Technical advances in proteomics mass spectrometry: Identification of post-translational modifications

Clinical Chemistry and Laboratory Medicine

Volumn 47, Issue 6, 2009, Pages 647-665

  Amoresano, Angela ^a   Carpentieri, Andrea ^a   Giangrande, Chiara ^a   Palmese, Angelo ^a   Chiappetta, Giovanni ^a   Marino, Gennaro ^a   Pucci, Piero ^a  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

Author keywords

Glycosylation; Nitration; Phosphorylation; Post translational modifications (PTMs); Proteomics; Tandem mass spectrometry (MS MS)

Indexed keywords

3 NITROTYROSINE; GLYCOPEPTIDE;

BIOSYNTHESIS; CELL FUNCTION; GLYCOSYLATION; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MICHAEL ADDITION; NITRATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEOMICS; REVIEW; TANDEM MASS SPECTROMETRY;

MASS SPECTROMETRY; PEPTIDES; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEINS; PROTEOMICS;

EID: 67650645750     PISSN: 14346621     EISSN: 14374331     Source Type: Journal    
DOI: 10.1515/CCLM.2009.154     Document Type: Review

References (115)

1. Godovac-Zimmermann J, Brown LR. Perspectives for mass spectrometry and functional proteomics. Mass Spectrom Rev 2001;20:1-57.
2. Patterson SD, Aebersold RH. Proteomics: the first decade and beyond. Nat Genet 2003;33:311-23.
3. Taylor SW, Fahy E, Ghosh SS. Global organellar proteo-mics. Trends Biotechnol 2003;21:82-8.
4. Mann M, Hendrickson RC, Pandey A. Analysis of proteins and proteomes by mass spectrometry. Annu Rev Biochem 2001;10:437-73.
5. Banks RE, Dunn MJ, Hochstrasser DF, Sanchez JC, Black-stock W, Pappin DJ, et al. Proteomics: new perspectives, new biomedical opportunities. Lancet 2000;356:1749-56.
6. Oda Y, Nagasu T, Chait BT. Enrichment analysis of phos-phorylated proteins as a tool for probing the phosphopro-teome. Nat Biotechnol 2001;19:379-82.
7. Riederer BM. Non-covalent and covalent protein labeling in two-dimensional gel electrophoresis. J Proteomics 2008;71:231-44.
8. Gesellchen F, Bertinetti O, Herberg FW. Analysis of post-translational modifications exemplified using protein kinase A. Biochim Biophys Acta 2006;1764:1788-800.
9. Han KK, Martinage A. Post-translational chemical modifications of proteins - III. Current developments in analytical procedures of identification and quantitation of post-translational chemically modified amino acid(s) and its derivatives. Int J Biochem 1993;25:957-70.
10. Karas M, Hillenkamp F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal Chem 1988;60:2299-301.
11. Beavis RC, Chait BT. Rapid, sensitive analysis of protein mixtures by mass spectrometry. Proc Natl Acad Sci USA 1990;87:6873-7.
12. Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM. Electrospray ionization for mass spectrometry of large biomolecules. Science 1989;246:64-71.
13. Chait BT, Kent SB. Weighing naked proteins: practical, high-accuracy mass measurement of peptides and proteins. Science 1992;257:1885-94.
14. Lee TD, Moore RE, Young MK. Introducing samples directly into electrospray ionization mass spectrometers using a nanospray interface. Curr Protoc Protein Sci 2001;5:unit 16.9.
15. Dal Piaz F, De Leo M, Braca A, De Simone F, Morelli I, De Tommasi N. Electrospray ionization mass spectrometry for identification and structural characterization of pregnane glycosides. Rapid Commun Mass Spectrom 2005;19:1041-52.
16. Schwartz JC, Jardine I. Quadrupole ion trap mass spectrometry. Methods Enzymol 1996;270:552-86.
17. Macek B, Waanders LF, Olsen JV, Mann M. Top-down protein sequencing and MS3 on a hybrid linear quadrupole ion trap-orbitrap mass spectrometer. Mol Cell Proteomics 2006;5:949-58.
18. Hager JW. A new linear ion trap mass spectrometer. Rapid Commun Mass Spectrom 2002;16:512-26.
19. Hager JW, LeBlanc JC. High-performance liquid chromatography-tandem mass spectrometry with a new quadrupole/linear ion trap instrument. J Chromatogr A 2003;1020:3-9.
20. Roepstorff P, Fohlman J. Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed Mass Spectrom 1984;11:601.
21. Hanrieder J, Nyakas A, Naessén T, Bergquist J. Proteomic analysis of human follicular fluid using an alternative bottom-up approach. J Proteome Res 2008;7: 443-9.
22. Monti M, Orrù S, Pagnozzi D, Pucci P. Interaction proteomics. Biosci Rep 2005;25:45-56.
23. Monti M, Orrù S, Pagnozzi D, Pucci P. Functional proteomics. Clin Chim Acta 2005;357:140-50.
24. Zhang K, Wrzesinski K, Fey SJ, Mose Larsen P, Zhang X, Roepstorff P. Assessing CMT cell line stability by two dimensional polyacrylamide gel electrophoresis and mass spectrometry based proteome analysis. J Proteomics 2008;71:160-7.
25. Li Z, Zhao X, Bai S, Wang Z, Chen L, Wei Y, et al. Proteomic identification of cyclophilin A as a potential prognostic factor and therapeutic target in endometrial carcinoma. Mol Cell Proteomics 2008. [Epub ahead of print].
26. Pucci P, Carestia C, Fioretti G, Mastrobuoni AM, Pagano L. Protein fingerprint by fast atom bombardment mass spectrometry: characterization of normal and variant human haemoglobins. Biochem Biophys Res Commun 1985;130:84-90.
27. Mead JA, Shadforth IP, Bessant C. Public proteomic MS repositories and pipelines: available tools and biological applications. Proteomics 2007;7:2769-86.
28. Macek B, Waanders LF, Olsen JV, Mann M. Top-down protein sequencing and MS3 on a hybrid linear quadrupole ion trap-orbitrap mass spectrometer. Mol Cell Proteomics 2006;5:949-58.
29. Gafken PR, Lampe PD. Methodologies for characterizing phosphoproteins by mass spectrometry. Cell Commun Adhes 2006;13:249-62.
30. Walsh TC. Posttranslational modification of proteins: expanding nature's Inventory. Roberts and Company Publishers, 2006:490 pp.
31. Walsh CT, Garneau-Tsodikova S, Gatto GJ Jr. Protein post-translational modifications: the chemistry of proteome diversifications. Angew Chem Int Ed Engl 2005; 44:7342-72.
32. Spiro RG. Protein glycosylation: nature, distribution, enzymatic formation, and disease implications of glycopeptide bonds. Glycobiology 2002;12:43R-56R.
33. Qiu R, Regnier FE. Comparative glycoproteomics of N-linked complex-type glycoforms containing sialic acid in human serum. Anal Chem 2005;77:7225-31.
34. Rademacher TW, Parekh RB, Dwek RA. Glycobiology. Annu Rev Biochem 1988;57:785-838.
35. Marshall RD. The nature and metabolism of the carbohydrate-peptide linkages of glycoproteins. Biochem Soc Symp 1974;17-26.
36. Kornfeld R, Kornfeld S. Assembly of asparagine-linked oligosaccharides. Annu Rev Biochem 1985;54:631-64.
37. Parodi AJ. Role of N-oligosaccharide endoplasmic reticulum processing reactions in glycoprotein folding and degradation. Biochem J 2000;348:1-13.
38. Dell A, Morris HR. Glycoprotein structure determination by mass spectrometry. Science 2001;291:2351-6.
39. Perez-Vilar J, Hidalgo J, Velasco A. Presence of terminal N-acetylgalactosamine residues in subregions of the endoplasmic reticulum is influenced by cell differentiation in culture. J Biol Chem 1991;266:23967-76.
40. Spiro RG. Glucose residues as key determinants in the biosynthesis and quality control of glycoproteins with N-linked oligosaccharides. J Biol Chem 2000;275:35657- 60.
41. Helenius A. How N-linked oligosaccharides affect glycoprotein folding in the endoplasmic reticulum. Mol Biol Cell 1994;5:253-65.
42. Trombetta ES. The contribution of N-glycans and their processing in the endoplasmic reticulum to glycoprotein biosynthesis. Glycobiology 2003;13:77R-91R.
43. Varki A. Biological roles of oligosaccharides: all of the theories are correct. Glycobiology 1993;3:97-130.
44. Gagneux P, Varki A. Evolutionary considerations in relating oligosaccharide diversity to biological function. Glycobiology 1999;9:747-55.
45. Karlsson KA. Microbial recognition of target-cell glycoconjugates. Curr Opin Struct Biol 1995;5:622-35.
46. Dell A, Morris HR. Glycoprotein structure determination by mass spectrometry. Science 2001;291:2351-6.
47. Bretthauer RK. Characterization of O-linked saccharides on glycoproteins. Methods Mol Biol 2007;389:107-18.
48. Xie Y, Liu J, Zhang J, Hedrick JL, Lebrilla CB. Method for the comparative glycomic analyses of O-linked, mucin-type oligosaccharides. Anal Chem 2004;76:5186- 97.
49. Freeze HH, Kranz C. Endoglycosidase and glycoamidase release of N-linked oligosaccharides. Curr Protoc Protein Sci 2006;12.
50. Zhang H, Li XJ, Martin DB, Aebersold R. Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat Biotechnol 2003;21:660-6.
51. Yang Z, Hancock WS. Approach to the comprehensive analysis of glycoproteins isolated from human serum using a multi-lectin affinity column. J Chromatogr A 2004;1053:79-88.
52. Zhao J, Simeone DM, Heidt D, Anderson MA, Lubman DM, et al. Comparative serum glycoproteomics using lectin selected sialic acid glycoproteins with mass spectrometric analysis: application to pancreatic cancer serum. J Proteome Res 2006;5:1792-802.
53. An HJ, Miyamoto S, Lancaster KS, Kirmiz C, Li B, Lam KS, et al. Profiling of glycans in serum for the discovery of potential biomarkers for ovarian cancer. J Proteome Res 2006;5:1626-35.
54. Durham M, Regnier FE. Targeted glycoproteomics: serial lectin affinity chromatography in the selection of O-glycosylation sites on proteins from the human blood proteome. J Chromatogr A 2006;1132:165-73.
55. Dalpathado DS, Desaire H. Glycopeptide analysis by mass spectrometry. Analyst 2008;133:731-8.
56. Ciardiello MA, D'Avino R, Amoresano A, Tuppo L, Carpentieri A, Carratore V, et al. The peculiar structural features of kiwi fruit pectin methylesterase: amino acid sequence, oligosaccharides structure, and modeling of the interaction with its natural proteinaceous inhibitor. Proteins 2008;71:195-206.
57. Amoresano A, Siciliano R, Orrù S, Napoleoni R, Altarocca V, De Luca E, et al. Structural characterisation of human recombinant glycohormones follitropin, lutropin and choriogonadotropin expressed in Chinese hamster ovary cells. Eur J Biochem 1996;242:608-18.
58. De Lorenzo C, Cozzolino R, Carpentieri A, Pucci P, Laccetti P, D'Alessio G. Biological properties of a human compact anti-ErbB2 antibody. Carcinogenesis 2005;26: 1890-5.
59. Lityńska A, Pocheć E, Hoja-Lukowicz D, Kremser E, Laidler P, Amoresano A, et al. The structure of the oligosaccharides of alpha3beta1 integrin from human ureter epithelium (HCV29) cell line. Acta Biochim Pol 2002; 49:491-500.
60. Inforzato A, Peri G, Doni A, Garlanda C, Mantovani A, Bastone A, et al. Structure and function of the long pentraxin PTX3 glycosidic moiety: fine-tuning of the interaction with C1q and complement activation. Biochemistry 2006;45:11540-51.
61. Zaia J. Mass spectrometry of oligosaccharides. Mass Spectrom Rev 2004;23:161-227.
62. Harvey DJ. Matrix-assisted laser desorption/ionisation mass spectrometry of oligosaccharides and glycoconjugates. J Chromatogr A 1996;720:429-46.
63. Domon B, Costello CE. A systematic nomenclature for carbohydrate fragmentations in FABMS/MS of glycoconjugates. Glycoconjugate J 1988;5:397-409.
64. Sandra K, Devreese B, Van Beeumen J, Stals I, Claeyssens M. The Q-Trap mass spectrometer, a novel tool in the study of protein glycosylation. J Am Soc Mass Spectrom 2004;15:413-23.
65. Meldrum DR. Tumor necrosis factor in the heart. Am J Physiol 1998;274:577-595.
66. Renkonen J, Tynninen O, Häyry P, Paavonen T, Renkonen R. Glycosylation might provide endothelial zip codes for organ-specific leukocyte traffic into inflammatory sites. Am J Pathol 2002;161:543-50.
67. Dube DH. Bertozzi CR. Glycans in cancer and inflammation - potential for therapeutics and diagnostics. Nat Rev Drug Discov 2005;4:477-88.
68. Unkenborg J, Pilch BJ, Podtelejnikov AV, Wiśniewski JR. Screening for N-glycosylated proteins by liquid chromatography mass spectrometry. Proteomics 2004;4: 454-65.
69. Nikov G, Bhat V, Wishnok JS, Tannenbaum SR. Analysis of nitrated proteins by nitrotyrosine-specific affinity probes and mass spectrometry. Anal Biochem 2003; 320:214-22.
70. Deonarain MP. Recombinant antibodies for cancer therapy. Expert Opin Biol Ther 2008;8:1123-41.
71. Go EP, Irungu J, Zhang Y, Dalpathado DS, Liao HX, Sutherland LL, et al. Glycosylation site-specific analysis of HIV envelope proteins (JR-FL and CON-S) reveals major differences in glycosylation site occupancy, glycoform profiles, and antigenic epitopes' accessibility. J Proteome Res 2008;7:1660-74.
72. Kumar GK, Prabhakar NR. Post-translational modification of proteins during intermittent hypoxia. Respir Physiol Neurobiol 2008. [Epub ahead of print].
73. Endoh H, Ishibashi Y, Yamaki E, Yoshida T, Yajima T, Kimura H, et al. Immunohistochemical analysis of phos-phorylated epidermal growth factor receptor might provide a surrogate marker of EGFR mutation. Lung Cancer 2008. [Epub ahead of print].
74. Sabetkar M, Low SY, Bradley NJ, Jacobs M, Naseem KM, Richard Bruckdorfer K. The nitration of platelet vasodilator stimulated phosphoprotein following exposure to low concentrations of hydrogen peroxide. Platelets 2008;19:282-92.
75. Larrainzar E, Urarte E, Auzmendi I, Ariz I, Arrese-Igor C, González EM, et al. Use of recombinant iron-superoxide dismutase as a marker of nitrative stress. Methods Enzymol 2008;437:605-18.
76. Baty JW, Hampton MB, Winterbourn CC. Proteomic detection of hydrogen peroxide-sensitive thiol proteins in Jurkat cells. Biochem J 2005;390:791-2.
77. Härtig W, Seeger J, Naumann T, Brauer K, Brü ckner G. Selective in vivo fluorescence labelling of cholinergic neurons containing p75(NTR) in the rat basal forebrain. Brain Res 1998;808:155-65.
78. Julka S, Regnier F. Quantification in proteomics through stable isotope coding: a review. J Proteome Res 2004; 3:350-63.
79. Amoresano A, Marino G, Cirulli C, Quemeneur E. Mapping phosphorylation sites: a new strategy based on the use of isotopically labelled DTT and mass spectrometry. Eur J Mass Spectrom 2004;10:401-12.
80. Steen H, Kuster B, Fernandez M, Pandey A, Mann M. Tyrosine phosphorylation mapping of the epidermal growth factor receptor signaling pathway. J Biol Chem 2002;277:1031-9.
81. Kalume DE, Molina H, Pandey A. Tackling the phospho-proteome: tools and strategies. Curr Opin Chem Biol 2003;7:64-9.
82. Mann M, Jensen ON. Proteomic analysis of post-trans-lational modifications. Nat Biotechnol 2003;21:255-61.
83. Jensen ON. Modification-specific proteomics: characterization of post-translational modifications by mass spec-trometry. Curr Opin Chem Biol 2004;8:33-41.
84. Amoresano A, Monti G, Cirulli C, Marino G. Selective detection and identification of phosphopeptides by dan-syl MS/MS/MS fragmentation. Rapid Commun Mass Spectrom 2006;20:1400-4.
85. Marino G, Buonocore V. Mass-spectrometric identification of 1-dimethylaminoaphthalene-5-sulphonyl-amino acids. Biochem J 1968;110:603-4.
86. LeBlanc JC, Hager JW, Ilisiu AM, Hunter C, Zhong F, Chu I. Unique scanning capabilities of a new hybrid linear ion trap mass spectrometer (Q TRAP) used for high sensitivity proteomics applications. Proteomics 2003;3:859- 69.
87. Hager JW, Yves Le Blanc JC. Product ion scanning using a Q-q-Q linear ion trap (Q TRAP) mass spectrometer. Rapid Commun Mass Spectrom 2003;17:1056-64.
88. Ben-Levy R, Leighton IA, Doza YN, Attwood P, Morrice N, Marshall CJ, et al. Identification of novel phosphory-lation sites required for activation of MAPKAP kinase-2. EMBO J 1995;14:5920-30.
89. Bouras T, Southey MC, Venter DJ. Overexpression of the steroid receptor coactivator AIB1 in breast cancer correlates with the absence of estrogen and progesterone receptors and positivity for p53 and HER2/neu. Cancer Res 2001;61:903-7.
90. Meimoun P, Ambard-Bretteville F, Colas-des Francs-Small C, Valot B, Vidal J. Analysis of plant phosphopro-teins. Anal Biochem 2007;371:238-46.
91. McLachlin DT, Chait BT. Analysis of phosphorylated proteins and peptides by mass spectrometry. Curr Opin Chem Biol 2001;5:591-602.
92. Lewandrowski U, Sickmann A, Cesaro L, Brunati AM, Toninello A, Salvi M. Identification of new tyrosine phosphorylated proteins in rat brain mitochondria. FEBS Lett 2008;582:1104-10.
93. Paradela A, Albar JP. Advances in the analysis of protein phosphorylation. J Proteome Res 2008;7:1809-18.
94. Pandey A, Andersen JS, Mann M. Use of mass spectrometry to study signaling pathways. Sci STKE 2000;2000:PL1.
95. Janek K, Wenschuh H, Bienert M, Krause E. Phospho-peptide analysis by positive and negative ion matrixassisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom 2001;15:1593-9.
96. Idris N, Carothers Carraway CA, Carraway KL. Differential localization of ErbB2 in different tissues of the rat female reproductive tract: implications for the use of specific antibodies for ErbB2 analysis. J Cell Physiol 2001;189:162-70.
97. Bendt AK, Burkovski A, Schaffer S, Bott M, Farwick M, Hermann T. Towards a phosphoproteome map of Cory-nebacterium glutamicum. Proteomics 2003;3:1637-46.
98. Gaberc-Porekar V, Menart V. Perspectives of immobilized-metal affinity chromatography. J Biochem Bio-phys Methods 2001;49:335-60.
99. Andersson L, Porath J. "Isolation of phosphoproteins by immobilized metal (Fe3+) affinity chromatography". Anal Biochem 1986;154:250-4.
100. Zhou H, Ye M, Dong J, Han G, Jiang X, Wu R, et al. Specific phosphopeptide enrichment with immobilized titanium ion affinity chromatography adsorbent for phosphoproteome analysis. J Proteome Res 2008. [Epub ahead of print].
101. Wilson-Grady JT, Villén J, Gygi SP. Phosphoproteome analysis of fission yeast. J Proteome Res 2008;7: 1088-97.
102. Zhang X, Ye J, Jensen ON, Roepstorff P. Highly efficient phosphopeptide enrichment by calcium phosphate precipitation combined with subsequent IMAC enrichment. Mol Cell Proteomics 2007;6:2032-42.
103. Oda Y, Nagasu T, Chait BT. Enrichment analysis of phosphorylated proteins as a tool for probing the phos-phoproteome. Nat Biotechnol 2001;19:379-82.
104. Zhou H, Watts JD, Aebersold R. A systematic approach to the analysis of protein phosphorylation. Nat Biotechnol 2001;19:375-8.
105. Mattila K, Siltainsuu J, Balaspiri L, Ora M, Lönnberg H. Derivatization of phosphopeptides with mercapto- and amino-functionalized conjugate groups by phosphate elimination and subsequent Michael addition. Org Biomol Chem 2005;3:3039-44.
106. Beckman JS, Koppenol WH. Nitric oxide, superoxide, and peroxynitrite: the good, the bad, and ugly. Am J Physiol 1996;271:1424-37.
107. Schopfer FJ, Baker PR, Freeman BA. NO-dependent protein nitration: a cell signaling event or an oxidative inflammatory response? Trends Biochem Sci 2003; 28:646-54.
108. Ischiropoulos H. Biological tyrosine nitration: a patho-physiological function of nitric oxide and reactive oxygen species. Arch Biochem Biophys 1998;356:1-11.
109. Greenacre SA, Ischiropoulos H. Tyrosine nitration: localisation, quantification, consequences for protein function and signal transduction. Free Radic Res 2001;34:541-81.
110. Castegna A, Thongboonkerd V, Klein JB, Lynn B, Mar-kesbery WR, Butterfield DA. Proteomic identification of nitrated proteins in Alzheimer's disease brain. J Neu-rochem 2003;85:1394-401.
111. Aulak KS, Koeck T, Crabb JW, Stuehr DJ. Dynamics of protein nitration in cells and mitochondria. Am J Phy-siol Heart Circ Physiol 2004;286:30-38.
112. Nikov G, Bhat V, Wishnok JS, Tannenbaum SR. Analysis of nitrated proteins by nitrotyrosine-specific affinity probes and mass spectrometry. Anal Biochem 2003;320:214-22.
113. Petersson AS, Steen H, Kalume DE, Caidahl K, Roep-storff P. Investigation of tyrosine nitration in proteins by mass spectrometry. J Mass Spectrom 2001;36:616- 25.
114. 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;79:2109-17.
115. Cirulli C, Marino G, Amoresano A. Membrane pro-teome in Escherichia coli probed by MS3 mass spec-trometry: a preliminary report. Rapid Commun Mass Spectrom 2007;21:2389-97.