LC/MS Analysis of Proteins and Peptides in Drug Discovery

HPLC for Pharmaceutical Scientists

Volumn , Issue , 2006, Pages 837-899

  Chen, Guodong ^a   Liu, Yan Hui ^a   Pramanik, Birendra N ^a  

^a MERCK RESEARCH LABORATORIES   (United States)

Author keywords

Biotechnology product and drug target applications; Drug discovery LC MS analysis of proteins and peptides; Proteins peptides general strategy analysis

Indexed keywords

EID: 84889287561     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470087954.ch19     Document Type: Chapter

References (140)

1. B. N. Pramanik, P. L. Bartner,and G. Chen, The role of mass spectrometry in thedrug discovery process, Curr. Opin. Drug Discovery Dev. 2 (1999), 401-417.
2. S. Nanda and J. M. Bathon, Etanercept: A clinical review of current and emergingindications. Expert Opin. Pharmacother. 5 (2004), 1175-1186.
3. N. J. Olsen and C. M. Stein, New drugs for rheumatoid arthritis, N. Engl. J. Med.350 (2004), 2167-2179.
4. E. H. Fischer, Cellular regulation by protein phosphorylation, Bull. Inst. Pasteur81 (1983), 7-31.
5. J. Axford, The impact of glycobiology on medicine, Trends Immunol. 22 (2001),237-239.
6. W. J.Wedemeyer, E.Welker,M. Narayan, and H.A. Scheraga, Disulfide bonds andprotein folding, Biochemistry 39 (2000), 4207-4216.
7. J. Godovac-Zimmermann and L. R. Brown, Perspectives for mass spectrometryand functional proteomics,Mass Spectrom. Rev. 20 (2001), 1-57.
8. R.W. A. Oliver, HPLC of Macromolecules: A Practical Approach, IRL Press atOxford University Press, Oxford, 1989.
9. K. Gooding and F. Regnier, HPLC of Biological Macromolecules, Marcel Dekker,New York, 1990.
10. G. B. Irvine, High-performance size-exclusion chromatography of peptides, J.Biochem. Biophys. Methods 56 (2003), 233-242.
11. T. Kawai, K. Saito,and W. Lee, Protein binding to polymer brush, based onion-exchange, hydrophobic, and affinity interactions, J. Chromatogr. B Analyst.Technol. Biomed. Life Sci. 790 (2003), 131-142.
12. P. D. McDonald, Improving our understanding of reversed-phase separations forthe 21st century,Adv. Chromatogr. 42 (2003), 323-375.
13. J. A. Queiroz, C. T. Tomaz,and J. M. Cabral, Hydrophobic interaction chromatographyof proteins. J. Biotechnol. 87 (2001), 143-159.
14. M. Girard and N. Mousseau, Analysis of human growth hormone by hydrophobicinteraction HPLC. Method development,validation, and comparative selectivityto reversed phase HPLC, J. Liq. Chrom. Relat. Technol. 22 (1999), 1103-1116.
15. N. E. Labrou, Design and selection of ligands for affinity chromatography,J. Chromatogr.B Analyt. Technol. Biomed. Life Sci. 790 (2003), 67-78.
16. R.G. Cooks,G. Chen, and P.Wong, Mass spectrometers, in G. L.Trigg (ed.), Encyclopediaof Applied Physics, VCH Publishers, New York, 1997, pp. 289-330.
17. J. B. Fenn, M. Mann, C. K. Meng, S. F.Wong, and C. M.Whitehouse, Electrosprayionization for mass spectrometry of large biomolecules, Science 246 (1989), 64-71.
18. B. N. Pramanik, A. K. Ganguly, and M. L. Gross, Applied Electrospray Mass Spectrometry,Marcel Dekker, New York, 2002.
19. F. Hillenkamp, M. Karas, R. C. Beavis, and B. T. Chait, Matrix-assisted laser desorption/ionization mass spectrometry of biopolymers, Anal. Chem. 63 (1991),1193A-1203A.
20. K. Tanaka, H. Waki,Y. Ido, S. Akita, Y. Yoshida, and T. Yoshida, Protein andpolymer analyses up to m/z 100,000 by laser ionization time-of-flight mass spectrometry,Rapid Commun. Mass Spectrom. 2 (1988), 151-153.
21. R.D. Smith, J.A. Loo,C.G. Edmonds,C. J. Barinaga, and H. R. Udseth, New developmentsin biochemical mass spectrometry: Electrospray ionization, Anal. Chem.62 (1990), 882-899.
22. F.W. McLafferty, Tandem mass spectrometry, Science 214 (1981), 280-287.
23. K. Hirayama, R.Takahashi, S. Akashi, K. Fukuhara,N. Oouchi, A. Murai, M.Arai,S. Murao,K.Tanaka, and I. Nojima, Primary structure of paim I, an alpha-amylaseinhibitor from Streptomyces corchorushii, determined by the combination ofEdman degradation and fast atom bombardment mass spectrometry, Biochemistry26 (1987), 6483-6488.
24. W. J. Henzel, T. M. Billeci, J. T. Stults, S. C.Wong, C. Grimley, and C.Watanable,Identifying proteins from two-dimensional gels by molecular mass searching ofpeptide fragments in protein sequence databases, Proc. Natl. Acad. Sci. USA 90(1993), 5011-5015.
25. N. L. Kelleher, Top-down proteomics, Anal. Chem. 76 (2004), 197A-203A.
26. D. F. Hunt, J. R. Yates III, J. Shabanowitz, S.Winston, and C. R. Hauer, Proteinsequencing by tandem mass spectrometry, Proc. Natl. Acad. Sci. USA 83 (1986),6233-6237.
27. J. R.Yates III, Mass spectrometry and the age of the proteome, J. Mass Spectrom.33 (1998), 1-19.
28. P. Roepstorff and J. Fohlman, Proposal for a common nomenclature for sequenceions in mass spectra of peptides, Biomedical Mass Spectrom. 11 (1984), 601.
29. R. W. Nelson, The use of bioreactive probes in protein characterization,MassSpectrom. Rev. 16 (1997), 353-376.
30. D. Metcalf, G. R. Johnson, and A.W. Burgess, Direct stimulation by purified GMCSFof the proliferation of multipotential and erythroid precursor cells, Blood 55(1980), 138-147.
31. A. Tsarbopoulos, B. N. Pramanik,J. Labdon, P. Reichert, G. Gitlin, S. Patel,V. Sardana, T. L. Nagabhushan, and P. P. Trotta, Isolation and characterization ofa resistant core peptide of recombinant human granulocyte-macrophage colonystimulatingfactor (GM-CSF); confirmation of the GM-CSF amino acid sequenceby mass spectrometry, Protein Sci. 2 (1993), 1948-1958.
32. P. C. Andrews and J. E. Dixon, A procedure for in situ alkylation of cysteineresidue on glass fiber prior to protein microsequence analysis, Anal. Biochem. 161(1987), 524-528.
33. R. Bordens, S. E. Grossberg, P. P. Trotta, and T. L. Nagabhushan, Molecular andbiologic characterization of recombinant interferon-a-2b, Semin. Oncol. 24(1997), S9-S51.
34. M. Streuli, S. Nagata, and C.Weissmann, At least three human type alpha interferons:Structure of alpha 2, Science 209 (1980), 1343-1347.
35. B.N. Pramanik,A.Tsarbopoulos, J. E. Labdon, P. P.Trotta, and T. L. Nagabhushan,Structural analysis of biologically active peptides and recombinant proteins andtheir modified counterparts by mass spectrometry, J. Chromatogr. 562 (1991),377-389.
36. E. P. Marbach and M. H. Weil, Rapid enzymatic measurement of blood lactateand pyruvate: Use and significance of metaphosphoric acid as a common precipitant,Clin. Chem. 13 (1967), 314-325.
37. G.W. Becker, P.M. Tackett,W.W. Bromer,D. S. Lefeber, and R. M. Riggin, Isolationand characterization of a sulfoxide and a desamido derivative of biosynthetichuman growth hormone, Biotechnol. Appl. Biochem. 10 (1988), 326-337.
38. K. Rose, M. G. Simona,L. A. Savoy, P. O. Regamey, B. N. Green, G. M. Clore,A. M. Gronenborn, and P.T.Wingfield, Pyruvic acid is attached through its centralcarbon atom to the amino terminus of the recombinant DNA-derived DNAbindingprotein Ner of Mu, J. Biol. Chem. 267 (1992), 19101-19106.
39. D. Prome,Y. Blouquit,C. Ponthus, J.C. Prome, and J. Rosa, Structure of the humanadult hemoglobin minor fraction A1b by electrospray and secondary ion massspectrometry. Pyruvic acid as amino-terminal blocking group, J. Biol. chem. 266(1991), 13050-13054.
40. R. Apweiler, H. Hermjakob, and N. Sharon, On the frequency of protein glycosylation,as deduced from analysis of the SWISS-PROT database, Biochim. Biophys.Acta 1473 (1999), 4-8.
41. B. S.Wojczyk, M. Stwora-Wojczyk, S. Shakin-Eshelman,W. H.Wunner, and S. L.Spitalnik,The role of site-specific N-glycosylation in secretion of soluble forms ofrabies virus glycoprotein, Glycobiology 8 (1998), 121-130.
42. M.V. Dwek, H. A. Ross, and A. J. Leathem, Proteome and glycosylation mappingidentifies post-translational modifications associated with aggressive breastcancer, Proteomics 1 (2001), 756-762.
43. P. M. Rudd, T. Elliott, P. Cresswell, I. A.Wilson, and R. A. Dwek, Glycosylationand the immune system, Science 291 (2001), 2370-2376.
44. R. Peracaula, G. Tabares, L. Royle, D. J. Harvey, R. A. Dwek, P. M. Rudd, and R.De Llorens, Altered glycosylation pattern allows the distinction between prostatespecificantigen (PSA) from normal and tumor origins, Glycobiology 13 (2003),457-470.
45. R. Peracaula, L. Royle, G. Tabares, G. Mallorqui-Fernandez, S. Barrabes, D. J.Harvey, R. Dwek, P. M. Rudd, and R. De Llorens, Glycosylation of human pancreaticribonuclease: Differences between normal and tumor states, Glycobiology13 (2002), 227-244.
46. P. M. Rudd,A. H. Merry,M.R.Wormald, and A. R. Dwek,Glycosylation and prionprotein, Curr. Opin. Struct. Biol. 12 (2002), 578-586.
47. M. Butler,D. Quelhas, A. J. Critchley,H. Carchon, H. F. Hebestreit, R.G. Hibbert,L.Vilarinto, E.Teles,G. Matthijs, E. Scholler, P. Argibay,D. J. Harvey,R. A. Dwek,J. Jaeken, and P. M. Rudd, Detailed glycan analysis of serum glycoproteins ofpatients with congenital disorders of glycosylation indicates the specific defectiveglycan processing step and provides an insight into pathogenesis, Glycobiology 13(2003), 601-622.
48. R. Kornfeld and S. Kornfeld, Assembly of asparagines-linked oligosaccharides,Annu. Rev. Biochem. 54 (1985), 631-664.
49. H. Schachter, Glycoproteins, in J. Montreuil, J. F.G.Vliegenthart, and H. Schachter(eds.), New Comprehensive Biochemistry,Vol. 29A, Elsevier,Amsterdam, 1995, pp.123-454.
50. H. J. An, T. R. Peavy, J. L. Hedrick, and C. B. Lebrilla, Determination of Nglycosylationsites and site heterogeneity in glycoproteins, Anal. Chem. 75 (2003),5628-5637.
51. M. J. Huddleston, M. F. Bean,and S. A. Carr, Collisional fragmentation of glycopeptidesby electrospray ionization LC/MS and LC/MS/MS: Methods for selectivedetection of glycopeptides in protein digests, Anal. Chem. 65 (1993), 877-884.
52. S. A. Carr, M. J. Huddleston,and M. F. Bean, Selective identification and differentiationof N- and O-linked oligosaccharides in glycoproteins by liquid chromatography-mass spectrometry, Protein Sci. 2 (1993), 183-196.
53. P.T. Jedrezejewski and W.D. Lehmann, Detection of modified peptides in enzymedigests by capillary liquid chromatography/electrospray mass spectrometry and aprogrammable skimmer CID acquisition routine,Anal. Chem. 69 (1997), 294-301.
54. J. Colangelo, V. Licon,J. Benen, J. Visser, C. Bergmann, and R. Orlando, Characterizationof the N-linked glycosylation site of recombinant pectate lyase, RapidCommun. Mass Spectrom. 13 (1999), 2382-2387.
55. A.W. Guzzetta, L. J. Basa,W. S. Hancock,B. A. Keyt, and W. F. Bennett, Identificationof carbohydrate structures in glycoprotein peptide maps by the use ofLC/MS with selected ion extraction with special reference to tissue plasminogenactivator and a glycosylation variant produced by site directed mutagenesis, Anal.Chem. 65 (1993), 2953-2962.
56. I. Mazsaroff,W.Yu, B.D.Kelley,and J. E.Vath, Quantitative comparison of globalcarbohydrate structures of glycoproteins using LC-MS and in-source fragmentation,Anal. Chem. 69 (1997), 2517-2524.
57. E. K. Fridriksson, A. Beavil, D. Holowka, H. J. Gould, B. Baird, and F. W.McLafferty, Heterogeneous glycosylation of immunoglobulin E constructs characterizationby top-down high-resolution 2-D mass spectrometry, Biochemistry 39(2000), 3369-3376.
58. P. Teng-umnuay, H. R. Morris,A. Dell, M. Panico, T. Paxton, and C. M.West, Thecytoplasmic F-box binding protein SKP1 contains a novel pentasaccharide linkedto hydroxyproline in Dictyostelium, J. Biol. Chem. 273 (1998), 18242-18249.
59. T. Kurahashi, A. Miyazaki,Y. Murakami,S. Suwan,T. Franz, M. Isobe, N.Tani, andH. Kai, Determination of a sugar chain and its linkage site on a glycoproteinTIME-EA4 from silkworm diapause eggs by means of LC-ESI-Q-TOF-MA andMS-MS, Bioorg. Med. Chem. 10 (2002), 1703-1710.
60. J. F. Nemeth, G. P. Hochensang, L. J. Marnett, and R. M. Capriolli, Characterizationof the glycosylation sites in cyclooxygenase-2 using mass spectrometry, Biochemistry40 (2001), 3109-3116.
61. J. Gonzalez, T. Takao,H. Hori, V. Besada, R. Rodriguez, G. Padron, and Y.Shimonishi, A method for determination of N-glycosylation sites in glycoproteinsby collision-induced dissociation analysis in fast atom bombardment mass spectrometry:Identification of the positions of carbohydrate-linked asparagine inrecombinant a-amylase by treatment with peptide-N-glycosidase F in 18O-labeledwater, Anal. Biochem. 205 (1992), 151-158.
62. B.Kuster and M. Mann, 18O-Labeling of N-glycosylation sites to improve the identificationof gel-separated glycoproteins using peptide mass mapping and databasesearching,Anal. Chem. 71 (1999), 1431-1440.
63. L. Xiong and F. Regnier, Use of a lectin affinity selector in the search for unusualglycosylation in proteomics, J. Chromatgr. B 782 (2002), 405-418.
64. H. Kaji, H. Saito, Y. Yamauchi, T. Shinkawa, M. Taoka, J. Hirabayashi, K. Kasai,N. Takahashi, and T. Isobe, Lectin affinity capture, isotope-coded tagging andmass spectrometry to identify N-linked glycoproteins, Nature Biotech. 21 (2003),667-672.
65. J. Bunkenborg, B. J. Pilch, A.V. Podteleinikov, and J. R.Wisniewski, Screening forN-glycosylated proteins by liquid chromatography mass spectrometry, Proteomics4 (2004), 454-465.
66. G. Reid, J. L. Stephenson,Jr., and S. A. McLuckey, Tandem mass spectrometry ofribonuclease A and B: N-linked glycosylation site analysis of whole protein ions,Anal. Chem. 74 (2002), 577-583.
67. A. Zlotnik, J. Ransom, G. Frank, M. Fischer, and M. Howard, Interleukin 4 is agrowth factor for activated thymocytes:Possible role in T-cell ontogeny, Proc. Natl.Acad. Sci. USA 84 (1987), 3856-3860.
68. H.V. Le, L. Ramanathan,J. E. Labdon, C. Mays-Ichinco, R. Syto, N. Arai, P. Hoy,Y. Takebe, T. L. Nagabhushan, and P. P. Trotta, Isolation and characterization ofmultiple variants of recombinant human interleukin 4 expressed in mammaliancells, J. Biol. Chem. 263 (1988), 10817-10823.
69. A. Tsarbopoulos, B. N. Pramanik,and T. L. Nagabhushan, Structural analysis ofthe CHO-derived interleukin-4 by liquid-chromatography/electrospray ionizationmass spectrometry, J. Mass Spectrom. 30 (1995), 1752-1763.
70. P. Cohen, The regulation of protein function by multisite phosphorylation-a 25year update,Trends Biochem. Sci. 25 (2000), 596-601.
71. J. D. Graves and E. D. Krebs, Protein phosphorylation and signal transduction,Pharmacol. Ther. 82 (1999), 111-121.
72. T. Hunter, Signaling-2000 and beyond, Cell 100 (2000), 113-127.
73. P. Blume-Jensen and T. Hunter, Oncogenic kinase signaling, Nature 411 (2001),355-365.
74. P. Cohen, Timeline: Protein kinases-The major drug targets of the twenty-firstcentry? Nature Rev. Drug Discovery 1 (2002), 309-315.
75. C.C.Kumar and V. Madison, Drugs targeted against protein kinases, Expert Opin.Emerging Drugs 6 (2001), 303-315.
76. T. Covey, B. Shushan, R. Bonner,W. Schroder, and F. Hucho, in H. Jornvall, J.-O.Hoog, and A.-M. Gustavsson (eds.), Methods in Protein Sequence Analysis,Birkhauser Verlag, Basel, 1991, p. 249.
77. E. J. Chang,V. Archambault, D. T. McLachlin,A. N. Krutchinsky, and B. T. Chait,Analysis of protein phosphorylation by hypothesis-driven multi-stage mass spectrometry,Anal. Chem. 76 (2004), 4472-4483.
78. M. J. Huddleston, R. S. Annan,M. F. Bean, and S. A. Carr, Selective detection ofphosphopeptides in complex mixtures by electrospray liquid chromatography/mass spectrometry, J. Am. Soc. Mass Spectrom. 4 (1993), 710-717.
79. R. S. Annan, M. J. Huddleston,R.Verma, R. J. Deshaies, and S. A. Carr,A multidimensionalelectrospray MS-based approach to phosphopeptide mapping, Anal.Chem. 73 (2001), 393-404.
80. G. Neubauer and M. Mann, Mapping of phosphorylation sites of gel-isolated proteinsby nanoelectrospray tandem mass spectrometry: Potentials and limitations,Anal. Chem. 71 (1999), 235-242.
81. J. Schlossmann, A. Ammendola, K. Ashman, X. Zong, A. Huber, G. Neubauer,G. X.Wang, H. D. Allescher,M. Korth, M.Wilm, F. Hofmann, and P. Ruth, Regulationof intracellular calcium by a signalling complex of IRAG, IP3 receptor andcGMP kinase Iβ, Nature 404 (2000), 197-201.
82. H. Steen, B. Kuster,and M. Mann, Quadrupole time-of-flight versus triplequadrupolemass spectrometry for the determination of phosphopeptides byprecursor ion scanning, J. Mass Spectrom. 36 (2001), 782-790.
83. S. D. Shi, M. E. Hemling,S. A. Carr, D. M. Horn, I. Lindh, and F.W. McLafferty,Phosphopeptide/phosphoprotein mapping by electron-capture dissociation massspectrometry, Anal. Chem. 73 (2001), 19-22.
84. L. Andersson and J. Porath, Isolation of phosphoproteins by immobilized metal(Fe3+) affinity chromatography,Anal. Biochem. 154 (1986), 250-254.
85. M. C. Posewitz and P. Tempst, Immobilized gallium (III) affinity chromatographyof phosphopeptides,Anal. Chem. 71 (1999), 2883-2892.
86. S. Ficarro, M. L. McCleland, P. T. Stukenberg, D. J. Burke, M. M. Ross,J. Shabanowitz, D. F. Hunt, and F. M.White, Phosphoproteome analysis by massspectrometry and its application to Saccharomyces cerevisiae, Nat. Biotechnol. 20(2002), 301-305.
87. A. Pandey, A. V. Podtelejnikov, B. Blagoev, X. R. Bustelo, M. Mann, and H. F.Lodish, Analysis of receptor signaling pathways by mass spectrometry: Identificationof Vav-2 as a substrate of the epidermal and platelet-derived growth factorreceptors, Proc. Natl. Acad. Sci. USA 97 (2000), 179-184.
88. M. Gronborg,T. Z. Kristiansen, A. Stensballe, J. S. Andersen, O. Ohara, M. Mann,O. N. Jensen, and A. Pandey, A mass spectrometry-based proteomic approach foridentification of serine/threonine-phosphorylated proteins by enrichment withphosphor-specific antibodies: Identification of a novel protein, Frigg, as a proteinkinase A substrate, Mol. Cell. Proteomics 1 (2002), 517-527.
89. H. Zhou, J. D.Watts,and R. A. Aebersold, A systematic approach to the analysisof protein phosphorylation, Nat. Biotechnol. 19 (2001), 375-378.
90. Y. Oda, T. Nagasu, and B. T. Chait, Enrichment analysis of phosphorylated proteinsas a tool for probing the phosphoproteome, Nat. Biotechnol. 19 (2001),379-382.
91. W. J. Qian, M. B. Goshe, D. G. Camp II, L.-R.Yu, K. Tang, and R. D. Smith, Phosphoproteinisotope-coded solid-phase tag approach for enrichment and quantitativeanalysis of phosphopeptides from complex mixtures, Anal. Chem. 75 (2003),5441-5450.
92. D. Bonenfant,T. Schmelze, E. Jacinto, J. L. Crespo,T. Mini, M.N. Hall, and P. Jenoe,Quantitation of changes in protein phosphorylation: a simple method based onstable isotope labeling and mass spectrometry, Proc. Natl. Acad. Sci. USA 100(2003), 880-885.
93. D.T. Mclachlin and B.T. Chait, Improved β-elimination-based affinity purificationstrategy for enrichment of phosphopeptides,Anal. Chem. 75 (2003), 6826-6836.
94. Z.A. Knight,B. Schilling,R.H.Row,D.M.Kenski,B.W. Gibson, and K. M. Shokat,Phosphospecific proteolysis for mapping sites of protein phosphorylation,Nat.Biotechnol. 21 (2003), 1047-1396.
95. E. S. Lander and R. A. Weinberg, Genomics: Journey to the center of biology,Science 287 (2000), 1777-1782.
96. G. Manning, D. B.Whyte, R. Martinez,T. Hunter, and S. Sudarsanam,The proteinkinase complement of the human genome, Science 298 (2002), 1912-1934.
97. S.Wang, Y. H. Liu, C. K. Smith, and B. N. Pramanik, Mass spectrometric characterizationof MEK1 phosphorylation during expression in insect cells, presentedat the 52nd ASMS Conference on Mass Spectrometry, May 23-27, 2004, Nashville,Tennessee.
98. R. C. Richter, D. Link, and H. M. S. Kingston, Microwave-enhanced chemistry,Anal. Chem. 73 (2001), 31A-37A.
99. P. Lidstrom, J.Tierney,B.Wathey,and J.Westman, Microwave-assisted organic synthesis,Tetrahedron Lett. 57 (2001), 9225-9283.
100. A. K. Bose, Y. H. Ing,N. Lavlinskaia, C. Sareen, B. N. Pramanik, P. L. Bartner,Y. H. Liu, and L. Heimark, Microwave enhanced Akabori reaction for peptideanalysis, J. Am. Soc. Mass Spectrom. 13 (2002), 839-850.
101. S. Akabori, K. Ohno, and K. Narita, On the hydrazinolysis of proteins and peptides:A method for the characterization of carboxy-terminal amino acids in proteins,Bull. Chem. Soc. Japan 25 (1952), 214-218.
102. B. N. Pramanik, Y. H. Ing,A. K. Bose, L. K. Zhang, Y. H. Liu, S. N. Ganguly, andP. L. Bartner, Rapid cyclopeptide analysis by microwave enhanced Akabori reaction,Tetrahedron Lett. 44 (2003), 2565-2568.
103. L. Ngoka and M. L. Gross, Multistep tandem mass spectrometry for sequencingcyclic peptides in an ion-trap mass spectrometer, J. Am. Soc. Mass Spectrom.10 (1999), 732-746.
104. J. Kuroda,T. Fukai, and T. Nomura,Collision-induced dissociation of ring-openedcyclic depsipeptides with a guanidino group by electrospray ionization/ion trapmass spectrometry, J. Mass Spectrom. 36 (2001), 30-37.
105. Y. H. Ing, L. K. Zhang, P. L. Bartner, A. K. Bose, and B. N. Pramanik, Rapidcyclopeptide analysis by microwave enhanced Akabori reaction. presented at the51st ASMS conference on mass spectrometry and allied topics, Montreal, Canada,2003.
106. B. N. Pramanik, U. A. Mirza, Y. H. Ing, Y. H. Liu, P. L. Bartner, P. C.Weber, andA. K. Bose, Microwave-enhanced enzyme reaction for protein mapping by massspectrometry: A new approach to protein digestion in minutes, Protein Science11 (2002), 2676-2687.
107. B. N. Pramanik, P. L. Bartner,U. A. Mirza,Y. H. Liu, and A. K. Ganguly, Electrosprayionization mass spectrometry for the study of non-covalent complexes: Anemerging technology, J. Mass Spectrom. 33 (1998), 911-920.
108. A. K. Ganguly, B. N. Pramanik, G. Chen, and A. Tsarbopoulos, Detection ofnoncovalent complexes by electrospray ionization mass spectrometry, in B. N.Pramanik, A. K. Ganguly, and M. L. Gross (eds.), Applied Electrospray MassSpectrometry, Marcel Dekker, New York, 2002, pp. 361-387.
109. D. C. Schriemer, D. R. Bundle,L. Li, and O. Hindsgaul, Micro-scale frontal affinitychromatography with mass spectrometric detection: A new method for thescreening of compound libraries, Angew. Chem. Int. Ed. 37 (1998), 3383-3387.
110. K. Kasai, Y. Oda,M. Nishikata, and S. Ishii, Frontal affinity chromatography:Theory for its application to studies on specific interactions of biomolecules, J.Chromatogr. Biomed. Appl. 376 (1986), 33-47.
111. M. A. Kelly, T. J. McLellan, and P. J. Rosner, Strategic use of affinity-based massspectrometry techniques in the drug discovery process, Anal. Chem. 74 (2002),1-9.
112. Y. M. Dunayevskiy, J. J. Lai,C. Quinn, F. Talley, and P. Vouros, Mass Spectromicidentification of ligands selected from combinatorial libraries using gel filtration,Rapid Commun. Mass Spectrom. 11 (1997), 1178-1184.
113. P. A. Wabnitz and J. A. Loo, Drug screening of pharmaceutical discovery compoundsby micro-size exclusion chromatography/mass spectrometry,RapidCommun. Mass Spectrom. 16 (2002), 85-91.
114. M. R.Wilkins, J. C. Sanchez,A. A. Gooley, R. D. Appel, I. Humphery-Smith, D. F.Hochstrasser, and K. L. Williams, Progress with proteome projects: Why allproteins expressed by a genome should be identified and how to do it, Biotechnol.Genet. Eng. Rev. 13 (1996), 19-50.
115. M.Tyers and M. Mann, From genomics to proteomics, Nature 422 (2003), 193-197.
116. P. G. Righetti, A. Castagna, and B. Herbert, Prefractionation techniques in proteomeanalysis, Anal. Chem. 73 (2001), 320A-326A.
117. P. G. Righetti, E.Wenisch,A. Jungbauer, H. Katinger, and M. Faupel, Preparativepurification of human monoclonal antibody isoforms in a multi-compartmentelectrolyser with immobiline membranes, J. Chromatogr. 500 (1990), 681-696.
118. M. Fountoulakis, H. Langen, C. Gray, and B. Takacs, Enrichment and purificationof proteins of Haemophilus influenzae by chromatofocusing, J. Chromatogr.A. 806(1998), 279-291.
119. M. Fountoulakis, M. F. Takacs, and B. Takacs, Enrichment of low-copy-numbergene products by hydrophobic interaction chromatography, J. Chromatogr.A. 833(1999), 157-168.
120. M. Fountoulakis and B.Takacs, Design of protein purification pathways: Applicationto the proteome of Haemophilus influenzae using heparin chromatography,Protein Expr. Purif. 14 (1998), 113-119.
121. P. H. O'Farrell, High resolution two-dimensional electrophoresis of proteins, J.Biol. Chem. 250 (1975), 4007-4021.
122. M. Hamdan and P. G. Righetti, Assessment of protein expression by means of2-D gel electrophoresis with and without mass spectrometry, Mass Spectrom. Rev.22 (2003), 272-284.
123. J. Klose and U. Kobalz,Two-dimensional electrophoresis of proteins: An updatedprotocol and implications for a functional analysis of the genome, Electrophoresis16 (1995), 1034-1059.
124. G. J. Opiteck, S. R. Ramirez, J.W. Jorgensen, and M. A. Moseley, Comprehensivetwo-dimensional high-performance liquid chromatography for the isolation ofoverexpressed proteins and proteome mapping, Anal. Biochem. 258 (1998),349-361.
125. W. H. McDonald and J. R. Yates III, Shotgun proteomics and biomarker discovery,Dis. Markers 18 (2002), 99-105.
126. W. S. Hancock, S. L.Wu, and P. Shieh, The challenges of developing a sound proteomicsstrategy, Proteomics 2 (2002), 352-359.
127. M. Geng, J. Ji,and F. E. Reginer, Signature-peptide approach to detecting proteinsin complex mixtures, J. Chromatogr.A. 870 (2000), 295-313.
128. S. P. Gygi, B. Rist,S. A. Gerber, F. Turecek, M. H. Gelb, and R. Aebersold, Quantitativeanalysis of complex protein mixtures using isotope-coded affinity tags, Nat.Biotechnol. 17 (1999), 994-999.
129. M. Munchbach, M. Quadroni,G. Miotto,and P. James, Quantitation and facilitatedde novo sequencing of proteins by isotopic N-terminal labeling of peptides witha fragmentation-directing moiety, Anal. Chem. 72 (2000), 4047-4057.
130. I. I. Stewart,T.Thomson, and D. Figeys, 18O labeling: A tool for proteomics, RapidCommun. Mass Spectrom. 15 (2001), 2456-2465.
131. L. J. Henry, D. Xia,M. E.Wilke, J. Deisenhofer, and R. D. Gerard, Characterizationof the knob domain of the adenovirus type 5 fiber protein expressed inEscherichia coli, J. Virol. 68 (1994), 5239-5246.
132. M. Green and M. Pina, Biochemical studies on adenovirus multiplication, VI.properties of highly purified tumorigenic human adenoviruses and their DNA,Proc. Natl. Acad. Sci. USA 51 (1964), 1251-1259.
133. M.Albrechtsen and M. Heide, Purification of plant viruses and virus coat proteinsby high performance liquid chromatography, J.Virol. Methods 28 (1990), 245-256.
134. M. Njayou and G. Quash, Purification of measles virus by affinity chromatographyand by ultracentrifugation: A comparative study, J.Virol. Methods 32 (1991),67-77.
135. P. W. Shabram, D. D. Giroux, A. M. Goudreau, R. J. Gregory, M. T. Horn, B. G.Huyghe, X. Liu, M. H. Nunnally, B. J. Sugarman, and S. Sutjipto, Analytical anionexchangeHPLC of recombinant type-5 adenoviral particles, Hum. Gene Ther. 8(1997), 453-465.
136. G. Vellekamp, F.W. Porter, S. Sutjipto, C. Cutler, L. Bondoc, Y. H. Liu, D.Wylie,S. Cannon-Carlson, J. T. Tang, A. Frei, M. Voloch, and S. Zhuang, Empty capsidsin column-purified recombinant adenovirus preparations, Hum. Gene Ther. 12(2001), 1923-1936.
137. B. G. Huyghe, X. Liu,S. Sutjipto, B. J. Sugarman, M. T. Horn, H. M. Shepard, C. J.Scandella, and P. Shabram, Purification of a type 5 recombinant adenovirus encodinghuman p53 by column chromatography, Hum. Gene Ther. 6 (1995), 1403-1416.
138. Y. H. Liu, G.Vellekamp,G. Chen, U. A. Mirza, D.Wylie, B. Twarowska, J. T. Tang,F.W. Porter, S.Wang, T. L. Nagabhushan, and B. N. Pramanik, Proteomic study ofrecombinant adenovirus 5 encoding human p53 by matrix-assisted laser desorption/ionization mass spectrometry in combination with database search, Int. J.Mass Spectrom. 226 (2003), 55-69.
139. U. A. Mirza, Y. H. Liu, J. T. Tang, F. Porter, L. Bondoc, G. Chen, and B. N.Pramanik, Nagabhushan, Extraction and characterization of adenovirus proteinsfrom sodium dodecylsulfide polyacrylamide gel electrophoresis by matrix-assistedlaser desorption/ionization mass spectrometry, J. Am. Soc. Mass Spectrom. 11(2000), 356-361.
140. F. Blanche, B. Monegier, D. Faucher, M. Duchesne, F. Audhuy, A. Barbot,S. Bouvier, G. Daude, H. Dubois, T. Guillemin, and L. Maton, Polypeptide compositionof an adenovirus type 5 used in cancer gene therapy, J. Chromatogr. A.921 (2001), 39-48.