloro, I., Durán, J. A., Elortza, F., Suárez, T., Evaluation of inter-day and inter-individual variability of tear peptide/protein profiles by MALDI-TOF MS analyses. Mol. Vis. 2012, 18, 1572-1582.
9. [No authors listed], The definition and classification of dry eye disease: report of the Definition and Classification Subcommittee of the International Dry Eye Workshop (2007). Ocul. Surf. 2007, 5, 75-92.
10. Schaumberg, D. A., Dana, R., Buring, J. E., Sullivan, D. A., Prevalence of dry eye disease among US men: estimates from the Physicians' Health Studies. Arch. Ophthalmol. 2009, 127, 763-768.
11. Schaumberg, D. A., Sullivan, D. A., Buring, J. E., Dana, M. R., Prevalence of dry eye syndrome among US women. Am. J. Ophthalmol. 2003, 136, 318-326.
12. Grus, F. H., Podust, V. N., Bruns, K., Lackner, K. et al., SELDI-TOF-MS ProteinChip array profiling of tears from patients with dry eye. Invest. Ophthalmol. Vis. Sci. 2005, 46, 863-876.
13. Tomosugi, N., Kitagawa, K., Takahashi, N., Sugai, S., Ishikawa, I., Diagnostic potential of tear proteomic patterns in Sjögren's syndrome. J. Proteome Res. 2005, 4, 820-825.
14. Zhou, L., Beuerman, R. W., Chan, C. M., Zhao, S. Z. et al., Identification of tear fluid biomarkers in dry eye syndrome using iTRAQ quantitative proteomics. J. Proteome Res. 2009, 8, 4889-4905.
15. Versura, P., Nanni, P., Bavelloni, A., Blalock, W. L. et al., Tear proteomics in evaporative dry eye disease. Eye 2010, 24, 1396-1402.
16. Tong, L., Zhou, L., Beuerman, R. W., Zhao, S. Z., Li, X. R., Association of tear proteins with Meibomian gland disease and dry eye symptoms. Br. J. Ophthalmol. 2011, 95, 848-852.
17. Cojocaru, V. M., Ciurtin, C., Uyy, E., Antohe, F., Nano-LC mass spectrometry proteomic tear secretion analysis in patients with secondary Sjögren's syndrome. Digest J. Nanomaterials Biostructures 2011, 6, 491-498.
18. Srinivasan, S., Thangavelu, M., Zhang, L., Green, K. B., Nichols, K. K., iTRAQ quantitative proteomics in the analysis of tears in dry eye patients. Invest. Ophthalmol. Vis. Sci. 2012, 53, 5052-5059.
19. Lema, I., Brea, D., Rodríguez-González, R., Díez-Feijoo, E., Sobrino, T., Proteomic analysis of the tear film in patients with keratoconus. Mol. Vis. 2010, 16, 2055-2061.
20. Pannebaker, C., Chandler, H. L., Nichols, J. J., Tear proteomics in keratoconus. Mol. Vis. 2010, 16, 1949-1957.
21. Acera, A., Vecino, E., Rodríguez-Agirretxe, I., Aloria, K. et al., Changes in tear protein profile in keratoconus disease. Eye 2011, 25, 1225-1233.
22. Okrojek, R., Grus, F. H., Matheis, N., Kahaly, G. J., Proteomics in autoimmune thyroid eye disease. Horm. Metab. Res. 2009, 41, 465-470.
23. Koo, B. S., Lee, D. Y, Ha, H. S., Kim, J. C., Kim, C. W., Comparative analysis of the tear protein expression in blepharitis patients using two-dimensional electrophoresis. J. Proteome Res. 2005, 4, 719-724.
24. Acera, A., Suárez, T., Rodríguez-Agirretxe, I., Vecino, E., Durán, J. A., Changes in tear protein profile in patients with conjunctivochalasis. Cornea 2011, 30, 42-49.
25. Csodouble acutesz, É., Boross, P., Csutak, A., Berta, A. et al., Quantitative analysis of proteins in the tear fluid of patients with diabetic retinopathy. J. Proteomics 2012, 75, 2196-2204.
26. Pieragostino, D., Bucci, S., Agnifili, L., Fasanella, V. et al., Differential protein expression in tears of patients with primary open angle and pseudoexfoliative glaucoma. Mol. Biosyst. 2012, 8, 1017-1028.
27. Markoulli, M., Papas, E., Cole, N., Holden, B., Differential gel electrophoresis of the tear proteome. Optom. Vis. Sci. 2012, 89, E875-E883.
28. Wong, T. T., Zhou, L., Li, J., Tong, L. et al., Proteomic profiling of inflammatory signaling molecules in the tears of patients on chronic glaucoma medication. Invest. Ophthalmol. Vis. Sci. 2011, 52, 7385-7391.
29. Zhou, L., Huang, L. Q., Beuerman, R. W., Grigg, M. E. et al., Proteomic analysis of human tears: defensin expression after ocular surface surgery. J. Proteome Res. 2004, 3, 410-416.
30. Karring, H., Thøgersen, I. B., Klintworth, G. K., Møller-Pedersen, T., Enghild, J. J., A dataset of human cornea proteins identified by peptide mass fingerprinting and tandem mass spectrometry. Mol. Cell. Proteomics 2005, 4, 1406-1408.
31. Galiacy, S. D., Froment, C., Mouton-Barbosa, E., Erraud, A. et al., Deeper in the human cornea proteome using nanoLC-Orbitrap MS/MS: an improvement for future studies on cornea homeostasis and pathophysiology. J. Proteomics 2011, 75, 81-92.
32. Dyrlund, T. F., Poulsen, E. T., Scavenius, C., Nikolajsen, C. L. et al., Human cornea proteome: identification and quantification of the proteins of the three main layers including epithelium, stroma, and endothelium. J. Proteome Res. 2012, 11, 4231-4239.
33. Whitcher, J. P., Srinivasan, M., Upadhyay, M. P., Corneal blindness: a global perspective. Bull. World Health Organ. 2011, 79, 214-221.
34. Darlington, J. K., Adrean, S. D., Schwab, I. R., Trends of penetrating keratoplasty in the United States from 1980 to 2004. Ophthalmology 2006, 113, 2171-2175.
35. Elhalis, H., Azizi, B., Jurkunas, U. V., Fuchs endothelial corneal dystrophy. Ocul. Surf. 2010, 8, 173-184.
36. Jurkunas, U. V., Rawe, I., Bitar, M. S., Zhu, C. et al., Decreased expression of peroxiredoxins in Fuchs' endothelial dystrophy. Invest. Ophthalmol. Vis. Sci. 2008, 49, 2956-2963.
37. Jurkunas, U. V., Bitar, M., Rawe, I., Colocalization of increased transforming growth factor-b-induced protein (TGFBIp) and clusterin in Fuchs endothelial corneal dystrophy. Invest. Ophthalmol. Vis. Sci. 2009, 50, 1129-1136.
38. Kennedy, R. H., Bourne, W. M., Dyer, J. A., A 48-year clinical and epidemiologic study of keratoconus. Am. J. Ophthalmol. 1986, 101, 267-273.
39. Nielsen, K., Vorum, H., Fagerholm, P., Birkenkamp-Demtröder, K. et al., Proteome profiling of corneal epithelium and identification of marker proteins for keratoconus, a pilot study. Exp. Eye Res. 2006, 82, 201-209.
40. Srivastava, O. P., Chandrasekaran, D., Pfister, R. R., Molecular changes in selected epithelial proteins in human keratoconus corneas compared to normal corneas. Mol. Vis. 2006, 12, 1615-1625.
41. Joseph, R., Srivastava, O. P., Pfister, R. R., Differential epithelial and stromal protein profiles in keratoconus and normal human corneas. Exp. Eye Res. 2011, 92, 282-298.
42. Lyngholm, M., Vorum, H., Nielsen, K., Ehlers, N., Honoré, B., Attempting to distinguish between endogenous and contaminating cytokeratins in a corneal proteomic study. BMC Ophthalmol. 2011, 11, 3.
43. Kannabiran, C., Klintworth, G. K., TGFBI gene mutations in corneal dystrophies. Hum. Mut. 2006, 27, 615-625.
44. Yang, J., Han, X., Huang, D., Yu, L. et al., Analysis of TGFBI gene mutations in Chinese patients with corneal dystrophies and review of the literature. Mol. Vis. 2010, 16, 1186-1193.
45. Karring, H., Runager, K., Thøgersen, I. B., Klintworth, G. K. et al., Composition and proteolytic processing of corneal deposits associated with mutations in the TGFBI gene. Exp. Eye. Res. 2012, 96, 163-170.
46. Richardson, M. R., Price, M. O., Price, F. W., Pardo, J. C. et al., Proteomic analysis of human aqueous humor using multidimensional protein identification technology. Mol. Vis. 2009, 15, 2740-2750.
47. Escoffier, P., Paris, L., Bodaghi, B., Danis, M. et al., Pooling aqueous humor samples: bias in 2D-LC-MS/MS strategy? J. Proteome Res. 2010, 9, 789-797.
48. Chowdhury, U. R., Madden, B. J., Charlesworth, M. C., Fautsch, M. P., Proteome analysis of human aqueous humor. Invest. Ophthalmol. Vis. Sci. 2010, 51, 4921-4931.
49. Bennett, K. L., Funk, M., Tschernutter, M., Breitwieser, F. P. et al., Proteomic analysis of human cataract aqueous humour: comparison of one-dimensional gel LCMS with two-dimensional LCMS of unlabelled and iTRAQ®-labelled specimens. J. Proteomics 2011, 74, 151-166.
50. Quigley, H. A., Broman, A. T., The number of people with glaucoma worldwide in 2010 and 2020. Br. J.Ophthalmol. 2006, 90, 262-267.
51. Grus, F. H., Joachim, S. C., Sandmann, S., Thiel, U. et al., Transthyretin and complex protein pattern in aqueous humor of patients with primary open-angle glaucoma. Mol. Vis. 2008, 14, 1437-1445.
52. Duan, X., Xue, P., Wang, N., Dong, Z. et al., Proteomic analysis of aqueous humor from patients with primary open angle glaucoma. Mol. Vis. 2010, 16, 2839-2846.
53. Izzotti, A., Longobardi, M., Cartiglia, C., Saccà, S. C., Proteome alterations in primary open angle glaucoma aqueous humor. J. Proteome Res. 2010, 9, 4831-4838.
54. Anshu, A., Price, M. O., Richardson, M. R., Segu, Z. M. et al., Alterations in the aqueous humor proteome in patients with a glaucoma shunt device. Mol. Vis. 2011, 17, 1891-1900.
55. Saccà, S. C., Centofanti, M., Izzotti, A., New proteins as vascular biomarkers in primary open angle glaucomatous aqueous humor. Invest. Ophthalmol. Vis. Sci. 2012, 53, 4242-4253.
56. Funding, M., Vorum, H., Honoré, B., Nexø, E., Ehlers, N., Proteomic analysis of aqueous humour from patients with acute corneal rejection. Acta Ophthalmol. Scand. 2005, 83, 31-39.
57. Duan, X., Lu, Q., Xue, P., Zhang, H. et al., Proteomic analysis of aqueous humor from patients with myopia. Mol. Vis. 2008, 14, 370-377.
58. Richardson, R. W., Segu, Z. M., Price, M. O., Lai, X. et al., Alterations in the aqueous humor proteome in patients with Fuchs endothelial corneal dystrophy. Mol. Vis. 2010, 16, 2376-2383.
59. Bouhenni, R. A., Al Shawan, S., Morales, J., Wakim, B. T. et al., Identification of differentially expressed proteins in the aqueous humor of primary congenital glaucoma. Exp. Eye Res. 2011, 92, 67-75.
60. Kim, T. W., Kang, J. W., Ahn, J., Lee, E. K. et al., Proteomic analysis of the aqueous humor in age-related macular degeneration (AMD) patients. J. Proteome Res. 2012, 11, 4034-4043.
61. Kyselova, Z., Mass spectrometry-based proteomics approaches applied in cataract research. Mass. Spectrometry Rev. 2011, 30, 1173-1184.
62. West, S. K., Looking forward to 20/20: a focus on the epidemiology of eye diseases. Epidemiol. Rev. 2000, 22, 64-70.
63. West, S., Epidemiology of cataract, accomplishments over 25 years and future directions. Ophthalmic Epidemiol. 2007, 14, 173-178.
64. MacCoss, M. J., McDonald, W. H., Saraf, A., Sadygov, R. et al., Shotgun identification of protein modifications from protein complexes and lens tissues. Proc. Natl. Acad. Sci. USA 2002, 99, 7900-7905.
65. Srivastava, O. P., Srivastava, K., Existence of deamidated aB-crystallin fragments in normal and cataractous human lenses. Mol. Vis. 2003, 9, 110-118.
66. Harrington, V., McCall, S., Huynh, S., Srivastava, K., Srivastava, O. P., Crystallins in water soluble-high molecular weight protein fractions and water insoluble protein fractions in aging and cataractous human lenses. Mol. Vis. 2003, 10, 476-489.
67. Wilmarth, P. A., Tanner, S., Dasari, S., Nagalla, S. R. et al., Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: does deamidation contribute to crystallin insolubility? J. Proteome Res. 2006, 5, 2554-2566.
68. Harrington, V., Srivastava, O. P., Kirk, M., Proteomic analysis of water insoluble proteins from normal and cataractous human lenses. Mol. Vis. 2007, 13, 1680-1694.
69. Zhang, C., Liu, P., Wang, N., Li, Y., Wang, L., Comparison of two tandem mass spectrometry-based methods for analyzing the proteome of healthy human lens fibers. Mol. Vis. 2007, 13, 1873-1877.
70. Srivastava, K., Chaves, J. M., Srivastava, O. P., Kirk, M., Multi-crystallin complexes exist in the water-soluble high molecular weight protein fractions of aging normal and cataractous human lenses. Exp. Eye Res. 2008, 87, 356-366.
71. Hains, P. G., Truscott, R. J. W., Proteome analysis of human foetal, aged and advanced nuclear cataract lenses. Proteomics Clin. Appl. 2008, 2, 1611-1619.
72. Hains, P. G., Truscott, R. J. W., Proteomic analysis of the oxidation of cysteine residues in human age-related nuclear cataract lenses. Biochim. Biophys. Acta 2008, 1784, 1959-1964.
73. Hains, P. G., Truscott, R. J. W., Age-dependent deamidation of lifelong proteins in the human lens. Invest. Ophthalmol. Vis. Sci. 2010, 51, 3107-3114.
74. Huang, C. H., Wang, Y. T., Tsai, C. F., Chen, Y. J. et al., Phosphoproteomics characterization of novel phosphorylation sites of lens proteins from normal and cataractous human eye lenses. Mol. Vis. 2011, 17, 186-198.
75. 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. Chromatog. B 2002, 776, 89-100.
76. Koyama, R., Nakanishi, T., Ikeda, T., Shimizu, A., Catalogue of soluble proteins in human vitreous humor by one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis and electrospray ionization mass spectrometry including seven angiogenesis-regulating factors. J. Chromatog. B 2003, 792, 5-21.
77. Yamane, K., Minamoto, A., Yamashita, H., Takamura, H. et al., Proteome analysis of human vitreous proteins. Mol. Cell. Proteomics 2003, 2, 1177-1187.
78. Ouchi, M., West, K., Crabb, J. W., Kinoshita, S., Kamei, M., Proteomic analysis of vitreous from diabetic macular edema. Exp. Eye Res. 2005, 81, 176-182.
79. Kim, S. J., Kim, S., Park, J., Lee, H. K. et al., Differential expression of vitreous proteins in proliferative diabetic retinopathy. Curr. Eye Res. 2006, 31, 231-240.
80. Kim, T., Kim, S. J., Kim, K., Kang, U. B. et al., Profiling of vitreous proteomes from proliferative diabetic retinopathy and nondiabetic patients. Proteomics 2007, 7, 4203-4215.
81. García-Ramírez, M., Canals, F., Hernández, C., Colomé, N. et al., 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, 1294-1303.
82. Gao, B. B., Chen, X., Timothy, N., Aiello, L. P., Feener, E. P., Characterization of the vitreous proteome in diabetes without diabetic retinopathy and diabetes with proliferative diabetic retinopathy. J. Proteome Res. 2008, 7, 2516-2525.
83. Shitama, T., Hayashi, H., Noge, S., Uchio, E. et al., Proteome profiling of vitreoretinal diseases by cluster analysis. Proteomics Clin. Appl. 2008, 2, 1265-1280.
84. Wang, H., Feng, L., Hu, J. W., Xie, C. L., Wang, F., Characterisation of the vitreous proteome in proliferative diabetic retinopathy. Proteome Sci. 2012, 10, 15.
85. Jager, R. D., Meiler, W. F., Miller, J. W., Age-related macular degeneration. N. Engl. J. Med. 2008, 358, 2606-2617.
86. Friedman, D. S., O'Colmain, B. J., Muñoz, B., Tomany, S. C. et al., Prevalence of age-related macular degeneration in the United States. Arch. Ophthalmol. 2004, 122, 564-572.
87. AMD Alliance International, The Global Economic Cost of Visual Impairment, AMD Alliance International, Canberra, 2010. Available at: http://www.amdalliance.org/cost-of-blindness.html [Accessed 11/08/2011].
88. Crabb, J. W., Miyagi, M., Gu, X., Shadrach, K. et al., Drusen proteome analysis: an approach to the etiology of age-related macular degeneration. Proc. Natl. Acad. Sci. 2002, 99, 14682-14687.
89. Ng, K. P., Gugiu, B., Renganathan, K., Davies, M. W. et al., Retinal pigment epithelium lipofuscin proteomics. Mol. Cell. Proteomics 2008, 7, 1397-1405.
90. Nordgaard, C. L., Berg, K. M., Kapphahn, R. J., Reilly, C. et al., 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.
91. Ethen, C. M., Reilly, C., Feng, X., Olsen, T. W., Ferrington, D. A., The proteome of central and peripheral retina with progression of age-related macular degeneration. Invest. Ophthalmol. Vis. Sci. 2006, 47, 2280-2290.
92. Nordgaard, C. L., Karunadharma, P. P., Feng, X., Olsen, T. W., Ferrington, D. A., Mitochondrial proteomics of the retinal pigment epithelium at progressive stages of age-related macular degeneration. Invest. Ophthalmol. Vis. Sci. 2008, 49, 2848-2855.
93. Alcazar, O., Hawkridge, A. M., Collier, T. S., Cousins, S. W. et al., Proteomics characterization of cell membrane blebs in human retinal pigment epithelium cells. Mol. Cell. Proteomics 2009, 8, 2201-2211.
94. Decanini, A., Karunadhrama, P. R., Nordgaard, C. L., Feng, X. et al., Human retinal pigment epithelium proteome changes in early diabetes. Diabetologia 2008, 51, 1051-1061.
95. Hernández, C., García-Ramírez, M., Colomé, N., Villarroel, M. et al., New pathogenic candidates for diabetic macular edema detected by proteomic analysis. Diabetes Care 2010, 33, e92.
96. Len, A. C. L., Powner, M. B., Zhu, L., Hageman, G. S. et al., Pilot application of iTRAQ to the retinal disease macular telangiectasia. J. Proteome Res. 2012, 11, 537-553.
97. 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.
98. Yuan, X., Gu, X., Crabb, J. S., Yue, X. et al., Quantitative proteomics: comparison of the macular Bruch membrane/choroid complex from age-related macular degeneration and normal eyes. Mol. Cell. Proteomics 2010, 9, 1031-1046.
99. Bhattacharya, S. K., Crabb, J. S., Bonilha, V. L., Gu, X. et al., Proteomics implicates peptidyl arginine deiminase 2 and optic nerve citrullination in glaucoma pathogenesis. Invest. Ophthalmol. Vis. Sci. 2006, 47, 2508-2514.
100. Rogers, R. S., Dharsee, M., Ackloo, S., Sivak, J. M., Flanagan, J. G., Proteomics analyses of human optic nerve head astrocytes following biomechanical strain. Mol. Cell. Proteomics 2012, 11, 1-17.
101. Rogers, R., Dharsee, M., Ackloo, S., Flanagan, J. G., Proteomics analyses of activated human optic nerve head lamina cribrosa cells following biomechanical strain. Invest. Ophthalmol. Vis. Sci. 2012, 53, 3806-3816.
102. Picciani, R., Junk, A. K., Bhattacharya, S. K., Technical brief: a novel strategy for enrichment of trabecular meshwork protease proteome. Mol. Vis. 2008, 14, 871-877.
103. Kersey, P. J., Duarte, J., Williams, A., Karavidopoulou, Y. et al., The International Protein Index: an integrated database for proteomics experiments. Proteomics 2004, 4, 1995-1998.
104. The UniProt Consortium, Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2012, 40, D71-D75.
105. Huang, Y., Niu, B., Gao, Y., Fu, L., Li, W., CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics 2010, 26, 680-682.
106. Dyrlund, T. F., Poulsen, E. T., Scavenius, C., Sanggaard, K. W., Enghild, J. J., MS Data Miners: a web-based software tool to analyze, compare, and share mass spectrometry protein identifications. Proteomics 2012, 12, 2792-2796.
107. Farrah, T., Deutsch, E. W., Omenn, G. S., Campbell, D. S. et al., A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol. Cell. Proteomics 2011, 10, 10.1074/mcp.M110.006353.
108. Smith, W., Assink, J., Klein, R., Mitchell, P. et al., Risk factors for age-related macular degeneration: pooled findings from three continents. Ophthalmology 2001, 108, 697-704.
109. Tomany, S. C., Wang, J. J., Van Leeuwen, R., Klein, R. et al., Risk factors for incident age-related macular degeneration: pooled findings from three continents. Ophthalmology 2004, 111, 1280-1287.
110. Semba, R. D., Handbook of Nutrition and Ophthalmology. Humana Press, Totowa, NJ, 2007.
111. DeAngelis, M. M., Silveira, A. C., Carr, E. A., Kim, I. K., Genetics of age-related macular degeneration: current concepts, future directions. Sem. Ophthalmol. 2011, 26, 77-93.
112. Hong, T., Tan, A. G., Mitchell, P., Wang, J. J., A review and meta-analysis of the association between C-reactive protein and age-related macular degeneration. Surv. Ophthalmol. 2011, 56, 184-194.
113. Gu, J., Pauer, G. J. T., Yu, X., Narendra, U. et al., Assessing susceptibility to age-related macular degeneration with proteomic and genomic biomarkers. Mol. Cell. Proteomics 2009, 8, 1338-1349.
114. Kwon, Y. H., Fingert, J. H., Kuehn, M. H., Alward, W. L. M., Primary open-angle glaucoma. N. Engl. J. Med. 2009, 360, 1113-1124.
115. Knepper, P. A., Samples, J. R., Yue, B. Y. J. T., Biomarkers of primary open-angle glaucoma. Expert Rev. Ophthalmol. 2010, 5, 731-742.
116. Kokotas, H., Kroupis, C., Chiras, D., Grigoriadou, M. et al., Biomarkers in primary open angle glaucoma. Clin. Chem. Lab. Med. 2012, 50, 2107-2119.
117. Mohamed, Q., Gillies, M. C., Wong, T. Y., Management of diabetic retinopathy: a systematic review. JAMA 2007, 298, 902-916.
118. Frank, R. N., Diabetic retinopathy. N. Engl. J. Med. 2004, 350, 48-58.
119. Nguyen, T. T., Alibrahim, E., Islam, F. M. A., Klein, R. et al., Inflammatory, hemostatic, and other novel biomarkers for diabetic retinopathy: the Multi-Ethnic Study of Atherosclerosis. Diabetes Care 2009, 32, 1704-1709.
120. Hu, Q., Noll, R. J., Makarov, A., Hardman, M., Graham Cooks, R., The Orbitrap: a new mass spectrometer. J. Mass. Spectrom. 2005, 40, 430-443.
121. Michalski, A., Damoc, E., Lange, O., Denisov, E. et al., Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes. Mol. Cell. Proteomics 2012, 11, O111.013698.
122. Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B. et al., Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 2004, 3, 1154-1169.
123. Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B. et al., Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 2002, 1, 376-386.
124. Smolka, M. B., Zhou, H., Purkayastha, S., Aebersold, R., Optimization of the isotope-coded affinity tag-labeling procedure for quantitative proteome analysis. Anal. Biochem. 2001, 297, 25-31.
125. Gerber, S. A., Rush, J., Stemman, O., Kirschner, M. W., Gygi, S. P., Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. USA 2003, 100, 6940-6945.
126. Picotti, P., Aebersold, R., Selected reaction monitoring-based proteomics, workflows, potential, pitfalls, and future directions. Nat. Methods 2012, 9, 555-566.
127. Gille, L. C., Navarro, P., Tate, S., Röst, H. et al., Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteomic analysis. Mol. Cell. Proteomics 2012, 11, 1-17.
128. Tress, M. L., Bodenmiller, B., Aebersold, R., Valencia, A., Proteomics studies confirm the presence of alternative isoforms on a large scale. Genome Biol. 2008, 9, R162.
129. Su, Z. D., Sun, L., Yu, D. X., Li, R. X. et al., Quantitative detection of single amino acid polymorphisms by targeted proteomics. J. Mol. Cell. Biol. 2011, 3, 309-315.
130. Stastna, M., Van Eyk, J. E., Analysis of protein isoforms: can we do it better? Proteomics J. 2012, 12, 2937-2948.
131. Menon, R., Roy, A., Mukherjee, S., Belkin, S. et al., Functional implications of structural predictions for alternative splice proteins expressed in Her2/neu-induced breast cancers. J. Proteome Res. 2011, 10, 5503-5511.
132. Palmisano, G., Thingholm, T. E., Strategies for quantitation of phosphoproteomic data. Expert Rev. Proteomics 2010, 7, 439-456.
133. Vertegaal, A. C. O., Uncovering ubiquitin and ubiquitin-like signaling networks. Chem. Rev. 2011, 111, 7923-7940.
134. Paruchuri, V. D., Zachara, N. E., Defining the heart and cardiovascular O-GlcNAcome: a review of approaches and methods. Circ. Cardiovasc. Genet. 2011, 4, 710.
135. De Ceuleneer, M., Van Steendam, K., Dhaenens, M., Deforce, D., In vivo relevance of citrullinated proteins and the challenges in their detection. Proteomics 2012, 12, 752-760.
136. Cristea, I. M., Williams, R., Chait, B. T., Rout, M. P., Fluorescent proteins as proteomic probes. Mol. Cell. Proteomics 2005, 4, 1933-1941.
137. Sardiu, M. E., Washburn, M. P., Building protein-protein interaction networks with proteomics and informatics tools. J. Biol. Chem. 2011, 286, 23645-23651.
138. Millward, S. W., Agnew, H. D., Lai, B., Lee, S. S. et al., In situ click chemistry: from small molecule discovery to synthetic antibodies. Integr. Biol. (Cambridge) 2013, 5, 87-95.
139. Sprung, R. W. Jr., Brock, J. W. C., Tanksley, J. P., Li, M. et al., Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis. Mol. Cell. Proteomics 2009, 8, 1988-1998.
140. Scicchitano, M. S., Dalmas, D. A., Boyce, R. W., Thomas, H. C., Frazier, K. S., Protein extraction of formalin-fixed, paraffin-embedded tissue enables robust proteomic profiles by mass spectrometry. J. Histochem. Cytochem. 2009, 57, 849-860.
141. Sprung, R. W., Martinez, M. A., Carpenter, K. L., Ham, A. J. L. et al., Precision of multiple reaction monitoring mass spectrometry analysis of formalin-fixed, paraffin-embedded tissue. J. Proteome. Res. 11, 3498-3505.
142. Rissin, D. M., Kan, C. W., Campbell, T. G., Howes, S. C. et al., Single-molecule enzyme-linked immunosorbent assay detects serum proteins at subfemtomolar concentrations. Nature Biotechnol. 2010, 28, 595-599.
143. Bancaud, A., Huet, S., Rabut, G, Ellenberg, J., Fluorescence perturbation techniques to study mobility and molecular dynamics of proteins in live cells: FRAP, photoactivation, photoconversion, and FLIP. Cold Spring Harb. Protoc. 2010, 2010, pdb.top90.