Proteomics quantification of protein nitration

Reviews in Analytical Chemistry

Volumn 32, Issue 3, 2013, Pages 173-187

  Evans, Adam R ^a   Robinson, Renã A S ^a  

^a UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

3 Nitrotyrosine; Mass spectrometry; Nitration; Proteomics; Redox proteomics

Indexed keywords

EID: 84888227184     PISSN: 07930135     EISSN: None     Source Type: Journal    
DOI: 10.1515/revac-2012-0041     Document Type: Review

References (140)

1. Abe, K.; Pan, L. H.; Watanabe, M.; Kato, T.; Itoyama, Y. Induction of nitrotyrosine-like immunoreactivity in the lower motor neuron of amyotrophic lateral sclerosis. Neurosci. Lett. 1995, 199, 152-154.
2. Abello, N.; Kerstjens, H. A.; Postma, D. S.; Bischoff, R. Protein tyrosine nitration: selectivity, physicochemical and biological consequences, denitration, and proteomics methods for the identification of tyrosine-nitrated proteins. J. Proteome Res. 2009, 8, 3222-3238.
3. Abello, N.; Barroso, B.; Kerstjens, H. A.; Postma, D. S.; Bischoff, R. Chemical labeling and enrichment of nitrotyrosine-containing peptides. Talanta 2010, 80, 1503-1512.
4. Adibhatla, R. M.; Hatcher, J. F. Lipid oxidation and peroxidation in CNS health and disease: from molecular mechanisms to therapeutic opportunities. Antioxid. Redox Signal. 2010, 12, 125-169.
5. Aebersold, R.; Mann, M. Mass spectrometry-based proteomics. Nature 2003, 422, 198-207.
6. Aksenova, M.; Butterfield, D. A.; Zhang, S. X.; Underwood, M.; Geddes, J. W. Increased protein oxidation and decreased creatine kinase BB expression and activity after spinal cord contusion injury. J. Neurotrauma 2002, 19, 491-502.
7. Alvarez, B.; Radi, R. Peroxynitrite reactivity with amino acids and proteins. Amino Acids 2003, 25, 295-311.
8. Amoresano, A.; Chiappetta, G.; Pucci, P.; D ' Ischia, M.; Marino, G. Bidimensional tandem mass spectrometry for selective identification of nitration sites in proteins. Anal. Chem. 2007, 79, 2109-2117.
9. Armirotti, A.; Damonte, G. Achievements and perspectives of top-down proteomics. Proteomics 2010, 10, 3566-3576.
10. Azad, N.; Rojanasakul, Y.; Vallyathan, V. Inflammation and lung cancer: roles of reactive oxygen/nitrogen species. J. Toxicol. Environ. Health B Crit. Rev. 2008, 11, 1-15.
11. Bantscheff, M.; Schirle, M.; Sweetman, G.; Rick, J.; Kuster, B. Quantitative mass spectrometry in proteomics: a critical review. Anal. Bioanal. Chem. 2007, 389, 1017-1031.
12. Bantscheff, M.; Lemeer, S.; Savitski, M. M.; Kuster, B. Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present. Anal. Bioanal. Chem. 2012, 404, 939-965.
13. Bayden, A. S.; Yakovlev, V. A.; Graves, P. R.; Mikkelsen, R. B.; Kellogg, G. E. Factors influencing protein tyrosine nitration-structure-based predictive models. Free Radic. Biol. Med. 2011, 50, 749-762.
14. Bayir, H.; Kagan, V. E.; Clark, R. S.; Janesko-Feldman, K.; Rafikov, R.; Huang, Z.; Zhang, X.; Vagni, V.; Billiar, T. R.; Kochanek, P. M. Neuronal NOS-mediated nitration and inactivation of manganese superoxide dismutase in brain after experimental and human brain injury. J. Neurochem. 2007, 101, 168-181.
15. Bigelow, D. J.; Qian, W. J. Quantitative proteome mapping of nitro tyrosines. Methods Enzymol. 2008, 440, 191-205.
16. Birnboim, H. C.; Lemay, A. M.; Lam, D. K.; Goldstein, R.; Webb, J. R. Cutting edge: MHC class II-restricted peptides containing the inflammation-Associated marker 3-nitrotyrosine evade central tolerance and elicit a robust cell-mediated immune response. J. Immunol. 2003, 171, 528-532.
17. Blackstock, W. P.; Weir, M. P. Proteomics: quantitative and physical mapping of cellular proteins. Trends Biotechnol. 1999, 17, 121-127.
18. Boersema, P. J.; Aye, T. T.; van Veen, T. A.; Heck, A. J.; Mohammed, S. Triplex protein quantification based on stable isotope labeling by peptide dimethylation applied to cell and tissue lysates. Proteomics 2008, 8, 4624-4632.
19. Bronte, V.; Kasic, T.; Gri, G.; Gallana, K.; Borsellino, G.; Marigo, I.; Battistini, L.; Iafrate, M.; Prayer-Galetti, T.; Pagano, F.; Viola, A. Boosting antitumor responses of T lymphocytes infiltrating human prostate cancers. J. Exp. Med. 2005, 201, 1257-1268.
20. Brown, J. R.; Hartley, B. S. Location of disulphide bridges by diagonal paper electrophoresis. The disulphide bridges of bovine chymotrypsinogen A. Biochem. J. 1966, 101, 214-228.
21. Browne, S. E.; Ferrante, R. J.; Beal, M. F. Oxidative stress in Huntington ' s disease. Brain Pathol. 1999, 9, 147-163.
22. Bubber, P.; Haroutunian, V.; Fisch, G.; Blass, J. P.; Gibson, G. E. Mitochondrial abnormalities in Alzheimer brain: mechanistic implications. Ann. Neurol. 2005, 57, 695-703.
23. Butterfield, D. A.; Dalle-Donne, I. Redox proteomics. Antioxid. Redox Signal. 2012, 17, 1487-1489.
24. Butterfield, D. A.; Reed, T.; Newman, S. F.; Sultana, R. Roles of amyloid beta-peptide-Associated oxidative stress and brain protein modifications in the pathogenesis of Alzheimer ' s disease and mild cognitive impairment. Free Radic. Biol. Med. 2007, 43, 658-677.
25. Butterfield, D. A.; Reed, T.; Sultana, R. Roles of 3-nitrotyrosine- and 4-hydroxynonenal-modified brain proteins in the progression and pathogenesis of Alzheimer ' s disease. Free Radic. Res. 2011, 45, 59-72.
26. Butterfield, D. A.; Perluigi, M.; Reed, T.; Muharib, T.; Hughes, C. P.; Robinson, R. A.; Sultana, R. Redox proteomics in selected neurodegenerative disorders: from its infancy to future applications. Antioxid. Redox Signal. 2012, 17, 1610-1655.
27. Butterfield, D. A.; Gu, L.; Domenico, F. D.; Robinson, R. A. S. The role of mass spectrometry in redox proteomics. Mass Spectrom. Rev. (in press
28. Casagrande, S.; Bonetto, V.; Fratelli, M.; Gianazza, E.; Eberini, I.; Massignan, T.; Salmona, M.; Chang, G.; Holmgren, A.; Ghezzi, P. Glutathionylation of human thioredoxin: a possible crosstalk between the glutathione and thioredoxin systems. Proc. Natl. Acad. Sci. USA 2002, 99, 9745- 9749.
29. Castegna, A.; Thongboonkerd, V.; Klein, J. B.; Lynn, B.; Markesbery, W. R.; Butterfield, D. A. Proteomic identification of nitrated proteins in Alzheimer ' s disease brain. J. Neurochem. 2003, 85, 1394-1401.
30. Castegna, A.; Lauderback, C. M.; Mohmmad-Abdul, H.; Butterfield, D. A. Modulation of phospholipid asymmetry in synaptosomal membranes by the lipid peroxidation products, 4-hydroxynonenal and acrolein: implications for Alzheimer ' s disease. Brain Res. 2004, 1004, 193-197.
31. Ceriello, A.; Mercuri, F.; Quagliaro, L.; Assaloni, R.; Motz, E.; Tonutti, L.; Taboga, C. Detection of nitrotyrosine in the diabetic plasma: evidence of oxidative stress. Diabetologia 2001, 44, 834-838.
32. Chen, H. J.; Chen, Y. C. Reactive nitrogen oxide species-induced post-translational modifications in human hemoglobin and the association with cigarette smoking. Anal. Chem. 2012, 84, 7881-7890.
33. Chen, H. J.; Chiu, W. L. Simultaneous detection and quantification of 3-nitrotyrosine and 3-bromotyrosine in human urine bystable isotope dilution liquid chromatography tandem mass spectrometry. Toxicol. Lett. 2008, 181, 31-39.
34. Chiappetta, G.; Corbo, C.; Palmese, A.; Galli, F.; Piroddi, M.; Marino, G.; Amoresano, A. Quantitative identification of protein nitration sites. Proteomics 2009, 9, 1524-1537.
35. Christoforou, A. L.; Lilley, K. S. Isobaric tagging approaches in quantitative proteomics: the ups and downs. Anal. Bioanal. Chem. 2012, 404, 1029-1037.
36. Coleman, P. D.; Flood, D. G. Neuron numbers and dendritic extent in normal aging and Alzheimer ' s disease. Neurobiol. Aging 1987, 8, 521-545.
37. Cookson, M. R.; Shaw, P. J. Oxidative stress and motor neurone disease. Brain Pathol. 1999, 9, 165-186.
38. Dalle-Donne, I.; Scaloni, A.; Butterfield, D. A. Redox Proteomics: From Protein Modifications to Cellular Dysfunction and Diseases; John Wiley and Sons: Hoboken, NJ, 2006.
39. Danielson, S. R.; Held, J. M.; Schilling, B.; Oo, M.; Gibson, B. W.; Andersen, J. K. Preferentially increased nitration of alphasynuclein at tyrosine-39 in a cellular oxidative model of Parkinson ' s disease. Anal. Chem. 2009, 81, 7823-7828.
40. Dekker, F.; Abello, N.; Wisastra, R.; Bischoff, R. Enrichment and detection of tyrosine-nitrated proteins. Curr. Protocols Protein Sci. 2012, 69, 14.13.1-14.13.19.
41. Dremina, E. S.; Li, X.; Galeva, N. A.; Sharov, V. S.; Stobaugh, J. F.; Schoneich, C. A methodology for simultaneous fluorogenic derivatization and boronate affinity enrichment of 3-nitrotyrosine-containing peptides. Anal. Biochem. 2011, 418, 184-196.
42. Duncan, M. W. A review of approaches to the analysis of 3-nitrotyrosine. Amino Acids 2003, 25, 351-361.
43. Feeney, M. B.; Schoneich, C. Tyrosine modifications in aging. Antioxid. Redox Signal. 2012, 17, 1571-1579.
44. Feeney, M. B.; Schoneich, C. Proteomic approaches to analyze protein tyrosine nitration. Antioxid. Redox Signal. 2013, 1-10.
45. Ferrante, R. J.; Shinobu, L. A.; Schulz, J. B.; Matthews, R. T.; Thomas, C. E.; Kowall, N. W.; Gurney, M. E.; Beal, M. F. Increased 3-nitrotyrosine and oxidative damage in mice with a human copper/zinc superoxide dismutase mutation. Ann. Neurol. 1997, 42, 326-334.
46. Franco Mdo, C.; Fortes, Z. B.; Akamine, E. H.; Kawamoto, E. M.; Scavone, C.; de Britto, L. R.; Muscara, M. N.; Teixeira, S. A.; Tostes, R. C.; Carvalho, M. H.; Nigro, D. Tetrahydrobiopterin improves endothelial dysfunction and vascular oxidative stress in microvessels of intrauterine undernourished rats. J. Physiol. 2004, 558 (Pt 1), 239-248.
47. Frost, M. T.; Halliwell, B.; Moore, K. P. Analysis of free and protein-bound nitrotyrosine in human plasma by a gas chromatography/mass spectrometry method that avoids nitration artifacts. Biochem. J. 2000, 345 (Pt 3), 453-458.
48. Ghesquiere, B.; Colaert, N.; Helsens, K.; Dejager, L.; Vanhaute, C.; Verleysen, K.; Kas, K.; Timmerman, E.; Goethals, M.; Libert, C.; Vandekerckhove, J.; Gevaert, K. In vitro and in vivo protein-bound tyrosine nitration characterized by diagonal chromatography. Mol. Cell. Proteomics 2009, 8, 2642-2652.
49. Good, P. F.; Hsu, A.; Werner, P.; Perl, D. P.; Olanow, C. W. Protein nitration in Parkinson ' s disease. J. Neuropathol. Exp. Neurol. 1998, 57, 338-342.
50. Guo, W.; Adachi, T.; Matsui, R.; Xu, S.; Jiang, B.; Zou, M. H.; Kirber, M.; Lieberthal, W.; Cohen, R. A. Quantitative assessment of tyrosine nitration of manganese superoxide dismutase in angiotensin II-infused rat kidney. Am. J. Physiol. Heart Circ. Physiol. 2003, 285, H1396- H1403.
51. Halejcia-Delophont, P.; Hoshiai, K.; Fukuyama, N.; Nakazawa, H. No evidence of NO-induced damage in potential donor organs after brain death. J. Heart Lung Transplant. 2001, 20, 71-79.
52. Han, X.; Aslanian, A.; Yates, J. R. 3rd. Mass spectrometry for proteomics. Curr. Opin. Chem. Biol. 2008, 12, 483-490.
53. Helman, M.; Givol, D. Isolation of nitrotyrosine-containing peptides by using an insoluble-Antibody column. Biochem. J. 1971, 125, 971-974.
54. Horiguchi, T.; Uryu, K.; Giasson, B. I.; Ischiropoulos, H.; LightFoot, R.; Bellmann, C.; Richter-Landsberg, C.; Lee, V. M.; Trojanowski, J. Q. Nitration of tau protein is linked to neurodegeneration in tauopathies. Am. J. Pathol. 2003, 163, 1021-1031.
55. Jin, H.; Webb-Robertson, B. J.; Peterson, E. S.; Tan, R.; Bigelow, D. J.; Scholand, M. B.; Hoidal, J. R.; Pounds, J. G.; Zangar, R. C. Smoking, COPD, and 3-nitrotyrosine levels of plasma proteins. Environ. Health Perspect. 2011, 119, 1314-1320.
56. Jovanovic, S. V.; Clements, D.; MacLeod, K. Biomarkers of oxidative stress are significantly elevated in Down syndrome. Free Radic. Biol. Med. 1998, 25, 1044-1048.
57. Kaur, H.; Halliwell, B. Evidence for nitric oxide-mediated oxidative damage in chronic inflammation. Nitrotyrosine in serum and synovial fluid from rheumatoid patients. FEBS Lett. 1994, 350, 9-12.
58. Kaur, H.; Lyras, L.; Jenner, P.; Halliwell, B. Artefacts in HPLC detection of 3-nitrotyrosine in human brain tissue. J. Neurochem. 1998, 70, 2220-2223.
59. Khan, J.; Brennand, D. M.; Bradley, N.; Gao, B.; Bruckdorfer, R.; Jacobs, M. 3-Nitrotyrosine in the proteins of human plasma determined by an ELISA method. Biochem. J. 1998, 330 (Pt 2), 795-801.
60. Kim, J. K.; Lee, J. R.; Kang, J. W.; Lee, S. J.; Shin, G. C.; Yeo, W. S.; Kim, K. H.; Park, H. S.; Kim, K. P. Selective enrichment and mass spectrometric identification of nitrated peptides using fluorinated carbon tags. Anal. Chem. 2011, 83, 157-163.
61. Kissner, R.; Nauser, T.; Bugnon, P.; Lye, P. G.; Koppenol, W. H. Formation and properties of peroxynitrite as studied by laser flash photolysis, high-pressure stopped-flow technique, and pulse radiolysis. Chem. Res. Toxicol. 1997, 10, 1285-1292.
62. Kong, S. K.; Yim, M. B.; Stadtman, E. R.; Chock, P. B. Peroxynitrite disables the tyrosine phosphorylation regulatory mechanism: lymphocyte-specific tyrosine kinase fails to phosphorylate nitrated cdc2(6-20)NH2 peptide. Proc. Natl. Acad. Sci. USA 1996, 93, 3377-3382.
63. Lee, J. R.; Kim, J. K.; Lee, S. J.; Kim, K. P. Role of protein tyrosine nitration in neurodegenerative diseases and atherosclerosis. Arch. Pharm. Res. 2009a, 32, 1109-1118.
64. Lee, J. R.; Lee, S. J.; Kim, T. W.; Kim, J. K.; Park, H. S.; Kim, D. E.; Kim, K. P.; Yeo, W. S. Chemical approach for specific enrichment and mass analysis of nitrated peptides. Anal. Chem. 2009b, 81, 6620-6626.
65. Leeuwenburgh, C.; Hardy, M. M.; Hazen, S. L.; Wagner, P.; Oh-ishi,S.; Steinbrecher, U. P.; Heinecke, J. W. Reactive nitrogen intermediates promote low density lipoprotein oxidation in human atherosclerotic intima. J. Biol. Chem. 1997, 272, 1433-1436.
66. Li, B.; Held, J. M.; Schilling, B.; Danielson, S. R.; Gibson, B. W. Confident identification of 3-nitrotyrosine modificationsin mass spectral data across multiple mass spectrometry platforms. J. Proteomics 2011, 74, 2510-2521.
67. Liu, H.; Sadygov, R. G.; Yates, J. R. 3rd. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 2004, 76, 4193-4201.
68. Liu, F.; Xiong, J.; Huang, G. Y.; Wang, W. [Study on the underlying mechanism of acupuncture in regulating neuroendocrine activity in dysmenorrhea rats]. Zhen Ci Yan Jiu 2009, 34, 3-8.
69. Marshall, A.; Lutfeaili, R.; Raval, A.; Chakravarti, D. N.; Chakravarti, B. Differential hepatic protein tyrosine nitration of mouse due to aging-effect on mitochondrial energy metabolism, quality control machinery of the endoplasmic reticulum and metabolism of drugs. Biochem. Biophys. Res. Commun. 2013, 430, 231-235.
70. Mazzola, J. L.; Sirover, M. A. Reduction of glyceraldehyde- 3-phosphate dehydrogenase activity in Alzheimer ' s disease and in Huntington ' s disease fibroblasts. J. Neurochem. 2001, 76, 442-429.
71. Monteiro, H. P.; Arai, R. J.; Travassos, L. R. Protein tyrosine phosphorylation and protein tyrosine nitration in redox signaling. Antioxid. Redox Signal. 2008, 10, 843-889.
72. Morrissey, B. M.; Schilling, K.; Weil, J. V.; Silkoff, P. E.; Rodman, D. M. Nitric oxide and protein nitration in the cystic fibrosis airway. Arch. Biochem. Biophys. 2002, 406, 33- 39.
73. Nemirovskiy, O. V.; Radabaugh, M. R.; Aggarwal, P.; F unckes- Shippy, C. L.; Mnich, S. J.; Meyer, D. M.; Sunyer, T.; Rodney Mathews, W.; Misko, T. P. Plasma 3-nitrotyrosine is a biomarker in animal models of arthritis: pharmacological dissection of iNOS ' role in disease. Nitric Oxide 2009, 20, 150-156.
74. Nikov, G.; Bhat, V.; Wishnok, J. S.; Tannenbaum, S. R. Analysis of nitrated proteins by nitrotyrosine-specific affinity probes and mass spectrometry. Anal. Biochem. 2003, 320, 214-222.
75. Nuriel, T.; Deeb, R. S.; Hajjar, D. P.; Gross, S. S. Protein 3-nitrotyrosine in complex biological samples: quantification by high-pressure liquid chromatography/electrochemical detection and emergence of proteomic approaches for unbiased identification of modification sites. Methods Enzymol. 2008, 441, 1- 17.
76. Ohshima, H.; Friesen, M.; Brouet, I.; Bartsch, H. Nitrotyrosine as a new marker for endogenous nitrosation and nitration of proteins. Food Chem. Toxicol. 1990, 28, 647-652.
77. Oldreive, C.; Bradley, N.; Bruckdorfer, R.; Rice-Evans, C. Lack of influence of dietary nitrate/nitrite on plasma nitrotyrosine levels measured using a competitive inhibition of binding ELISA assay. Free Radic. Res. 2001, 35, 377-386.
78. Pacher, P.; Beckman, J. S.; Liaudet, L. Nitric oxide and peroxynitrite in health and disease. Physiol. Rev. 2007, 87, 315-424.
79. Pan, S.; Aebersold, R.; Chen, R.; Rush, J.; Goodlett, D. R.; McIntosh, M. W.; Zhang, J.; Brentnall, T. A. Mass spectrometry based targeted protein quantification: methods and applications. J. Proteome Res. 2009, 8, 787-797.
80. Pannala, A. S.; Mani, A. R.; Spencer, J. P.; Skinner, V.; Bruckdorfer, K. R.; Moore, K. P.; Rice-Evans, C. A. The effect of dietary nitrate on salivary, plasma, and urinary nitrate metabolism in humans. Free Radic. Biol. Med. 2003, 34, 576- 584.
81. Patton, W. F. Detection technologies in proteome analysis. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2002, 771, 3-31.
82. Pavlovic, R. S. E.; Chiesa, L. M.; Biandi, P. A. New procedure for the determination of 3-nitrotyrosine in plasma by GC-ECD. Chromatographia 2009, 70, 637-641.
83. Peluffo, G.; Radi, R. Biochemistry of protein tyrosine nitration in cardiovascular pathology. Cardiovasc. Res. 2007, 75, 291-302.
84. Petruzzelli, S.; Puntoni, R.; Mimotti, P.; Pulera, N.; Baliva, F.; Fornai, E.; Giuntini, C. Plasma 3-nitrotyrosine in cigarette smokers. Am. J. Respir. Crit. Care Med. 1997, 156, 1902-1907.
85. Qu, L. N.; Yang, T. B.; Yuan, Y. H.; Zhong, P.; Yang, B.; Zhao, H. A novel competitive ELISA for both free and protein-bound nitrotyrosine. Hybrid. Hybridomics 2003, 22, 401-406.
86. Radi, R. Nitric oxide, oxidants, and protein tyrosine nitration. Proc. Natl. Acad. Sci. USA 2004, 101, 4003-4008.
87. Radi, R. Protein tyrosine nitration: biochemical mechanisms and structural basis of functional effects. Acc. Chem. Res. 2013, 46, 550-559.
88. Reed, T. T.; Pierce, W. M. Jr.; Turner, D. M.; Markesbery, W. R.; Butterfield, D. A. Proteomic identification of nitrated brain proteins in early Alzheimer ' s disease inferior parietal lobule. J. Cell. Mol. Med. 2009, 13, 2019-2029.
89. Reynolds, M. R.; Berry, R. W.; Binder, L. I. Nitration in neurodegeneration: deciphering the " Hows" " nYs". Biochemistry 2007, 46, 7325-7336.
90. Riggs, L.; Seeley, E. H.; Regnier, F. E. Quantification of phosphoproteins with global internal standard technology. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2005, 817, 89-96.
91. Righetti, P. G.; Antonioli, P.; Simo, C.; Citterio, A. Gel-based proteomics. In: Plant Proteomics: Technologies, Strategies, and Applications. Agrawal, G. K.; Rakwal, R., Eds. John Wiley and Sons Inc.: Hoboken, NJ, USA, 2008, pp. 9-31.
92. Robinson, R. A.; Evans, A. R. Enhanced sample multiplexing for nitrotyrosine-modified proteins using combined precursor isotopic labeling and isobaric tagging. Anal. Chem. 2012, 84, 4677-4686.
93. Ross, P. L.; Huang, Y. N.; Marchese, J. N.; Williamson, B.; Parker, K.; Hattan, S.; Khainovski, N.; Pillai, S.; Dey, S.; Daniels, S.; Purkayastha, S.; Juhasz, P.; Martin, S.; Bartlet-Jones, M.; He, F.; Jacobson, A.; Pappin, D. J. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 2004, 3, 1154-1169.
94. Rubbo, H.; Radi, R. Protein and lipid nitration: role in redox signaling and injury. Biochim. Biophys. Acta 2008, 1780, 1318-1324.
95. Ruse, C. I.; Willard, B.; Jin, J. P.; Haas, T.; Kinter, M.; Bond, M. Quantitative dynamics of site-specific protein phosphorylation determined using liquid chromatography electrospray ionization mass spectrometry. Anal. Chem. 2002, 74, 1658- 1664.
96. Ryberg, H.; Caidahl, K. Chromatographic and mass spectrometric methods for quantitative determination of 3-nitrotyrosine in biological samples and their application to human samples. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2007, 851, 160-171.
97. Sandhu, J. K.; Robertson, S.; Birnboim, H. C.; Goldstein, R. Distribution of protein nitrotyrosine in synovial tissues of patients with rheumatoid arthritis and osteoarthritis. J. Rheumatol. 2003, 30, 1173-1181.
98. Sharov, V. S.; Dremina, E. S.; Pennington, J.; Killmer, J.; Asmus, C.; Thorson, M.; Hong, S. J.; Li, X.; Stobaugh, J. F.; Schoneich, C. Selective fluorogenic derivatization of 3-nitrotyrosine and 3,4-dihydroxyphenylalanine in peptides: a method designed for quantitative proteomic analysis. Methods Enzymol. 2008, 441, 19-32.
99. Sharov, V. S.; Dremina, E. S.; Galeva, N. A.; Gerstenecker, G. S.; Li, X.; Dobrowsky, R. T.; Stobaugh, J. F.; Sch ö neich, C. Fluorogenic tagging of peptide and protein 3-nitrotyrosine with 4-(aminomethyl)-benzenesulfonic acid for quantitative analysis of protein tyrosine nitration. Chromatographia 2010, 71, 37-53.
100. Sly, W. S.; Hu, P. Y. Human carbonic anhydrases and carbonic anhydrase deficiencies. Ann. Review Biochem. 1995, 64, 375-401.
101. Smith, R. D.; Anderson, G. A.; Lipton, M. S.; Pasa-Tolic, L.; Shen, Y.; Conrads, T. P.; Veenstra, T. D.; Udseth, H. R. An accurate mass tag strategy for quantitative and high-throughput proteome measurements. Proteomics 2002, 2, 513-523.
102. Soderling, A. S.; Hultman, L.; Delbro, D.; Hojrup, P.; Caidahl, K. Reduction of the nitro group during sample preparation may cause underestimation of the nitration level in 3-nitrotyrosine immunoblotting. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2007, 851, 277-286.
103. Sokolovsky, M.; Riordan, J. F.; Vallee, B. L. Conversion of 3-nitrotyrosine to 3-Aminotyrosine in peptides and proteins. Biochem. Biophys. Res. Commun. 1967, 27, 20-25.
104. Souza, J. M.; Peluffo, G.; Radi, R. Protein tyrosine nitration- functional alteration or just a biomarker ? Free Radic. Biol. Med. 2008, 45, 357-366.
105. Sowell, R. A.; Butterfield, D. A. Insights from proteomics into mild cognitive impairment, likely the earliest stage of Alzheimer ' s disease. In Cognitive Impairment: Causes, Diagnosis and Treatment. Landow, M. L., Ed. Nova Science Publishers Inc: Hauppauge, NY, 2010.
106. Spickett, C. M.; Pitt, A. R. Protein oxidation: role in signalling and detection by mass spectrometry. Amino Acids 2012, 42, 5-21.
107. Squier, T. C. Oxidative stress and protein aggregation during biological aging. Exp. Gerontol. 2001, 36, 1539-1550.
108. Sucu, N.; Unlu, A.; Tamer, L.; Aytacoglu, B.; Ercan, B.; Dikmengil, M.; Atik, U. 3-Nitrotyrosine in atherosclerotic blood vessels. Clin. Chem. Lab. Med 2003, 41, 23-25.
109. Sugiura, H.; Ichinose, M.; Tomaki, M.; Ogawa, H.; Koarai, A.; Kitamuro, T.; Komaki, Y.; Akita, T.; Nishino, H.; Okamoto, S.; Akaike, T.; Hattori, T. Quantitative assessment of proteinbound tyrosine nitration in airway secretions from patients with inflammatory airway disease. Free Radic. Res. 2004, 38, 49-57.
110. Sultana, R.; Reed, T.; Perluigi, M.; Coccia, R.; Pierce, W. M.; Butterfield, D. A. Proteomic identification of nitrated brain proteins in amnestic mild cognitive impairment: a regional study. J. Cell. Mol. Med. 2007, 11, 839-851.
111. Sultana, R.; Sowell, R. A.; Butterfield, D. A. Nitrated proteins in the progression of Alzheimer ' s disease: a proteomics comparison of mild cognitive impairment and Alzheimer ' s disease brain. In Oxidative Neural Injury. Veasey, S. C., Ed. Humana Press Inc.: New York, NY, 2009, pp. 137-157.
112. Surmeli, N. B.; Litterman, N. K.; Miller, A. F.; Groves, J. T. Peroxynitrite mediates active site tyrosine nitration in manganese superoxide dismutase. Evidence of a role for the carbonate radical anion. J. Am. Chem. Soc. 2010, 132, 17174-17185.
113. Thangaswamy, S.; Bridenbaugh, E. A.; Gashev, A. A. Evidence of increased oxidative stress in aged mesenteric lymphatic vessels. Lymphat. Res. Biol. 2012, 10, 53-62.
114. Thompson, A.; Schafer, J.; Kuhn, K.; Kienle, S.; Schwarz, J.; Schmidt, G.; Neumann, T.; Johnstone, R.; Mohammed, A. K.; Hamon, C. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem. 2003, 75, 1895-1904.
115. Ting, L.; Rad, R.; Gygi, S. P.; Haas, W. MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat. Methods 2011, 8, 937-940.
116. Tsikas, D. Analytical methods for 3-nitrotyrosine quantification in biological samples: the unique role of tandem mass spectrometry. Amino Acids 2012, 42, 45-63.
117. Tsikas, D.; Caidahl, K. Recent methodological advances in the mass spectrometric analysis of free and protein-Associated 3-nitrotyrosine in human plasma. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2005, 814, 1-9.
118. Tsumoto, H.; Taguchi, R.; Kohda, K. Efficient identification and quantification of peptides containing nitrotyrosine by matrix-Assisted laser desorption/ionization time-of-flight mass spectrometry after derivatization. Chem. Pharm. Bull. 2010, 58, 488- 494.
119. Turko, I. V.; Murad, F. Protein nitration in cardiovascular diseases. Pharmacol. Rev. 2002, 54, 619-634.
120. Turko, I. V.; Li, L.; Aulak, K. S.; Stuehr, D. J.; Chang, J. Y.; Murad, F. Protein tyrosine nitration in the mitochondria from diabetic mouse heart. Implications to dysfunctional mitochondria in diabetes. J. Biol. Chem. 2003, 278, 33972-33977.
121. Uchida, K.; Stadtman, E. R. Covalent attachment of 4-hydroxynonenal to glyceraldehyde-3-phosphate dehydrogenase. A possible involvement of intra- and intermolecular cross-linking reaction. J. Biol. Chem. 1993, 268, 6388-6393.
122. Ungvari, Z.; Gupte, S. A.; Recchia, F. A.; Batkai, S.; Pacher, P. Role of oxidative-nitrosative stress and downstream pathways in various forms of cardiomyopathy and heart failure. Curr. Vasc. Pharmacol. 2005, 3, 221-229.
123. Upmacis, R. K. Atherosclerosis: a link between lipid intake and protein tyrosine nitration. Lipid Insights 2008, 2, 75-88.
124. Van den Bergh, G.; Arckens, L. Fluorescent two-dimensional difference gel electrophoresis unveils the potential of gel-based proteomics. Curr. Opin. Biotechnol. 2004, 15, 38-43.
125. van Haandel, L.; Killmer, J.; Li, X.; Schoneich, C.; Stobaugh, J. F. Phenylisothiocyanate as a multiple chemical dimension reagent for the relative quantitation of protein nitrotyrosine. Chromatographia 2008, 68, 507-516.
126. Viera, L.; Ye, Y. Z.; Estevez, A. G.; Beckman, J. S. Immunohistochemical methods to detect nitrotyrosine. Methods Enzymol. 1999, 301, 373-381.
127. Wasinger, V. C.; Zeng, M.; Yau, Y. Current status and advances in quantitative proteomic mass spectrometry. Int. J. Proteomics 2013, 2013, 180605.
128. Wayenberg, J. L.; Ransy, V.; Vermeylen, D.; Damis, E.; Bottari, S. P. Nitrated plasma albumin as a marker of nitrative stress and neonatal encephalopathy in perinatal asphyxia. Free Radic. Biol. Med. 2009, 47, 975-982.
129. Weber, D.; Kneschke, N.; Grimm, S.; Bergheim, I.; Breusing, N.; Grune, T. Rapid and sensitive determination of proteinnitrotyrosine by ELISA: application to human plasma. Free Radic. Res. 2012, 46, 276-285.
130. Wenger, C. D.; Lee, M. V.; Hebert, A. S.; McAlister, G. C.; Phanstiel, D. H.; Westphall, M. S.; Coon, J. J. Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging. Nat. Methods 2011, 8, 933- 935.
131. Willard, B. B.; Ruse, C. I.; Keightley, J. A.; Bond, M.; Kinter, M. Site-specific quantitation of protein nitration using liquid chromatography/tandem mass spectrometry. Anal. Chem. 2003, 75, 2370-2376.
132. Wisastra, R.; Poelstra, K.; Bischoff, R.; Maarsingh, H.; Haisma, H. J.; Dekker, F. J. Antibody-free detection of protein tyrosine nitration in tissue sections. Chembiochem 2011, 12, 2016- 2020.
133. Xie, F.; Liu, T.; Qian, W. J.; Petyuk, V. A.; Smith, R. D. Liquid chromatography- mass spectrometry-based quantitative proteomics. J. Biol. Chem. 2011, 286, 25443-25449.
134. Yamakura, F.; Taka, H.; Fujimura, T.; Murayama, K. Inactivation of human manganese-superoxide dismutase by peroxynitrite is caused by exclusive nitration of tyrosine 34 to 3-nitrotyrosine. J. Biol. Chem. 1998, 273, 14085-14089.
135. Yates, J. R.; Ruse, C. I.; Nakorchevsky, A. Proteomics by mass spectrometry: approaches, advances, and applications. Annu. Rev. Biomed. Eng. 2009, 11, 49-79.
136. Zhan, X.; Desiderio, D. M. Nitroproteins from a human pituitary adenoma tissue discovered with a nitrotyrosine affinity column and tandem mass spectrometry. Anal. Biochem. 2006, 354, 279-289.
137. Zhang, R.; Regnier, F. E. Minimizing resolution of isotopically coded peptides in comparative proteomics. J. Proteome Res. 2002, 1, 139-147.
138. Zhang, Q.; Qian, W. J.; Knyushko, T. V.; Clauss, T. R.; Purvine, S. O.; Moore, R. J.; Sacksteder, C. A.; Chin, M. H.; Smith, D. J.; Camp, D. G. 2nd; Bigelow, D. J.; Smith, R. D. A method for selective enrichment and analysis of nitrotyrosine-containing peptides in complex proteome samples. J. Proteome Res. 2007, 6, 2257-2268.
139. Zhu, W.; Smith, J. W.; Huang, C. M. Mass spectrometry-based label-free quantitative proteomics. J. Biomed. Biotechnol. 2010, 2010, 840518.
140. Zingarelli, B.; Szabo, C.; Salzman, A. L. Reduced oxidative and nitrosative damage in murine experimental colitis in the absence of inducible nitric oxide synthase. Gut 1999, 45, 199-209.