Gygi SP, Rochon Y, Franza BR and Aebersold R: Correlation between protein and mRNA abundance in yeast. Mol Cell Biol. 19:1720–1730. 1999. View Article : Google Scholar : PubMed/NCBI

Black DL: Mechanisms of alternative pre-messenger RNA splicing. Ann Rev Biochem. 72:291–336. 2003. View Article : Google Scholar : PubMed/NCBI

Belle A, Tanay A, Bitincka L, Shamir R and O'Shea EK: Quantification of protein half-lives in the budding yeast proteome. Proc Natl Acad Sci USA. 103:pp. 13004–13009. 2006; View Article : Google Scholar : PubMed/NCBI

Higgins SJ and Hames BD: Post-translational Processing: A Practical Approach. Oxford University Press; Oxford: 1999

Amniai L, Barbier P, Sillen A, Wieruszeski JM, Peyrot V, Lippens G and Landrieu I: Alzheimer disease specific phosphoepitopes of Tau interfere with assembly of tubulin but not binding to microtubules. FASEB J. 23:1146–1152. 2009. View Article : Google Scholar : PubMed/NCBI

Augustinack JC, Schneider A, Mandelkow EM and Hyman BT: Specific tau phosphorylation sites correlate with severity of neuronal cytopathology in Alzheimer's disease. Acta Neuropathol. 103:26–35. 2002. View Article : Google Scholar : PubMed/NCBI

Kyselova Z, Mechref Y, Al Bataineh MM, Dobrolecki LE, Hickey RJ, Vinson J, Sweeney CJ and Novotny MV: Alterations in the serum glycome due to metastatic prostate cancer. J Proteome Res. 6:1822–1832. 2007. View Article : Google Scholar : PubMed/NCBI

Zhao J, Qiu W, Simeone DM and Lubman DM: N-linked glycosylation profiling of pancreatic cancer serum using capillary liquid phase separation coupled with mass spectrometric analysis. J Proteome Res. 6:1126–1138. 2007. View Article : Google Scholar : PubMed/NCBI

Rombouts Y, Willemze A, Van Beers JJ, Shi J, Kerkman PF, Van Toorn L, Janssen GM, Zaldumbide A, Hoeben RC, Pruijn GJ, et al: Extensive glycosylation of ACPA-IgG variable domains modulates binding to citrullinated antigens in rheumatoid arthritis. Ann Rheum Dis. 75:578–585. 2016. View Article : Google Scholar : PubMed/NCBI

Ceciliani F, Eckersall D, Burchmore R and Lecchi C: Proteomics in veterinary medicine: Applications and trends in disease pathogenesis and diagnostics. Vet Pathol. 51:351–362. 2014. View Article : Google Scholar : PubMed/NCBI

Rabilloud T: Two-dimensional gel electrophoresis in proteomics: Old, old fashioned, but it still climbs up the mountains. Proteomics. 2:3–10. 2002. View Article : Google Scholar : PubMed/NCBI

Williams A and Frasca V: Ion-Exchange Chromatography. Curr Protoc Protein Sci Chapter. 8:Unit8.22001.

Queiroz J, Tomaz C and Cabral J: Hydrophobic interaction chromatography of proteins. J Biotechnol. 87:143–159. 2001. View Article : Google Scholar : PubMed/NCBI

Lecchi P, Gupte AR, Perez RE, Stockert LV and Abramson FP: Size-exclusion chromatography in multidimensional separation schemes for proteome analysis. J Biochem Biophys Methods. 56:141–152. 2003. View Article : Google Scholar : PubMed/NCBI

Lee WC and Lee KH: Applications of affinity chromatography in proteomics. Anal Biochem. 324:1–10. 2004. View Article : Google Scholar : PubMed/NCBI

McCue JT: Theory and use of hydrophobic interaction chromatography in protein purification applications. Methods Enzymol. 463:405–414. 2009. View Article : Google Scholar : PubMed/NCBI

Issaq HJ, Chan KC, Blonder J, Ye X and Veenstra TD: Separation, detection and quantitation of peptides by liquid chromatography and capillary electrochromatography. J Chromatogr A. 1216:1825–1837. 2009. View Article : Google Scholar : PubMed/NCBI

Petrovic M and Barceló D: Liquid chromatography-mass spectrometry in the analysis of emerging environmental contaminants. Anal Bioanal Chem. 385:422–424. 2006. View Article : Google Scholar : PubMed/NCBI

Rivier L: Criteria for the identification of compounds by liquid chromatography-mass spectrometry and liquid chromatography-multiple mass spectrometry in forensic toxicology and doping analysis. Analytica Chimica Acta. 492:69–82. 2003. View Article : Google Scholar

Chace DH: Mass spectrometry in the clinical laboratory. Chem Rev. 101:445–477. 2001. View Article : Google Scholar : PubMed/NCBI

Deutsch EW, Lam H and Aebersold R: Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics. Physiol Genomics. 33:18–25. 2008. View Article : Google Scholar : PubMed/NCBI

Zaluzec EJ, Gage DA and Watson JT: Matrix-assisted laser desorption ionization mass spectrometry: Applications in peptide and protein characterization. Protein Expr Purif. 6:109–123. 1995. View Article : Google Scholar : PubMed/NCBI

Kaufmann R: Matrix-assisted laser desorption ionization (MALDI) mass spectrometry: A novel analytical tool in molecular biology and biotechnology. J Biotechnol. 41:155–175. 1995. View Article : Google Scholar : PubMed/NCBI

Dole M, Mack LL and more RL Hines: Molecular beams of macroions. J Chemical Physics. 49:22401968. View Article : Google Scholar

Yamashita M and Fenn JB: Electrospray ion source. Another variation on the free-jet theme. J Phys Chem. 88:4451–4459. 1984. View Article : Google Scholar

Kinter M and Sherman NE: Protein Sequencing and Identification Using Tandem Mass Spectrometry. Wiley-Interscience; 2000, View Article : Google Scholar

Kraj A and Silberring J: Proteomics: Introduction to Methods and Applications. John Wiley & Sons; Hoboken, NJ: 2008

Elviri L: ETD and ECD mass spectrometry fragmentation for the characterization of protein post translational modificationsTandem Mass Spectrometry-Applications and Principles. Prasain JK: InTech; pp. 161–178. 2012

Quan L and Liu M: CID, ETD and HCD fragmentation to study protein post-translational modifications. Mod Chem Appl. 1:e1022013.

Hayakawa S, Matsumoto S, Hashimoto M, Iwamoto K, Nagao H, Toyoda M, Shigeri Y, Tajiri M and Wada Y: High-energy electron transfer dissociation (HE-ETD) using alkali metal targets for sequence analysis of post-translational peptides. J Am Soc Mass Spectrom. 21:1482–1489. 2010. View Article : Google Scholar : PubMed/NCBI

Guthals A and Bandeira N: Peptide identification by tandem mass spectrometry with alternate fragmentation modes. Mol Cell Proteomics. 11:550–557. 2012. View Article : Google Scholar : PubMed/NCBI

Altelaar AM, Mohammed S, Brans MA, Adan RA and Heck AJ: Improved identification of endogenous peptides from murine nervous tissue by multiplexed peptide extraction methods and multiplexed mass spectrometric analysis. J Proteome Res. 8:870–876. 2009. View Article : Google Scholar : PubMed/NCBI

van den Toorn HW, Mohammed S, Gouw JW, van Breukelen B and Heck AJ: Targeted scx based peptide fractionation for optimal sequencing by collision induced, and electron transfer dissociation. J Proteomics Bioinform. 1:379–388. 2008. View Article : Google Scholar

Jedrychowski MP, Huttlin EL, Haas W, Sowa ME, Rad R and Gygi SP: Evaluation of HCD- and CID-type fragmentation within their respective detection platforms for murine phosphoproteomics. Mol Cell Proteomics. 10:M111.0099102011. View Article : Google Scholar : PubMed/NCBI

Nagaraj N, D'Souza RC, Cox J, Olsen JV and Mann M: Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation. J Proteome Res. 9:6786–6794. 2010. View Article : Google Scholar

Saba J, Dutta S, Hemenway E and Viner R: Increasing the productivity of glycopeptides analysis by using higher-energy collision dissociation-accurate mass-product-dependent electron transfer dissociation. Int J Proteomics. 2012:5603912012. View Article : Google Scholar :

Liu M, Talmadge JE and Ding SJ: Development and application of site-specific proteomic approach for study protein S-nitrosylation. Amino acids. 42:1541–1551. 2012. View Article : Google Scholar

Palumbo AM, Tepe JJ and Reid GE: Mechanistic insights into the multistage gas-phase fragmentation behavior of phosphoserine- and phosphothreonine-containing peptides. J Proteome Res. 7:771–779. 2008. View Article : Google Scholar

Scott NE, Parker BL, Connolly AM, Paulech J, Edwards AV, Crossett B, Falconer L, Kolarich D, Djordjevic SP, Højrup P, et al: Simultaneous glycan-peptide characterization using hydrophilic interaction chromatography and parallel fragmentation by CID, higher energy collisional dissociation, and electron transfer dissociation MS applied to the N-linked glycoproteome of Campylobacter jejuni. Mol Cell Proteomics. 10:M000031–MCP201. 2011. View Article : Google Scholar

Sobott F, Watt SJ, Smith J, Edelmann MJ, Kramer HB and Kessler BM: Comparison of CID versus ETD based MS/MS fragmentation for the analysis of protein ubiquitination. J Am Soc Mass Spectrom. 20:1652–1659. 2009. View Article : Google Scholar

Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, et al: Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics. 3:1154–1169. 2004. View Article : Google Scholar

Paradela A, Marcilla M, Navajas R, Ferreira L, Ramos-Fernandez A, Fernández M, Mariscotti JF, García-del Portillo F and Albar JP: Evaluation of isotope-coded protein labeling (ICPL) in the quantitative analysis of complex proteomes. Talanta. 80:1496–1502. 2010. View Article : Google Scholar

Hsu JL, Huang SY and Chen SH: Dimethyl multiplexed labeling combined with microcolumn separation and MS analysis for time course study in proteomics. Electrophoresis. 27:3652–3660. 2006. View Article : Google Scholar

Liu H, Sadygov RG and Yates JR III: A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem. 76:4193–4201. 2004. View Article : Google Scholar

Bondarenko PV, Chelius D and Shaler TA: Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry. Anal Chem. 74:4741–4749. 2002. View Article : Google Scholar

Huang Q, Yang L, Luo J, Guo L, Wang Z, Yang X, Jin W, Fang Y, Ye J, Shan B and Zhang Y: SWATH enables precise label-free quantification on proteome-scale. Proteomics. 15:1215–1223. 2015. View Article : Google Scholar

Mueller LN, Brusniak MY, Mani DR and Aebersold R: An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J Proteome Res. 7:51–61. 2008. View Article : Google Scholar

Rajcevic U, Niclou SP and Jimenez CR: Proteomics strategies for target identification and biomarker discovery in cancer. Front Biosci (Landmark Ed). 14:3292–3303. 2009. View Article : Google Scholar

Räst HL, Rosenberger G, Navarro P, Gillet L, Miladinović SM, Schubert OT, Wolski W, Collins BC, Malmström J, Malmström L and Aebersold R: OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nat Biotechnol. 32:219–223. 2014. View Article : Google Scholar

Khoury GA, Baliban RC and Floudas CA: Proteome-wide post-translational modification statistics: Frequency analysis and curation of the swiss-prot database. Sci Rep. 1:pii: srep000902011. View Article : Google Scholar

Yarbrough ML and Orth K: AMPylation is a new post-translational modiFICation. Nat Chem Biol. 5:378–379. 2009. View Article : Google Scholar

Mann M and Jensen ON: Proteomic analysis of post-translational modifications. Nat Biotechnol. 21:255–261. 2003. View Article : Google Scholar

Manning G, Plowman GD, Hunter T and Sudarsanam S: Evolution of protein kinase signaling from yeast to man. Trends Biochem Sci. 27:514–520. 2002. View Article : Google Scholar

Graves JD and Krebs EG: Protein phosphorylation and signal transduction. Pharmacol Ther. 82:111–121. 1999. View Article : Google Scholar

Hunter T: Protein kinases and phosphatases: The yin and yang of protein phosphorylation and signaling. Cell. 80:225–236. 1995. View Article : Google Scholar

Cohen P: The regulation of protein function by multisite phosphorylation-a 25 year update. Trends Biochem Sci. 25:596–601. 2000. View Article : Google Scholar

Kersten B, Agrawal GK, Iwahashi H and Rakwal R: Plant phosphoproteomics: A long road ahead. Proteomics. 6:5517–5528. 2006. View Article : Google Scholar

Jung K, Fried L, Behr S and Heermann R: Histidine kinases and response regulators in networks. Curr Opin Microbiol. 15:118–124. 2012. View Article : Google Scholar

Kruppa M and Calderone R: Two-component signal transduction in human fungal pathogens. FEMS Yeast Res. 6:149–159. 2006. View Article : Google Scholar

Klumpp S and Krieglstein J: Reversible phosphorylation of histidine residues in proteins from vertebrates. Sci Signal. 2:pe132009. View Article : Google Scholar

Han SX, Wang LJ, Zhao J, Zhang Y, Li M, Zhou X, Wang J and Zhu Q: 14-kDa Phosphohistidine phosphatase plays an important role in hepatocellular carcinoma cell proliferation. Oncol Lett. 4:658–664. 2012.

Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, et al: The sequence of the human genome. Science. 291:1304–1351. 2001. View Article : Google Scholar

Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al: Initial sequencing and analysis of the human genome. Nature. 409:860–921. 2001. View Article : Google Scholar

Vasan S, Zhang X, Zhang X, Kapurniotu A, Bernhagen J, Teichberg S, Basgen J, Wagle D, Shih D, Terlecky I, et al: An agent cleaving glucose-derived protein crosslinks in vitro and in vivo. Nature. 382:275–278. 1996. View Article : Google Scholar

Blom N, Sicheritz-Pontén T, Gupta R, Gammeltoft S and Brunak S: Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics. 4:1633–1649. 2004. View Article : Google Scholar

Tian Y and Zhang H: Characterization of disease-associated N-linked glycoproteins. Proteomics. 13:504–511. 2013. View Article : Google Scholar

Cylwik B, Lipartowska K, Chrostek L and Gruszewska E: Congenital disorders of glycosylation. Part II. Defects of protein O-glycosylation. Acta Biochim Pol. 60:361–368. 2013.

Furmanek A and Hofsteenge J: Protein C-mannosylation: Facts and questions. Acta Biochim Pol. 47:781–789. 2000.

Kinoshita T, Fujita M and Maeda Y: Biosynthesis, remodelling and functions of mammalian GPI-anchored proteins: Recent progress. J Biochem. 144:287–294. 2008. View Article : Google Scholar

Wong CH: Protein glycosylation: New challenges and opportunities. J Org Chem. 70:4219–4225. 2005. View Article : Google Scholar

Murakami Y: Pathogenesis of paroxysmal nocturnal hemoglobinuria. Rinsho Ketsueki. 57:1900–1907. 2016.

Lee RT, Lauc G and Lee YC: Glycoproteomics: Protein modifications for versatile functions. Meeting on glycoproteomics. EMBO Rep. 6:1018–1022. 2005. View Article : Google Scholar :

Hart GW and Copeland RJ: Glycomics hits the big time. Cell. 143:672–676. 2010. View Article : Google Scholar :

Shahbazian MD and Grunstein M: Functions of site-specific histone acetylation and deacetylation. Annu Rev Biochem. 76:75–100. 2007. View Article : Google Scholar

Brooks CL and Gu W: Ubiquitination, phosphorylation and acetylation: The molecular basis for p53 regulation. Curr Opin Cell Biol. 15:164–171. 2003. View Article : Google Scholar

Hammond JW, Cai D and Verhey KJ: Tubulin modifications and their cellular functions. Curr Opin Cell Biol. 20:71–76. 2008. View Article : Google Scholar :

Arnesen T, Van Damme P, Polevoda B, Helsens K, Evjenth R, Colaert N, Varhaug JE, Vandekerckhove J, Lillehaug JR, Sherman F and Gevaert K: Proteomics analyses reveal the evolutionary conservation and divergence of N-terminal acetyltransferases from yeast and humans. Proc Natl Acad Sci USA. 106:pp. 8157–8162. 2009; View Article : Google Scholar :

Van Damme P, Hole K, Pimenta-Marques A, Helsens K, Vandekerckhove J, Martinho RG, Gevaert K and Arnesen T: NatF contributes to an evolutionary shift in protein N-terminal acetylation and is important for normal chromosome segregation. PLoS Genet. 7:e10021692011. View Article : Google Scholar :

Brown JL: A comparison of the turnover of alpha-N-acetylated and nonacetylated mouse L-cell proteins. J Biol Chem. 254:1447–1449. 1979.

Guo L, Münzberg H, Stuart RC, Nillni EA and Bjørbæk C: N-acetylation of hypothalamic alpha-melanocyte-stimulating hormone and regulation by leptin. Proc Natl Acad Sci USA. 101:pp. 11797–11802. 2004; View Article : Google Scholar :

Hwang CS, Shemorry A and Varshavsky A: N-terminal acetylation of cellular proteins creates specific degradation signals. Science. 327:973–977. 2010. View Article : Google Scholar :

Behnia R, Panic B, Whyte JR and Munro S: Targeting of the Arf-like GTPase Arl3p to the Golgi requires N-terminal acetylation and the membrane protein Sys1p. Nat Cell Biol. 6:405–413. 2004. View Article : Google Scholar

Forte GM, Pool MR and Stirling CJ: N-terminal acetylation inhibits protein targeting to the endoplasmic reticulum. PLoS Biol. 9:e10010732011. View Article : Google Scholar :

Gromyko D, Arnesen T, Ryningen A, Varhaug JE and Lillehaug JR: Depletion of the human Nα-terminal acetyltransferase A induces p53-dependent apoptosis and p53-independent growth inhibition. Int J Cancer. 127:2777–2789. 2010. View Article : Google Scholar

Yi CH, Pan H, Seebacher J, Jang IH, Hyberts SG, Heffron GJ, Heiden MG Vander, Yang R, Li F, Locasale JW, et al: Metabolic regulation of protein N-alpha-acetylation by Bcl-xL promotes cell survival. Cell. 146:607–620. 2011. View Article : Google Scholar :

Kamita M, Kimura Y, Ino Y, Kamp RM, Polevoda B, Sherman F and Hirano H: N(α)-Acetylation of yeast ribosomal proteins and its effect on protein synthesis. J Proteomics. 74:431–441. 2011. View Article : Google Scholar

Allfrey VG, Faulkner R and Mirsky AE: Acetylation and methylation of histones and their possible role in the regulation of rna synthesis. Proc Natl Acad Sci USA. 51:pp. 786–794. 1964; View Article : Google Scholar :

Gershey EL, Vidali G and Allfrey VG: Chemical studies of histone acetylation. The occurrence of epsilon-N-acetyllysine in the f2a1 histone. J Biol Chem. 243:5018–5022. 1968.

Yang XJ and Seto E: Lysine acetylation: Codified crosstalk with other posttranslational modifications. Mol Cell. 31:449–461. 2008. View Article : Google Scholar :

Haberland M, Montgomery RL and Olson EN: The many roles of histone deacetylases in development and physiology: Implications for disease and therapy. Nat Rev Genet. 10:32–42. 2009. View Article : Google Scholar :

Shakespear MR, Halili MA, Irvine KM, Fairlie DP and Sweet MJ: Histone deacetylases as regulators of inflammation and immunity. Trends Immunol. 32:335–343. 2011. View Article : Google Scholar

Villagra A, Sotomayor E and Seto E: Histone deacetylases and the immunological network: Implications in cancer and inflammation. Oncogene. 29:157–173. 2010. View Article : Google Scholar

Mukherjee S, Hao YH and Orth K: A newly discovered post-translational modification-the acetylation of serine and threonine residues. Trends Biochem Sci. 32:210–216. 2007. View Article : Google Scholar

Paquette N, Conlon J, Sweet C, Rus F, Wilson L, Pereira A, Rosadini CV, Goutagny N, Weber AN, Lane WS, et al: Serine/threonine acetylation of TGFβ-activated kinase (TAK1) by Yersinia pestis YopJ inhibits innate immune signaling. Proc Natl Acad Sci USA. 109:pp. 12710–12715. 2012; View Article : Google Scholar :

Ciechanover A and Iwai K: The ubiquitin system: From basic mechanisms to the patient bed. IUBMB Life. 56:193–201. 2004. View Article : Google Scholar

Stieren ES, El Ayadi A, Xiao Y, Siller E, Landsverk ML, Oberhauser AF, Barral JM and Boehning D: Ubiquilin-1 is a molecular chaperone for the amyloid precursor protein. J Biol Chem. 286:35689–35698. 2011. View Article : Google Scholar :

Ciechanover A and Brundin P: The ubiquitin proteasome system in neurodegenerative diseases: Sometimes the chicken, sometimes the egg. Neuron. 40:427–446. 2003. View Article : Google Scholar

Scheffner M, Werness BA, Huibregtse JM, Levine AJ and Howley PM: The E6 oncoprotein encoded by human papillomavirus types 16 and 18 promotes the degradation of p53. Cell. 63:1129–1136. 1990. View Article : Google Scholar

Dantuma NP and Masucci MG: The ubiquitin/proteasome system in Epstein-Barr virus latency and associated malignancies. Semin Cancer Biol. 13:69–76. 2003. View Article : Google Scholar

Karin M and Ben-Neriah Y: Phosphorylation meets ubiquitination: The control of NF-[kappa]B activity. Annu Rev Immunol. 18:621–663. 2000. View Article : Google Scholar

Shamu CE, Story CM, Rapoport TA and Ploegh HL: The pathway of US11-dependent degradation of MHC class I heavy chains involves a ubiquitin-conjugated intermediate. J Cell Biol. 147:45–58. 1999. View Article : Google Scholar :

Sarge KD and Park-Sarge OK: Sumoylation and human disease pathogenesis. Trends Biochem Sci. 34:200–205. 2009. View Article : Google Scholar :

Desterro JM, Rodriguez MS, Kemp GD and Hay RT: Identification of the enzyme required for activation of the small ubiquitin-like protein SUMO-1. J Biol Chem. 274:10618–10624. 1999. View Article : Google Scholar

Gong L, Kamitani T, Fujise K, Caskey LS and Yeh ET: Preferential interaction of sentrin with a ubiquitin-conjugating enzyme, Ubc9. J Biol Chem. 272:28198–28201. 1997. View Article : Google Scholar

Reverter D and Lima CD: Insights into E3 ligase activity revealed by a SUMO-RanGAP1-Ubc9-Nup358 complex. Nature. 435:687–692. 2005. View Article : Google Scholar :

Zhao J: Sumoylation regulates diverse biological processes. Cell Mol Life Sci. 64:3017–3033. 2007. View Article : Google Scholar

Kim KI and Baek SH: SUMOylation code in cancer development and metastasis. Mol Cells. 22:247–253. 2006.

Lin X, Sun B, Liang M, Liang YY, Gast A, Hildebrand J, Brunicardi FC, Melchior F and Feng XH: Opposed regulation of corepressor CtBP by SUMOylation and PDZ binding. Mol Cell. 11:1389–1396. 2003. View Article : Google Scholar

Sternsdorf T, Jensen K, Reich B and Will H: The nuclear dot protein sp100, characterization of domains necessary for dimerization, subcellular localization, and modification by small ubiquitin-like modifiers. J Biol Chem. 274:12555–12566. 1999. View Article : Google Scholar

Kamitani T, Kito K, Nguyen HP, Wada H, Fukuda-Kamitani T and Yeh ET: Identification of three major sentrinization sites in PML. J Biol Chem. 273:26675–26682. 1998. View Article : Google Scholar

Melchior F: SUMO-nonclassical ubiquitin. Annu Rev Cell Dev Biol. 16:591–626. 2000. View Article : Google Scholar

Zheng G and Yang YC: ZNF76, a novel transcriptional repressor targeting TATA-binding protein, is modulated by sumoylation. J Biol Chem. 279:42410–42421. 2004. View Article : Google Scholar

Pichler A, Knipscheer P, Oberhofer E, Van Dijk WJ, Körner R, Olsen JV, Jentsch S, Melchior F and Sixma TK: SUMO modification of the ubiquitin-conjugating enzyme E2-25K. Nat Struct Mol Biol. 12:264–269. 2005. View Article : Google Scholar

Matunis MJ, Coutavas E and Blobel G: A novel ubiquitin-like modification modulates the partitioning of the Ran-GTPase-activating protein RanGAP1 between the cytosol and the nuclear pore complex. J Cell Biol. 135:1457–1470. 1996. View Article : Google Scholar :

Mahajan R, Delphin C, Guan T, Gerace L and Melchior F: A small ubiquitin-related polypeptide involved in targeting RanGAP1 to nuclear pore complex protein RanBP2. Cell. 88:97–107. 1997. View Article : Google Scholar

Cheng TS, Chang LK, Howng SL, Lu PJ, Lee CI and Hong YR: SUMO-1 modification of centrosomal protein hNinein promotes hNinein nuclear localization. Life Sci. 78:1114–1120. 2006. View Article : Google Scholar

Desterro JM, Rodriguez MS and Hay RT: SUMO-1 modification of IkappaBalpha inhibits NF-kappaB activation. Mol Cell. 2:233–239. 1998. View Article : Google Scholar

Stadtman ER: Protein oxidation and aging. Science. 257:1220–1224. 1992. View Article : Google Scholar

Chang TC, Chou WY and Chang GG: Protein Oxidation and Turnover. J Biomed Sci. 7:357–363. 2000. View Article : Google Scholar

Lee DY, Teyssier C, Strahl BD and Stallcup MR: Role of protein methylation in regulation of transcription. Endocr Rev. 26:147–170. 2005. View Article : Google Scholar

Aletta JM, Cimato TR and Ettinger MJ: Protein methylation: A signal event in post-translational modification. Trends Biochem Sci. 23:89–91. 1998. View Article : Google Scholar

Nadolski MJ and Linder ME: Protein lipidation. FEBS J. 274:5202–5210. 2007. View Article : Google Scholar

Casey P: Protein lipidation in cell signaling. Science. 268:221–225. 1995. View Article : Google Scholar

Rikova K, Guo A, Zeng Q, Possemato A, Yu J, Haack H, Nardone J, Lee K, Reeves C, Li Y, et al: Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell. 131:1190–1203. 2007. View Article : Google Scholar

Ong SE, Mittler G and Mann M: Identifying and quantifying in vivo methylation sites by heavy methyl SILAC. Nat Methods. 1:119–126. 2004. View Article : Google Scholar

Zhang J, Sprung R, Pei J, Tan X, Kim S, Zhu H, Liu CF, Grishin NV and Zhao Y: Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli. Mol Cell Proteomics. 8:215–225. 2009. View Article : Google Scholar :

Vocadlo DJ, Hang HC, Kim EJ, Hanover JA and Bertozzi CR: A chemical approach for identifying O-GlcNAc-modified proteins in cells. Proc Natl Acad Sci USA. 100:pp. 9116–9121. 2003; View Article : Google Scholar :

Kaji H, Saito H, Yamauchi Y, Shinkawa T, Taoka M, Hirabayashi J, Kasai K, Takahashi N and Isobe T: Lectin affinity capture, isotope-coded tagging and mass spectrometry to identify N-linked glycoproteins. Nat Biotechnol. 21:667–672. 2003. View Article : Google Scholar

Derakhshan B, Wille PC and Gross SS: Unbiased identification of cysteine S-nitrosylation sites on proteins. Nat Protoc. 2:1685–1691. 2007. View Article : Google Scholar

Sprung R, Nandi A, Chen Y, Kim SC, Barma D, Falck JR and Zhao Y: Tagging-via-substrate strategy for probing O-GlcNAc modified proteins. J Proteome Res. 4:950–957. 2005. View Article : Google Scholar

Kostiuk MA, Corvi MM, Keller BO, Plummer G, Prescher JA, Hangauer MJ, Bertozzi CR, Rajaiah G, Falck JR and Berthiaume LG: Identification of palmitoylated mitochondrial proteins using a bio-orthogonal azido-palmitate analogue. FASEB J. 22:721–732. 2008. View Article : Google Scholar

Xiong L, Andrews D and Regnier F: Comparative proteomics of glycoproteins based on lectin selection and isotope coding. J Proteome Res. 2:618–625. 2003. View Article : Google Scholar

Yang Z, Harris LE, Palmer-Toy DE and Hancock WS: Multilectin affinity chromatography for characterization of multiple glycoprotein biomarker candidates in serum from breast cancer patients. Clin Chem. 52:1897–1905. 2006. View Article : Google Scholar

Madera M, Mann B, Mechref Y and Novotny MV: Efficacy of glycoprotein enrichment by microscale lectin affinity chromatography. J Sep Sci. 31:2722–2732. 2008. View Article : Google Scholar :

Andersson L and Porath J: Isolation of phosphoproteins by immobilized metal (Fe3+) affinity chromatography. Anal Biochem. 154:250–254. 1986. View Article : Google Scholar

Posewitz MC and Tempst P: Immobilized gallium(III) affinity chromatography of phosphopeptides. Anal Chem. 71:2883–2892. 1999. View Article : Google Scholar

Dubrovska A and Souchelnytskyi S: Efficient enrichment of intact phosphorylated proteins by modified immobilized metal-affinity chromatography. Proteomics. 5:4678–4683. 2005. View Article : Google Scholar

Pinkse MW, Uitto PM, Hilhorst MJ, Ooms B and Heck AJ: Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns. Anal Chem. 76:3935–3943. 2004. View Article : Google Scholar

Larsen MR, Thingholm TE, Jensen ON, Roepstorff P and Jørgensen TJD: Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Molecular Cellular Proteomics. 4:873–886. 2005. View Article : Google Scholar

Thingholm TE, Jensen ON, Robinson PJ and Larsen MR: SIMAC (sequential elution from IMAC), a phosphoproteomics strategy for the rapid separation of monophosphorylated from multiply phosphorylated peptides. Mol Cell Proteomics. 7:661–671. 2008. View Article : Google Scholar

Moshirfar M, Pierson K, Hanamaikai K, Santiago-Caban L, Muthappan V and Passi SF: Artificial tears potpourri: A literature review. Clin Ophthalmol. 8:1419–1433. 2014.

Okrojek R, Grus FH, Matheis N and Kahaly GJ: Proteomics in autoimmune thyroid eye disease. Horm Metab Res. 41:465–470. 2009. View Article : Google Scholar

Zhou L, Beuerman RW, Chew AP, Koh SK, Cafaro TA, Urrets-Zavalia EA, Urrets-Zavalia JA, Li SF and Serra HM: Quantitative Analysis of N-Linked Glycoproteins in Tear Fluid of Climatic Droplet Keratopathy by Glycopeptide Capture and iTRAQ. J Proteome Res. 8:1992–2003. 2009. View Article : Google Scholar

de Souza GA, de Godoy LM and Mann M: Identification of 491 proteins in the tear fluid proteome reveals a large number of proteases and protease inhibitors. Genome Biol. 7:R722006. View Article : Google Scholar :

Zhou L, Zhao SZ, Koh SK, Chen L, Vaz C, Tanavde V, Li XR and Beuerman RW: In-depth analysis of the human tear proteome. J Proteomics. 75:3877–3885. 2012. View Article : Google Scholar

Zhou L, Beuerman RW, Chan CM, Zhao SZ, Li XR, Yang H, Tong L, Liu S, Stern ME and Tan D: Identification of tear fluid biomarkers in dry eye syndrome using iTRAQ quantitative proteomics. J Proteome Res. 8:4889–4905. 2009. View Article : Google Scholar

Lema I, Brea D, Rodríguez-González R, Díez-Feijoo E and Sobrino T: Proteomic analysis of the tear film in patients with keratoconus. Mol Vis. 16:2055–2061. 2010.

Csősz É, Boross P, Csutak A, Berta A, Tóth F, Póliska S, Török Z and Tőzsér J: Quantitative analysis of proteins in the tear fluid of patients with diabetic retinopathy. J Proteomics Proteomics Proteomics. 75:2196–2204. 2012. View Article : Google Scholar

Wong TT, Zhou L, Li J, Tong L, Zhao SZ, Li XR, Yu SJ, Koh SK and Beuerman RW: Proteomic profiling of inflammatory signaling molecules in the tears of patients on chronic glaucoma medication. Invest Ophthalmol Vis Sci. 52:7385–7391. 2011. View Article : Google Scholar

Argueso P and Sumiyoshi M: Characterization of a carbohydrate epitope defined by the monoclonal antibody H185: Sialic acid O-acetylation on epithelial cell-surface mucins. Glycobiology. 16:1219–1228. 2006. View Article : Google Scholar :

Lei Z, Beuerman RW, Chew AP, Koh SK, Cafaro TA, Urrets-Zavalia EA, Urrets-Zavalia JA, Li SF and Serra HM: Quantitative analysis of N-linked glycoproteins in tear fluid of climatic droplet keratopathy by glycopeptide capture and iTRAQ. J Proteome Res. 8:1992–2003. 2009. View Article : Google Scholar

You J, Fitzgerald A, Cozzi PJ, Zhao Z, Graham P, Russell PJ, Walsh BJ, Willcox M, Zhong L, Wasinger V and Li Y: Post-translation modification of proteins in tears. Electrophoresis. 31:1853–1861. 2010. View Article : Google Scholar

Vieira AC, An HJ, Ozcan S, Kim JH, Lebrilla CB and Mannis MJ: Glycomic analysis of tear and saliva in ocular rosacea patients: The search for a biomarker. Ocul Surf. 10:184–192. 2012. View Article : Google Scholar

Dickinson DP and Thiesse M: A major human lacrimal gland mRNA encodes a new proline-rich protein family member. Invest Ophthalmol Vis Sci. 36:2020–2031. 1995.

Perumal N, Funke S, Pfeiffer N and Grus FH: Characterization of Lacrimal Proline-Rich Protein 4 (PRR4) in human tear proteome. Proteomics. 14:1698–1709. 2014. View Article : Google Scholar

Dyrlund TF, Poulsen ET, Scavenius C, Nikolajsen CL, Thøgersen IB, Vorum H and Enghild JJ: Human cornea proteome: Identification and quantitation of the proteins of the three main layers including epithelium, stroma and endothelium. J Proteome Res. 11:4231–4239. 2012. View Article : Google Scholar :

Narayan M, Mirza SP and Twining SS: Identification of phosphorylation sites on extracellular corneal epithelial cell maspin. Proteomics. 11:1382–1390. 2011. View Article : Google Scholar :

Kehasse A, Rich CB, Lee A, McComb ME, Costello CE and Trinkaus-Randall V: Epithelial wounds induce differential phosphorylation changes in response to purinergic and EGF receptor activation. Am J Pathol. 183:1841–1852. 2013. View Article : Google Scholar

Iwatsuka K, Iwamoto H, Kinoshita M, Inada K, Yasueda S and Kakehi K: Comparative studies of N-glycans and glycosaminoglycans present in SIRC (Statens Seruminstitut rabbit cornea) cells and corneal epithelial cells from rabbit eyes. Curr Eye Res. 39:686–694. 2014. View Article : Google Scholar

Truscott RJ: Age-related nuclear cataract-oxidation is the key. Exp Eye Res. 80:709–725. 2005. View Article : Google Scholar

Michael R and Bron AJ: The ageing lens and cataract: A model of normal and pathological ageing. Philos Trans R Soc Lond B Biol Sci. 366:1278–1292. 2011. View Article : Google Scholar :

Lampi KJ, Wilmarth PA, Murray MR and David LL: Lens β-crystallins: The role of deamidation and related modifications in aging and cataract. Prog Biophys Mol Biol. 115:21–31. 2014. View Article : Google Scholar :

Sharma KK and Santhoshkumar P: Lens aging: Effects of crystallins. Biochim Biophys Acta. 1790:1095–1108. 2009. View Article : Google Scholar :

Asomugha CO, Gupta R and Srivastava OP: Identification of crystallin modifications in the human lens cortex and nucleus using laser capture microdissection and CyDye labeling. Mol Vis. 16:476–494. 2010.

Fujii N, Sakaue H and Sasaki H: A rapid, comprehensive liquid chromatography-mass spectrometry (LC-MS)-based survey of the Asp isomers in crystallins from human cataract lenses. J Biol Chem. 287:39992–40002. 2012. View Article : Google Scholar :

Hains PG and Truscott RJ: Post-translational modifications in the nuclear region of young, aged, and cataract human lenses. J Proteome Res. 6:3935–3943. 2007. View Article : Google Scholar

Kamei A, Takeuchi N, Nagai M and Mori S: Post-translational modification of betaH-crystallin of bovine lens with aging. Biol Pharm Bull. 26:1715–1720. 2003. View Article : Google Scholar

Schaefer H, Chamrad DC, Herrmann M, Stuwe J, Becker G, Klose J, Blueggel M, Meyer HE and Marcus K: Study of posttranslational modifications in lenticular alphaA-Crystallin of mice using proteomic analysis techniques. Biochim Biophys Acta. 1764:1948–1962. 2006. View Article : Google Scholar

Truscott RJ, Mizdrak J, Friedrich MG, Hooi MY, Lyons B, Jamie JF, Davies MJ, Wilmarth PA and David LL: Is protein methylation in the human lens a result of non-enzymatic methylation by S-adenosylmethionine? Exp Eye Res. 99:48–54. 2012. View Article : Google Scholar :

Ueda Y, Duncan MK and David LL: Lens proteomics: The accumulation of crystallin modifications in the mouse lens with age. Invest Ophthalmol Vis Sci. 43:205–215. 2002.

Yanshole LV, Cherepanov IV, Snytnikova OA, Yanshole VV, Sagdeev RZ and Tsentalovich YP: Cataract-specific posttranslational modifications and changes in the composition of urea-soluble protein fraction from the rat lens. Mol Vis. 19:2196–2208. 2013.

Chiou SH, Huang CH, Lee IL, Wang YT, Liu NY, Tsay YG and Chen YJ: Identification of in vivo phosphorylation sites of lens proteins from porcine eye lenses by a gel-free phosphoproteomics approach. Mol Vis. 16:294–302. 2010.

Huang CH, Wang YT, Tsai CF, Chen YJ, Lee JS and Chiou SH: Phosphoproteomics characterization of novel phosphorylated sites of lens proteins from normal and cataractous human eye lenses. Mol Vis. 17:186–198. 2011.

Ball LE, Garland DL, Crouch RK and Schey KL: Post-translational modifications of aquaporin 0 (AQP0) in the normal human lens: Spatial and temporal occurrence. Biochemistry. 43:9856–9865. 2004. View Article : Google Scholar

Wang Z, Han J and Schey KL: Spatial differences in an integral membrane proteome detected in laser capture microdissected samples. J Proteome Res. 7:2696–2702. 2008. View Article : Google Scholar :

Schey KL, Gutierrez DB, Wang Z, Wei J and Grey AC: Novel fatty acid acylation of lens integral membrane protein aquaporin-0. Biochemistry. 49:9858–9865. 2010. View Article : Google Scholar

Kim T, Kim SJ, Kim K, Kang UB, Lee C, Park KS, Yu HG and Kim Y: Profiling of vitreous proteomes from proliferative diabetic retinopathy and nondiabetic patients. Proteomics. 7:4203–4215. 2007. View Article : Google Scholar

Bahk SC, Jang JU, Choi CU, Lee SH, Park ZY, Yang JY, Kim JD, Yang YS and Chung HT: Post-translational modification of crystallins in vitreous body from experimental autoimmune uveitis of rats. J Proteome Res. 6:3891–3898. 2007. View Article : Google Scholar

Hong SM and Yang YS: A potential role of crystallin in the vitreous bodies of rats after ischemia-reperfusion injury. Korean J Ophthalmol. 26:248–254. 2012. View Article : Google Scholar :

Griciuc A, Roux MJ, Merl J, Giangrande A, Hauck SM, Aron L and Ueffing M: Proteomic survey reveals altered energetic patterns and metabolic failure prior to retinal degeneration. J Neurosci. 34:2797–2812. 2014. View Article : Google Scholar

Keenan TD, Clark SJ, Unwin RD, Ridge LA, Day AJ and Bishop PN: Mapping the differential distribution of proteoglycan core proteins in the adult human retina, choroid, and sclera. Invest Ophthalmol Vis Sci. 53:7528–7538. 2012. View Article : Google Scholar :

Tababat-Khani P, de la Torre C, Canals F, Bennet H, Simo R, Hernandez C, Fex M, Agardh CD, Hansson O and Agardh E: Photocoagulation of human retinal pigment epithelium in vitro: Unravelling the effects on ARPE-19 by transcriptomics and proteomics. Acta ophthalmol. 93:348–354. 2015. View Article : Google Scholar

Zhang SY, Li BY, Li XL, Cheng M, Cai Q, Yu F, Wang WD, Tan M, Yan G, Hu SL and Gao HQ: Effects of phlorizin on diabetic retinopathy according to isobaric tags for relative and absolute quantification-based proteomics in db/db mice. Mol Vis. 19:812–821. 2013.

Ablonczy Z, Goletz P, Knapp DR and Crouch RK: Mass spectrometric analysis of porcine rhodopsin. Photochem Photobiol. 75:316–321. 2002. View Article : Google Scholar

Saraswathy S and Rao NA: Posttranslational modification of differentially expressed mitochondrial proteins in the retina during early experimental autoimmune uveitis. Mol Vis. 17:1814–1821. 2011.

Chen F, Ng PS, Faull KF and Lee RH: Cone photoreceptor betagamma-transducin: Posttranslational modification and interaction with phosducin. Invest Ophthalmol Vis Sci. 44:4622–4629. 2003. View Article : Google Scholar

Kassai H, Satomi Y, Fukada Y and Takao T: Top-down analysis of protein isoprenylation by electrospray ionization hybrid quadrupole time-of-flight tandem mass spectrometry; the mouse Tgamma protein. Rapid Commun Mass Spectrom. 19:269–274. 2005. View Article : Google Scholar

Salom D, Wang B, Dong Z, Sun W, Padayatti P, Jordan S, Salon JA and Palczewski K: Post-translational modifications of the serotonin type 4 receptor heterologously expressed in mouse rod cells. Biochemistry. 51:214–224. 2011. View Article : Google Scholar :

Tsybovsky Y, Wang B, Quazi F, Molday RS and Palczewski K: Posttranslational modifications of the photoreceptor-specific ABC transporter ABCA4. Biochemistry. 50:6855–6866. 2011. View Article : Google Scholar :

Zhao X, Sidoli S, Wang L, Wang W, Guo L, Jensen ON and Zheng L: Comparative proteomic analysis of histone post-translational modifications upon ischemia/reperfusion-induced retinal injury. J Proteome Res. 13:2175–2186. 2014. View Article : Google Scholar

Morgan IG, Ohno-Matsui K and Saw SM: Myopia. Lancet. 379:1739–1748. 2012. View Article : Google Scholar

Pan CW, Ramamurthy D and Saw SM: Worldwide prevalence and risk factors for myopia. Ophthalmic Physiol Opt. 32:3–16. 2012. View Article : Google Scholar

Lin LL, Shih YF, Hsiao CK and Chen CJ: Prevalence of myopia in Taiwanese schoolchildren: 1983 to 2000. Ann Acad Med Singapore. 33:27–33. 2004.

Sun J, Zhou J, Zhao P, Lian J, Zhu H, Zhou Y, Sun Y, Wang Y, Zhao L, Wei Y, et al: High prevalence of myopia and high myopia in 5060 Chinese university students in Shanghai. Invest Ophthalmol Vis Sci. 53:7504–7509. 2012. View Article : Google Scholar

Wallman J, Gottlieb MD, Rajaram V and Fugate-Wentzek LA: Local retinal regions control local eye growth and myopia. Science. 237:73–77. 1987. View Article : Google Scholar

Hodos W and Kuenzel WJ: Retinal-image degradation produces ocular enlargement in chicks. Invest Ophthalmol Vis Sci. 25:652–659. 1984.

Lam TC, Li KK, Lo SC, Guggenheim JA and To CH: Application of fluorescence difference gel electrophoresis technology in searching for protein biomarkers in chick myopia. J Proteome Res. 6:4135–4149. 2007. View Article : Google Scholar

Jostrup R, Shen W, Burrows JT, Sivak JG, McConkey BJ and Singer TD: Identification of myopia-related marker proteins in tilapia retinal, RPE, and choroidal tissue following induced form deprivation. Curr Eye Res. 34:966–975. 2009. View Article : Google Scholar

Barathi VA, Chaurasia SS, Poidinger M, Koh SK, Tian D, Ho C, Iuvone PM, Beuerman RW and Zhou L: Involvement of GABA transporters in atropine-treated myopic retina as revealed by iTRAQ quantitative proteomics. J Proteome Res. 13:4647–4658. 2014. View Article : Google Scholar :

Chen B, Yu F, Li KK, Chun RK, Lam TC and To CH: Qualitative and quantitative phosphoproteomics analysis of chick retina of Tio2-enriched strategy. Presented at the 13th Annual World Congress of the Human Proteome Organization. 2014; http://hdl.handle.net/10397/59149

Lee H, Chung H, Lee SH and Jahng WJ: Light-induced phosphorylation of crystallins in the retinal pigment epithelium. Int J Biol Macromol. 48:194–201. 2011. View Article : Google Scholar

Kanan Y, Siefert JC, Kinter M and Al-Ubaidi MR: Complement factor H, vitronectin, and opticin are tyrosine-sulfated proteins of the retinal pigment epithelium. PLoS One. 9:e1054092014. View Article : Google Scholar :

Lee H, Chung H, Arnouk H, Lamoke F, Hunt RC, Hrushesky WJ, Wood PA, Lee SH and Jahng WJ: Cleavage of the retinal pigment epithelium-specific protein RPE65 under oxidative stress. Int J Biol Macromol. 47:104–108. 2010. View Article : Google Scholar :

Yuan Q, Kaylor JJ, Miu A, Bassilian S, Whitelegge JP and Travis GH: Rpe65 isomerase associates with membranes through an electrostatic interaction with acidic phospholipid headgroups. J Biol Chem. 285:988–999. 2010. View Article : Google Scholar

DiMauro MA, Nandi SK, Raghavan CT, Kar RK, Wang B, Bhunia A, Nagaraj RH and Biswas A: Acetylation of Gly1 and Lys2 promotes aggregation of human γD-crystallin. Biochemistry. 53:7269–7282. 2014. View Article : Google Scholar :