Applications of current proteomics techniques in modern drug design

Current Computer-Aided Drug Design

Volumn 6, Issue 3, 2010, Pages 147-164

  Zhang, Cheng Cheng ^a   Kast, Juergen ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

Drug design; Drug target discovery; Drug target interaction; Mass spectrometry; Post translational modifications; Protein interaction networks; Proteomics

Indexed keywords

CELL SIGNALING; CHEMICAL ANALYSIS; DATA HANDLING; DESIGN; DRUG INTERACTIONS; MASS SPECTROMETRY; MOLECULAR BIOLOGY;

DRUG ACTION; DRUG COMPOUNDS; DRUG DESIGN; DRUG TARGET DISCOVERY; DRUG TARGETS; DRUG-TARGET INTERACTIONS; POST-TRANSLATIONAL MODIFICATIONS; PROTEIN INTERACTION NETWORKS; PROTEOMIC TECHNIQUES; PROTEOMICS;

PROTEINS;

2,4 DIMETHYL 5 (2 OXO 1H INDOL 3 YLMETHYLENE) 3 PYRROLEPROPIONIC ACID; 4 (4 FLUOROPHENYL) 2 (4 METHYLSULFINYLPHENYL) 5 (4 PYRIDYL)IMIDAZOLE; BISINDOLYLMALEIMIDE; BOSUTINIB; DASATINIB; GEFITINIB; IMATINIB; PYRIDO[2,3 D]PYRIMIDINE DERIVATIVE; STABLE ISOTOPE; TITANIUM DIOXIDE; LIGAND;

ACTIVITY BASED PROBE PROFILING; AFFINITY PURIFICATION MASS SPECTROMETRY; ARTICLE; CHEMICAL PHENOMENA; CHEMICAL REACTION; COLLISIONALLY ACTIVATED DISSOCIATION; COMPOUND CENTRIC CHEMICAL PROTEOMICS; DIFFERENTIAL IN GEL ELECTROPHORESIS; DRUG DESIGN; DRUG TARGETING; GEL ELECTROPHORESIS; IMMOBILIZED METAL AFFINITY CHROMATOGRAPHY; IMMUNOPRECIPITATION; ISOTOPE TAGS FOR RELATIVE AND ABSOLUTE QUANTIFICATION; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FRAGMENT COMPLEMENTATION ASSAY; PROTEIN INTERACTION; PROTEIN PHOSPHORYLATION; PROTEOMICS; SIGNAL TRANSDUCTION; STRONG CATION EXCHANGE; TANDEM MASS SPECTROMETRY; TWO DIMENSIONAL GEL ELECTROPHORESIS; TWO DIMENSIONAL POLYACRYLAMIDE GEL ELECTROPHORESIS; ANIMAL; COMPUTER AIDED DESIGN; COMPUTER SIMULATION; DRUG EFFECT; GENE EXPRESSION REGULATION; HUMAN; METHODOLOGY; PROTEIN DOMAIN; REVIEW;

ANIMALS; COMPUTER SIMULATION; COMPUTER-AIDED DESIGN; DRUG DESIGN; GENE EXPRESSION REGULATION; HUMANS; LIGANDS; MASS SPECTROMETRY; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN INTERACTION MAPPING; PROTEOMICS; SIGNAL TRANSDUCTION;

EID: 78049521236     PISSN: 15734099     EISSN: None     Source Type: Journal    
DOI: 10.2174/157340910791760064     Document Type: Article

References (202)

1. Landry, Y.; Gies, J.P. Drugs and their molecular targets: an updated overview. Fundam. Clin. Pharmacol., 2008, 22, 1-18.
2. Overington, J.P.; Al-Lazikani, B.; Hopkins, A.L. How many drug targets are there? Nat. Rev. Drug Discov., 2006, 5, 993-996.
3. Liebler, D.C.; Guengerich, F.P. Elucidating mechanisms of drug induced toxicity. Nat. Rev. Drug Discov., 2005, 4, 410-420.
4. Anderson, N.L.; Anderson, N.G. Proteome and proteomics: new technologies, new concepts, and new words. Electrophoresis, 1998, 19, 1853-1861.
5. Blackstock, W.P.; Weir, M.P. Proteomics: quantitative and physical mapping of cellular proteins. Trends Biotechnol., 1999, 17, 121-127.
6. Cravatt, B.F.; Simon, G.M.; Yates, J.R. The biological impact of mass-spectrometry-based proteomics. Nature, 2007, 450, 991-1000.
7. Song, C.M.; Lim, S.J.; Tong, J.C. Recent advances in computeraided drug design. Brief. Bioinform., 2009, 10, 579-591.
8. Taft, C.A.; Da Silva, V.B.; Da Silva, C.H. Current topics in computer-aided drug design. J. Pharm. Sci., 2008, 97, 1089-1098.
9. Cohen, P. The regulation of protein function by multisite phosphorylation-a 25 year update. Trends Biochem. Sci., 2000, 25, 596-601.
10. Pawson, T.; Scott, J.D. Protein phosphorylation in signaling-50 years and counting. Trends Biochem. Sci., 2005, 30, 286-290.
11. Domon, B.; Aebersold, R. Mass spectrometry and protein analysis. Science, 2006, 312, 212-217.
12. Hager, J.W. A new linear ion trap mass spectrometer. Rapid Commun. Mass Spectrom., 2002, 16, 512-540.
13. Lange, V.; Picotti, P.; Domon, B.; Aebersold, R. Selected reaction monitoring for quantitative proteomics: a tutorial. Mol. Syst. Biol., 2008, 4, 222.
14. Marshall, A.G.; Hendrickson, C.L.; Jackson, G.S. Fourier transform ion cyclotron resonance mass spectrometry: a primer. Mass Spectrom. Rev., 1998, 17, 1-35.
15. Senko, M.W.; Hendrickson, C.L.; Emmett, M.R.; Shi, S.D.H.; Marshall, A.G. External accumulation of ions for enhanced electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. J. Am. Soc. Mass. Spectrom., 1997, 8, 970-976.
16. Hardman, M.; Makarov, A.A. Interfacing the orbitrap mass analyzer to an electrospray ion source. Anal. Chem., 2003, 75, 1699-1705.
17. Hu, Q.; Noll, R.J.; Li, H.; Makarov, A.; Hardman, M.; Graham Cooks, R. The Orbitrap: a new mass spectrometer. J. Mass Spectrom., 2005, 40, 430-443.
18. Aebersold, R.; Mann, M. Mass spectrometry-based proteomics. Nature, 2003, 422, 198-207.
19. Fenn, J.B.; Mann, M.; Meng, C.K.; Wong, S.F.; Whitehouse, C.M. Electrospray ionization for mass spectrometry of large biomolecules. Science, 1989, 246, 64-71.
20. Karas, M.; Hillenkamp, F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem., 1988, 60, 2299-2301.
21. Steen, H.; Mann, M. The ABC's (and XYZ's) of peptide sequencing. Nat. Rev. Mol. Cell Biol., 2004, 5, 699-711.
22. Wells, J.M.; McLuckey, S.A. Collision-induced dissociation (CID) of peptides and proteins. Methods Enzymol., 2005, 402, 148-185.
23. McLafferty, F. W.; Horn, D.M.; Breuker, K.; Ge, Y.; Lewis, M.A.; Cerda, B.; Zubarev, R.A.; Carpenter, B.K. Electron capture dissociation of gaseous multiply charged ions by Fourier-transform ion cyclotron resonance. J. Am. Soc. Mass. Spectrom., 2001, 12, 245-249.
24. Syka, J.E.P.; Coon, J.J.; Schroeder, M.J.; Shabanowitz, J.; Hunt, D.F. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. USA, 2004, 101, 9528-9533.
25. Mikesh, L.M.; Ueberheide, B.; Chi, A.; Coon, J.J.; Syka, J.E.P.; Shabanowitz, J.; Hunt, D.F. The utility of ETD mass spectrometry in proteomic analysis. Biochim. Biophys. Acta., 2006, 1764, 1811-1822.
26. Eng, J.K.; McCormack, A.L.; Yates, J.R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass. Spectrom., 1994, 5, 976-989.
27. Perkins, D.N.; Pappin, D.J.C.; Creasy, D.M.; Cottrell, J.S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis, 1999, 20, 3551-3567.
28. Clauser, K.R.; Baker, P.; Burlingame, A.L. Role of accurate mass measurement (+/10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal. Chem., 1999, 71, 2871-2882.
29. Craig, R.; Beavis, R.C. TANDEM: matching proteins with tandem mass spectra. Bioinformatics, 2004, 20, 1466-1467.
30. Geer, L.Y.; Markey, S.P.; Kowalak, J.A.; Wagner, L.; Xu, M.; Maynard, D.M.; Yang, X.; Shi, W.; Bryant, S.H. Open mass spectrometry search algorithm. J. Proteome Res., 2004, 3, 958-964.
31. Nesvizhskii, A.I.; Vitek, O.; Aebersold, R. Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat. Methods, 2007, 4, 787-797.
32. Sze, S.K.; Ge, Y.; Oh, H.B.; McLafferty, F.W. Top-down mass spectrometry of a 29-kDa protein for characterization of any posttranslational modification to within one residue. Proc. Natl. Acad. Sci. USA, 2002, 99, 1774-1779.
33. Han, X.; Jin, M.; Breuker, K.; McLafferty, F.W. Extending topdown mass spectrometry to proteins with masses greater than 200 kilodaltons. Science, 2006, 314, 109-112.
34. Chait, B.T. Mass Spectrometry: Bottom-Up or Top-Down? Science, 2006, 314, 65-66.
35. Siuti, N.; Kelleher, N.L. Decoding protein modifications using topdown mass spectrometry. Nat. Methods, 2007, 4, 817-821.
36. 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.
37. Ong, S.E.; Mann, M. Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol., 2005, 1, 252-262.
38. Ishihama, Y.; Oda, Y.; Tabata, T.; Sato, T.; Nagasu, T.; Rappsilber, J.; Mann, M. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol. Cell Proteomics, 2005, 4, 1265-1272.
39. Rappsilber, J.; Ryder, U.; Lamond, A.I.; Mann, M. Large-scale proteomic analysis of the human spliceosome. Genome Res., 2002, 12, 1231-1245.
40. Ong, S.E.; Blagoev, B.; Kratchmarova, I.; Kristensen, D.B.; Steen, H.; Pandey, A.; Mann, M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell Proteomics, 2002, 1, 376-386.
41. Gruhler, A.; Olsen, J.V.; Mohammed, S.; Mortensen, P.; Faergeman, N.J.; Mann, M.; Jensen, O.N. Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol. Cell Proteomics, 2005, 4, 310-327.
42. Mann, M. Functional and quantitative proteomics using SILAC. Nat. Rev. Mol. Cell Biol., 2006, 7, 952-958.
43. Olsen, J.V.; Blagoev, B.; Gnad, F.; Macek, B.; Kumar, C.; Mortensen, P.; Mann, M. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell, 2006, 127, 635-648.
44. Park, K.S.; Mohapatra, D.P.; Misonou, H.; Trimmer, J.S. Graded regulation of the Kv2. 1 potassium channel by variable phosphorylation. Science, 2006, 313, 976-979.
45. Blagoev, B.; Ong, S.E.; Kratchmarova, I.; Mann, M. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat. Biotechnol., 2004, 22, 1139-1145.
46. Hinsby, A.M.; Olsen, J.V.; Mann, M. Tyrosine phosphoproteomics of fibroblast growth factor signaling: a role for insulin receptor substrate-4. J. Biol. Chem., 2004, 279, 46438-46447.
47. Harsha, H.C.; Molina, H.; Pandey, A. Quantitative proteomics using stable isotope labeling with amino acids in cell culture. Nat. Protoc., 2008, 3, 505-516.
48. Krüger, M.; Moser, M.; Ussar, S.; Thievessen, I.; Luber, C.A.; Forner, F.; Schmidt, S.; Zanivan, S.; F ssler, R.; Mann, M. SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell, 2008, 134, 353-364.
49. Julka, S.; Regnier, F. Quantification in proteomics through stable isotope coding: a review. J. Proteome Res., 2004, 3, 350-363.
50. Gygi, S.P.; Rist, B.; Gerber, S.A.; Turecek, F.; Gelb, M.H.; Aebersold, R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol., 1999, 17, 994-999.
51. 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.
52. Schulze, W.X.; Mann, M. A novel proteomic screen for peptideprotein interactions. J. Biol. Chem., 2004, 279, 10756-10764.
53. Han, D.K.; Eng, J.; Zhou, H.; Aebersold, R. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol., 2001, 19, 946-951.
54. Cox, J.; Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteomewide protein quantification. Nat. Biotechnol., 2008, 26, 1367-1372.
55. MacCoss, M.J.; Wu, C.C.; Liu, H.; Sadygov, R.; Yates, J.R. A correlation algorithm for the automated quantitative analysis of shotgun proteomics data. Anal. Chem., 2003, 75, 6912-6921.
56. Keller, A.; Eng, J.; Zhang, N.; Li, X.; Aebersold, R. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst. Biol., 2005, 1, 2005.0017.
57. Lin, W.T.; Hung, W.N.; Yian, Y.H.; Wu, K.P.; Han, C.L.; Chen, Y.R.; Chen, Y.J.; Sung, T.Y.; Hsu, W.L. Multi-Q: a fully automated tool for multiplexed protein quantitation. J. Proteome Res., 2006, 5, 2328-2338.
58. Shadforth, I.P.; Dunkley, T.P.J.; Lilley, K.S.; Bessant, C. i-Tracker: For quantitative proteomics using iTRAQ. BMC Genomics, 2005, 6, 145.
59. Sleno, L.; Emili, A. Proteomic methods for drug target discovery. Curr. Opin. Chem. Biol., 2008, 12, 46-54.
60. Veenstra, T.D. Proteomic approaches in drug discovery. Drug Discov. Today: Technol., 2006, 3, 433-440.
61. Conrads, T.P.; Hood, B.L.; Veenstra, T.D. Sampling and analytical strategies for biomarker discovery using mass spectrometry. BioTechniques, 2006, 40, 799-805.
62. Carrette, O.; Burkhard, P.R.; Sanchez, J.C.; Hochstrasser, D.F. State-of-the-art two-dimensional gel electrophoresis: a key tool of proteomics research. Nat. Protoc., 2006, 1, 812-823.
63. Pietrogrande, M.C.; Marchetti, N.; Dondi, F.; Righetti, P.G. Decoding 2D-PAGE complex maps: Relevance to proteomics. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci., 2006, 833, 51-62.
64. Campostrini, N.; Areces, L.B.; Rappsilber, J.; Pietrogrande, M.C.; Dondi, F.; Pastorino, F.; Ponzoni, M.; Righetti, P.G. Spot overlapping in two-dimensional maps: a serious problem ignored for much too long. Proteomics, 2004, 5, 2385-2395.
65. Pietrogrande, M.C.; Marchetti, N.; Tosi, A.; Dondi, F.; Righetti, P.G. Decoding two-dimensional polyacrylamide gel electrophoresis complex maps by autocovariance function: a simplified approach useful for proteomics. Electrophoresis, 2005, 26, 2739-2748.
66. Alban, A.; David, S.O.; Bjorkesten, L.; Andersson, C.; Sloge, E.; Lewis, S.; Currie, I. A novel experimental design for comparative two-dimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics, 2003, 3, 36-44.
67. Kanamoto, T.; Hellman, U.; Heldin, C.H.; Souchelnytskyi, S. Functional proteomics of transforming growth factor 1-stimulated Mv1Lu epithelial cells: Rad51 as a target of TGF 1-dependent regulation of DNA repair. EMBO J., 2002, 21, 1219-1230.
68. Imamura, T.; Kanai, F.; Kawakami, T.; Amarsanaa, J.; Ijichi, H.; Hoshida, Y.; Tanaka, Y.; Ikenoue, T.; Tateishi, K.; Kawabe, T.; Arakawa, Y.; Miyagishi, M.; Taira, K.; Yokosuka, O.; Omata, M. Proteomic analysis of the TGF-beta signaling pathway in pancreatic carcinoma cells using stable RNA interference to silence Smad4 expression. Biochem. Biophys. Res. Commun., 2004, 318, 289-296.
69. Holly, M.K.; Dear, J.W.; Hu, X.; Schechter, A.N.; Gladwin, M.T.; Hewitt, S.M.; Yuen, P.S.T.; Star, R.A. Biomarker and drug target discovery using proteomics in a new rat model of sepsis-induced acute renal failure. Kidney Int., 2006, 70, 496-506.
70. Dear, J.W.; Leelahavanichkul, A.; Aponte, A.; Hu, X.; Constant, S.L.; Hewitt, S.M.; Yuen, P.S.T.; Star, R.A. Liver proteomics for therapeutic drug discovery: inhibition of the cyclophilin receptor CD147 attenuates sepsis-induced acute renal failure. Crit. Care Med., 2007, 35, 2319-2328.
71. Boyd, R.S.; Adam, P.J.; Patel, S.; Loader, J.A.; Berry, J.; Redpath, N.T.; Poyser, H.R.; Fletcher, G.C.; Burgess, N.A.; Stamps, A.C.; Hudson, L.; Smith, P.; Griffiths, M.; Willis, T.G.; Karran, E.L.; Oscier, D.G.; Catovsky, D.; Terrett, J.A.; Dyer, M.J. Proteomic analysis of the cell-surface membrane in chronic lymphocytic leukemia: identification of two novel proteins, BCNP1 and MIG2B. Leukemia, 2003, 17, 1605-1612.
72. Schubert, P.; Thon, J.N.; Walsh, G.M.; Chen, C.H.I.; Moore, E.D.; Devine, D.V.; Kast, J. A signaling pathway contributing to platelet storage lesion development: targeting PI3-kinase-dependent Rap1 activation slows storage-induced platelet deterioration. Transfusion, 2009, 49, 1944-1955.
73. Lamb, J.; Crawford, E.D.; Peck, D.; Modell, J.W.; Blat, I.C.; Wrobel, M.J.; Lerner, J.; Brunet, J. P.; Subramanian, A.; Ross, K.N.; Reich, M.; Hieronymus, H.; Wei, G.; Armstrong, S.A.; Haggarty, S.J.; Clemons, P.A.; Wei, R.; Carr, S.A.; Lander, E.S.; Golub, T.R. The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science, 2006, 313, 1929-1935.
74. Becker, F.; Murthi, K.; Smith, C.; Come, J.; Costa-Roldán, N.; Kaufmann, C.; Hanke, U.; Degenhart, C.; Baumann, S.; Wallner, W.; Huber, A.; Dedier, S.; Dill, S.; Kinsman, D.; Hediger, M.; Bockovich, N.; Meier-Ewert, S.; Kluge, A.F.; Kley, N. A threehybrid approach to scanning the proteome for targets of small molecule kinase inhibitors. Chem. Biol., 2004, 11, 211-223.
75. Caligiuri, M.; Molz, L.; Liu, Q.; Kaplan, F.; Xu, J.P.; Majeti, J.Z.; Ramos-Kelsey, R.; Murthi, K.; Lievens, S.; Tavernier, J.; Kley, N. MASPIT: three-hybrid trap for quantitative proteome fingerprinting of small molecule-protein interactions in mammalian cells. Chem. Biol., 2006, 13, 711-722.
76. Hillenmeyer, M.E.; Fung, E.; Wildenhain, J.; Pierce, S.E.; Hoon, S.; Lee, W.; Proctor, M.; St Onge, R.P.; Tyers, M.; Koller, D.; Altman, R.B.; Davis, R.W.; Nislow, C.; Giaever, G. The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science, 2008, 320, 362-365.
77. Zon, L.I.; Peterson, R.T. In vivo drug discovery in the zebrafish. Nat. Rev. Drug Discov., 2005, 4, 35-44.
78. Rix, U.; Superti-Furga, G. Target profiling of small molecules by chemical proteomics. Nat. Chem. Biol., 2009, 5, 616-624.
79. Bantscheff, M.; Scholten, A.; Heck, A.J. Revealing promiscuous drug-target interactions by chemical proteomics. Drug Discov. Today, 2009, 14, 1021-1029.
80. Barglow, K.T.; Cravatt, B.F. Activity-based protein profiling for the functional annotation of enzymes. Nat. Methods, 2007, 4, 822-827.
81. Hagenstein, M.C.; Mussgnug, J.H.; Lotte, K.; Plessow, R.; Brockhinke, A.; Kruse, O.; Sewald, N. Affinity-based tagging of protein families with reversible inhibitors: a concept for functional proteomics. Angew. Chem. Int. Ed., 2003, 42, 5635-5638.
82. Ge, X.; Sem, D.S. Affinity-based chemical proteomic probe for dehydrogenases: Fluorescence and visible binding assays in gels. Anal. Biochem., 2007, 370, 171-179.
83. Sadaghiani, A.M.; Verhelst, S.H.L.; Bogyo, M. Tagging and detection strategies for activity-based proteomics. Curr. Opin. Chem. Biol., 2007, 11, 20-28.
84. Hagenstein, M.C.; Sewald, N. Chemical tools for activity-based proteomics. J. Biotechnol., 2006, 124, 56-73.
85. Doucet, A.; Butler, G.S.; Rodriguez, D.; Prudova, A.; Overall, C.M. Metadegradomics: toward in vivo quantitative degradomics of proteolytic post-translational modifications of the cancer proteome. Mol. Cell Proteomics, 2008, 7, 1925-1951.
86. Brehmer, D.; Godl, K.; Zech, B.; Wissing, J.; Daub, H. Proteomewide identification of cellular targets affected by bisindolylmaleimide-type protein kinase C inhibitors. Mol. Cell Proteomics, 2004, 3, 490-500.
87. Bach, S.; Knockaert, M.; Reinhardt, J.; Lozach, O.; Schmitt, S.; Baratte, B.; Koken, M.; Coburn, S.P.; Tang, L.; Jiang, T.; Liang, D.C.; Galons, H.; Dierick, J.F.; Pinna, L.A.; Meggio, F.; Totzke, F.; Schächtele, C.; Lerman, A.S.; Carnero, A.; Wan, Y.; Gray, N.; Meijer, L. Roscovitine targets, protein kinases and pyridoxal kinase. J. Biol. Chem., 2005, 280, 31208-31219.
88. Rix, U.; Hantschel, O.; Dürnberger, G.; Remsing Rix, L.L.; Planyavsky, M.; Fernbach, N.V.; Kaupe, I.; Bennett, K.L.; Valent, P.; Colinge, J.; Köcher, T.; Superti-Furga, G. Chemical proteomic profiles of the BCR-ABL inhibitors imatinib, nilotinib, and dasatinib reveal novel kinase and nonkinase targets. Blood, 2007, 110, 4055-4063.
89. Godl, K.; Wissing, J.; Kurtenbach, A.; Habenberger, P.; Blencke, S.; Gutbrod, H.; Salassidis, K.; Stein-Gerlach, M.; Missio, A.; Cotten, M.; Daub, H. An efficient proteomics method to identify the cellular targets of protein kinase inhibitors. Proc. Natl. Acad. Sci. USA, 2003, 100, 15434-15439.
90. Wissing, J.; Godl, K.; Brehmer, D.; Blencke, S.; Weber, M.; Habenberger, P.; Stein-Gerlach, M.; Missio, A.; Cotten, M.; Müller, S.; Daub, H. Chemical proteomic analysis reveals alternative modes of action for pyrido[2,3-d]pyrimidine kinase inhibitors. Mol. Cell Proteomics, 2004, 3, 1181-1193.
91. Godl, K.; Gruss, O.J.; Eickhoff, J.; Wissing, J.; Blencke, S.; Weber, M.; Degen, H.; Brehmer, D.; Orfi, L.; Horváth, Z.; Kéri, G.; Müller, S.; Cotten, M.; Ullrich, A.; Daub, H. Proteomic characterization of the angiogenesis inhibitor SU6668 reveals multiple impacts on cellular kinase signaling. Cancer Res., 2005, 65, 6919-6926.
92. Brehmer, D.; Greff, Z.; Godl, K.; Blencke, S.; Kurtenbach, A.; Weber, M.; Müller, S.; Klebl, B.; Cotten, M.; Kéri, G.; Wissing, J.; Daub, H. Cellular targets of gefitinib. Cancer Res., 2005, 65, 379-382.
93. Zhang, J.; Yang, P.L.; Gray, N.S. Targeting cancer with small molecule kinase inhibitors. Nat. Rev. Cancer, 2009, 9, 28-39.
94. Ghoreschi, K.; Laurence, A.; O'Shea, J.J. Selectivity and therapeutic inhibition of kinases: to be or not to be? Nat. Immunol., 2009, 10, 356-360.
95. Bain, J.; Plater, L.; Elliott, M.; Shpiro, N.; Hastie, C.J.; McLauchlan, H.; Klevernic, I.; Arthur, J.S.C.; Alessi, D.R.; Cohen, P. The selectivity of protein kinase inhibitors: a further update. Biochem. J., 2007, 408, 297-315.
96. Bantscheff, M.; Eberhard, D.; Abraham, Y.; Bastuck, S.; Boesche, M.; Hobson, S.; Mathieson, T.; Perrin, J.; Raida, M.; Rau, C.; Reader, V.; Sweetman, G.; Bauer, A.; Bouwmeester, T.; Hopf, C.; Kruse, U.; Neubauer, G.; Ramsden, N.; Rick, J.; Kuster, B.; Drewes, G. Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat. Biotechnol., 2007, 25, 1035-1044.
97. Daub, H.; Olsen, J.V.; Bairlein, M.; Gnad, F.; Oppermann, F.S.; Krner, R.; Greff, Z.; Kéri, G.; Stemmann, O.; Mann, M. Kinaseselective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle. Mol. Cell., 2008, 31, 438-448.
98. Ong, S.E.; Schenone, M.; Margolin, A.A.; Li, X.; Do, K.; Doud, M.K.; Mani, D.R.; Kuai, L.; Wang, X.; Wood, J.L.; Tolliday, N.J.; Koehler, A.N.; Marcaurelle, L.A.; Golub, T.R.; Gould, R.J.; Schreiber, S.L.; Carr, S.A. Identifying the proteins to which smallmolecule probes and drugs bind in cells. Proc. Natl. Acad. Sci. USA, 2009, 106, 4617-4622.
99. Jensen, O.N. Interpreting the protein language using proteomics. Nat. Rev. Mol. Cell Biol., 2006, 7, 391-403.
100. Macek, B.; Mann, M.; Olsen, J.V. Global and site-specific quantitative phosphoproteomics: principles and applications. Annu. Rev. Pharmacol. Toxicol., 2009, 49, 199-221.
101. Collins, M.O.; Yu, L.; Choudhary, J.S. Analysis of protein phosphorylation on a proteome-scale. Proteomics, 2007, 7, 2751-2768.
102. Wilson, N.L.; Schulz, B.L.; Karlsson, N.G.; Packer, N.H. Sequential analysis of N-and O-linked glycosylation of 2D-PAGE separated glycoproteins. J. Proteome Res., 2002, 1, 521-529.
103. Harvey, D.J. Proteomic analysis of glycosylation: structural determination of N-and O-linked glycans by mass spectrometry. Exp. Rev. Proteomics, 2005, 2, 87-101.
104. Abbosh, P.H.; Montgomery, J.S.; Starkey, J.A.; Novotny, M.; Zuhowski, E.G.; Egorin, M.J.; Moseman, A.P.; Golas, A.; Brannon, K.M.; Balch, C.; Huang, T.H.; Nephew, K.P. Dominant-negative histone H3 lysine 27 mutant derepresses silenced tumor suppressor genes and reverses the drug-resistant phenotype in cancer cells. Cancer Res., 2006, 66, 5582-5591.
105. Farzan, M.; Mirzabekov, T.; Kolchinsky, P.; Wyatt, R.; Cayabyab, M.; Gerard, N.P.; Gerard, C.; Sodroski, J.; Choe, H. Tyrosine sulfation of the amino terminus of CCR5 facilitates HIV-1 entry. Cell, 1999, 96, 667-676.
106. Hunter, T. Protein kinases and phosphatases: the yin and yang of protein phosphorylation and signaling. Cell, 1995, 80, 225-236.
107. Schlessinger, J. Cell signaling by receptor tyrosine kinases. Cell, 2000, 103, 211-225.
108. Cohen, P. Protein kinases-the major drug targets of the twenty first century? Nat. Rev. Drug Discov., 2002, 1, 309-315.
109. Deininger, M.W.; Druker, B.J. Specific targeted therapy of chronic myelogenous leukemia with imatinib. Pharmacol. Rev., 2003, 55, 401-423.
110. Salomon, A.R.; Ficarro, S.B.; Brill, L.M.; Brinker, A.; Phung, Q.T.; Ericson, C.; Sauer, K.; Brock, A.; Horn, D.M.; Schultz, P.G.; Peters, E.C. Profiling of tyrosine phosphorylation pathways in human cells using mass spectrometry. Proc. Natl. Acad. Sci. USA, 2003, 100, 443-448.
111. Rush, J.; Moritz, A.; Lee, K.A.; Guo, A.; Goss, V.L.; Spek, E.J.; Zhang, H.; Zha, X.M.; Polakiewicz, R.D.; Comb, M.J. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nat. Biotechnol., 2005, 23, 94-101.
112. Rikova, K.; Guo, A.; Zeng, Q.; Possemato, A.; Yu, J.; Haack, H.; Nardone, J.; Lee, K.; Reeves, C.; Li, Y.; Hu, Y.; Tan, Z.; Stokes, M.; Sullivan, L.; Mitchell, J.; Wetzel, R.; Macneill, J.; Ren, J.M.; Yuan, J.; Bakalarski, C.E.; Villen, J.; Kornhauser, J.M.; Smith, B.; Li, D.; Zhou, X.; Gygi, S.P.; Gu, T.L.; Polakiewicz, R.D.; Rush, J.; Comb, M.J. Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell, 2007, 131, 1190-1203.
113. Gronborg, M.; Kristiansen, T.Z.; Stensballe, A.; Andersen, J.S.; Ohara, O.; Mann, M.; Jensen, O.N.; Pandey, A. A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies: identification of a novel protein, Frigg, as a protein kinase A substrate. Mol. Cell Proteomics, 2002, 1, 517-527.
114. Posewitz, M.C.; Tempst, P. Immobilized gallium (III) affinity chromatography of phosphopeptides. Anal. Chem., 1999, 71, 2883-2892.
115. Stensballe, A.; Andersen, S.; Jensen, O.N. Characterization of phosphoproteins from electrophoretic gels by nanoscale Fe (III) affinity chromatography with off-line mass spectrometry analysis. Proteomics, 2001, 1, 207-222.
116. Ficarro, S.B.; McCleland, M.L.; Stukenberg, P.T.; Burke, D.J.; Ross, M.M.; Shabanowitz, J.; Hunt, D.F.; White, F.M. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol., 2002, 20, 301-305.
117. Nuhse, T.S.; Stensballe, A.; Jensen, O.N.; Peck, S.C. Large-scale analysis of in vivo phosphorylated membrane proteins by immobilized metal ion affinity chromatography and mass spectrometry. Mol. Cell Proteomics, 2003, 2, 1234-1243.
118. Zhang, Y.; Wolf-Yadlin, A.; Ross, P.L.; Pappin, D.J.; Rush, J.; Lauffenburger, D.A.; White, F.M. Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules. Mol. Cell Proteomics, 2005, 4, 1240-1250.
119. Collins, M.O.; Yu, L.; Coba, M.P.; Husi, H.; Campuzano, I.; Blackstock, W.P.; Choudhary, J.S.; Grant, S.G. Proteomic analysis of in vivo phosphorylated synaptic proteins. J. Biol. Chem., 2004, 280, 5972-5982.
120. Larsen, M.R.; Thingholm, T.E.; Jensen, O.N.; Roepstorff, P.; Jørgensen, T.J. Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol. Cell Proteomics, 2005, 4, 873-886.
121. Pinkse, M.W.H.; Uitto, P.M.; Hilhorst, M.J.; Ooms, B.; Heck, A.J.R. Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI MS/MS and titanium oxide precolumns. Anal. Chem., 2004, 76, 3935-3943.
122. Beausoleil, S.A.; Jedrychowski, M.; Schwartz, D.; Elias, J.E.; Villén, J.; Li, J.; Cohn, M.A.; Cantley, L.C.; Gygi, S.P. Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc. Natl. Acad. Sci. USA, 2004, 101, 12130-12135.
123. Villén, J.; Beausoleil, S.A.; Gerber, S.A.; Gygi, S.P. Large-scale phosphorylation analysis of mouse liver. Proc. Natl. Acad. Sci. USA, 2007, 104, 1488-1493.
124. Chi, A.; Huttenhower, C.; Geer, L.Y.; Coon, J.J.; Syka, J.E.P.; Bai, D.L.; Shabanowitz, J.; Burke, D.J.; Troyanskaya, O.G.; Hunt, D.F. Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc. Natl. Acad. Sci. USA, 2007, 104, 2193-2198.
125. Zubarev, R.A.; Horn, D.M.; Fridriksson, E.K.; Kelleher, N.L.; Kruger, N.A.; Lewis, M.A.; Carpenter, B.K.; McLafferty, F.W. Electron capture dissociation for structural characterization of multiply charged protein cations. Anal. Chem., 2000, 72, 563-573.
126. Stensballe, A.; Jensen, O.N.; Olsen, J.V.; Haselmann, K.F.; Zubarev, R.A. Electron capture dissociation of singly and multiply phosphorylated peptides. Rapid Commun. Mass Spectrom., 2000, 14, 1793-1800.
127. Good, D.M.; Wirtala, M.; McAlister, G.C.; Coon, J.J. Performance characteristics of electron transfer dissociation mass spectrometry. Mol. Cell Proteomics, 2007, 6, 1942-1951.
128. Guo, A.; Villén, J.; Kornhauser, J.; Lee, K.A.; Stokes, M.P.; Rikova, K.; Possemato, A.; Nardone, J.; Innocenti, G.; Wetzel, R.; Wang, Y.; MacNeill, J.; Mitchell, J.; Gygi, S.P.; Rush, J.; Polakiewicz, R.D.; Comb, M.J. Signaling networks assembled by oncogenic EGFR and c-Met. Proc. Natl. Acad. Sci. USA, 2008, 105, 692-697.
129. Bose, R.; Molina, H.; Patterson, A.S.; Bitok, J.K.; Periaswamy, B.; Bader, J.S.; Pandey, A.; Cole, P.A. Phosphoproteomic analysis of Her2/neu signaling and inhibition. Proc. Natl. Acad. Sci. USA, 2006, 103, 9773-9778.
130. Calderwood, M.A.; Venkatesan, K.; Xing, L.; Chase, M.R.; Vazquez, A.; Holthaus, A.M.; Ewence, A.E.; Li, N.; Hirozane Kishikawa, T.; Hill, D.E.; Vidal, M.; Kieff, E.; Johannsen, E. Epstein-Barr virus and virus human protein interaction maps. Proc. Natl. Acad. Sci. USA, 2007, 104, 7606-7611.
131. Limviphuvadh, V.; Tanaka, S.; Goto, S.; Ueda, K.; Kanehisa, M. The commonality of protein interaction networks determined in neurodegenerative disorders (NDDs). Bioinformatics, 2007, 23, 2129-2138.
132. Lim, J.; Hao, T.; Shaw, C.; Patel, A.J.; Szabó, G.; Rual, J.F.; Fisk, C.J.; Li, N.; Smolyar, A.; Hill, D.E.; Barabási, A.L.; Vidal, M.; Zoghbi, H.Y. A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell, 2006, 125, 801-814.
133. Uetz, P.; Dong, Y.A.; Zeretzke, C.; Atzler, C.; Baiker, A.; Berger, B.; Rajagopala, S.V.; Roupelieva, M.; Rose, D.; Fossum, E.; Haas, J. Herpesviral protein networks and their interaction with the human proteome. Science, 2006, 311, 239-242.
134. Schadt, E.E.; Friend, S.H.; Shaywitz, D.A. A network view of disease and compound screening. Nat. Rev. Drug Discov., 2009, 8, 286-295.
135. Köcher, T.; Superti-Furga, G. Mass spectrometry-based functional proteomics: from molecular machines to protein networks. Nat. Methods, 2007, 4, 807-815.
136. Ideker, T.; Sharan, R. Protein networks in disease. Genome. Res., 2008, 18, 644-652.
137. Figeys, D. Mapping the human protein interactome. Cell Res., 2008, 18, 716-724.
138. Kast, J. Making connections for life: an in vivo map of the yeast interactome. HFSP J., 2008, 2, 244-250.
139. Fields, S.; Song, O. A novel genetic system to detect protein protein interactions. Nature, 1989, 340, 245-246.
140. von Mering, C.; Krause, R.; Snel, B.; Cornell, M.; Oliver, S.G.; Fields, S.; Bork, P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature, 2002, 417, 399-403.
141. Cai, Y.D.; Chou, K.C. Predicting 22 protein localizations in budding yeast. Biochem. Biophys. Res. Commun., 2004, 323, 425-428.
142. Chou, K.C.; Cai, Y.D. Predicting protein localization in budding yeast. Bioinformatics, 2005, 21, 944-950.
143. Chou, K.C.; Shen, H.B. Euk-mPLoc: a fusion classifier for largescale eukaryotic protein subcellular location prediction by incorporating multiple sites. J. Proteome Res., 2007, 6, 1728-1734.
144. Suter, B.; Kittanakom, S.; Stagljar, I. Two-hybrid technologies in proteomics research. Curr. Opin. Biotechnol., 2008, 19, 316-323.
145. Vidal, M.; Brachmann, R.K.; Fattaey, A.; Harlow, E.; Boeke, J.D. Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions. Proc. Natl. Acad. Sci. USA, 1996, 93, 10315-10320.
146. Hirst, M.; Ho, C.; Sabourin, L.; Rudnicki, M.; Penn, L.; Sadowski, I. A two-hybrid system for transactivator bait proteins. Proc. Natl. Acad. Sci. USA, 2001, 98, 8726-8731.
147. Licitra, E.J.; Liu, J.O. A three-hybrid system for detecting small ligand-protein receptor interactions. Proc. Natl. Acad. Sci. USA, 1996, 93, 12817-12821.
148. Eyckerman, S.; Verhee, A.; Van der Heyden, J.; Lemmens, I.; Van Ostade, X.; Vandekerckhove, J.; Tavernier, J. Design and application of a cytokine-receptor-based interaction trap. Nat. Cell Biol., 2001, 3, 1114-1119.
149. Pelletier, J.N.; Campbell-Valois, F.X.; Michnick, S.W. Oligomerization domain-directed reassembly of active dihydrofolate reductase from rationally designed fragments. Proc. Natl. Acad. Sci. USA, 1998, 95, 12141-12146.
150. Remy, I.; Michnick, S.W. Clonal selection and in vivo quantitation of protein interactions with protein-fragment complementation assays. Proc. Natl. Acad. Sci. USA, 1999, 96, 5394-5399.
151. Tarassov, K.; Messier, V.; Landry, C.R.; Radinovic, S.; Molina, M.M.S.; Shames, I.; Malitskaya, Y.; Vogel, J.; Bussey, H.; Michnick, S.W. An in vivo map of the yeast protein interactome. Science, 2008, 320, 1465-1470.
152. Michnick, S.W.; Remy, I.; Campbell-Valois, F.X.; Vallée-Bélisle, A.; Pelletier, J.N. Detection of protein-protein interactions by protein fragment complementation strategies. Methods Enzymol., 2000, 328, 208-230.
153. Galarneau, A.; Primeau, M.; Trudeau, L.E.; Michnick, S.W. Betalactamase protein fragment complementation assays as in vivo and in vitro sensors of protein-protein interactions. Nat. Biotechnol., 2002, 20, 619-622.
154. Wehrman, T.; Kleaveland, B.; Her, J.H.; Balint, R.F.; Blau, H.M. Protein-protein interactions monitored in mammalian cells via complementation of -lactamase enzyme fragments. Proc. Natl. Acad. Sci. USA, 2002, 99, 3469-3474.
155. Ghosh, I.; Hamilton, A.D.; Regan, L. Antiparallel leucine zipperdirected protein reassembly: application to the green fluorescent protein. J. Am. Chem. Soc., 2000, 122, 5658-5659.
156. Michnick, S.W.; Ear, P.H.; Manderson, E.N.; Remy, I.; Stefan, E. Universal strategies in research and drug discovery based on protein-fragment complementation assays. Nat. Rev. Drug Discov., 2007, 6, 569-582.
157. Gingras, A.C.; Gstaiger, M.; Raught, B.; Aebersold, R. Analysis of protein complexes using mass spectrometry. Nat. Rev. Mol. Cell Biol., 2007, 8, 645-654.
158. Puig, O.; Caspary, F.; Rigaut, G.; Rutz, B.; Bouveret, E.; Bragado Nilsson, E.; Wilm, M.; Séraphin, B. The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods, 2001, 24, 218-229.
159. Guerrero, C.; Tagwerker, C.; Kaiser, P.; Huang, L. An integrated mass spectrometry-based proteomic approach: quantitative analysis of tandem affinity-purified in vivo cross-linked protein complexes (QTAX) to decipher the 26 S proteasome-interacting network. Mol. Cell Proteomics, 2006, 5, 366-378.
160. Vasilescu, J.; Guo, X.; Kast, J. Identification of protein-protein interactions using in vivo cross-linking and mass spectrometry. Proteomics, 2004, 4, 3845-3854.
161. Sinz, A. Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions. Mass Spectrom. Rev., 2006, 25, 663-682.
162. Trakselis, M.A.; Alley, S.C.; Ishmaels, F.T. Identification and mapping of protein-protein interactions by a combination of crosslinking, cleavage, and proteomics. Bioconjug. Chem., 2005, 16, 741-750.
163. Rinner, O.; Seebacher, J.; Walzthoeni, T.; Mueller, L.; Beck, M.; Schmidt, A.; Mueller, M.; Aebersold, R. Identification of crosslinked peptides from large sequence databases. Nat. Methods, 2008, 5, 315-318.
164. Ihling, C.; Schmidt, A.; Kalkhof, S.; Schulz, D.M.; Stingl, C.; Mechtler, K.; Haack, M.; Beck-Sickinger, A.G.; Cooper, D.M.; Sinz, A. Isotope-labeled cross-linkers and Fourier transform ion cyclotron resonance mass spectrometry for structural analysis of a protein/peptide complex. J. Am. Soc. Mass. Spectrom., 2006, 17, 1100-1113.
165. Seebacher, J.; Mallick, P.; Zhang, N.; Eddes, J.S.; Aebersold, R.; Gelb, M.H. Protein cross-linking analysis using mass spectrometry, isotope-coded cross-linkers, and integrated computational data processing. J. Proteome Res., 2006, 5, 2270-2282.
166. Schmitt-Ulms, G.; Hansen, K.; Liu, J.; Cowdrey, C.; Yang, J.; DeArmond, S.J.; Cohen, F.E.; Prusiner, S.B.; Baldwin, M.A. Timecontrolled transcardiac perfusion cross-linking for the study of protein interactions in complex tissues. Nat. Biotechnol., 2004, 22, 724-731.
167. Sutherland, B.W.; Toews, J.; Kast, J. Utility of formaldehyde crosslinking and mass spectrometry in the study of protein-protein interactions. J. Mass Spectrom., 2008, 43, 699-715.
168. Huang, J.; Schreiber, S.L. A yeast genetic system for selecting small molecule inhibitors of protein-protein interactions in nanodroplets. Proc. Natl. Acad. Sci. USA, 1997, 94, 13396-13401.
169. Joshi, P.B.; Hirst, M.; Malcolm, T.; Parent, J.; Mitchell, D.; Lund, K.; Sadowski, I. Identification of protein interaction antagonists using the repressed transactivator two-hybrid system. Biotechniques, 2007, 42, 635-644.
170. Eyckerman, S.; Lemmens, I.; Catteeuw, D.; Verhee, A.; Vandekerckhove, J.; Lievens, S.; Tavernier, J. Reverse MAPPIT: screening for protein-protein interaction modifiers in mammalian cells. Nat. Methods, 2005, 2, 427-433.
171. Selbach, M.; Mann, M. Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK). Nat. Methods, 2006, 3, 981-983.
172. Chen, H.K.; Fernandez-Funez, P.; Acevedo, S.F.; Lam, Y.C.; Kaytor, M.D.; Fernandez, M.H.; Aitken, A.; Skoulakis, E.M.C.; Orr, H.T.; Botas, J.; Zoghbi, H.Y. Interaction of Aktphosphorylated ataxin-1 with 14-3-3 mediates neurodegeneration in spinocerebellar ataxia type 1. Cell, 2003, 113, 457-468.
173. Fernández, E.; Collins, M.O.; Uren, R.T.; Kopanitsa, M.V.; Komiyama, N.H.; Croning, M.D.R.; Zografos, L.; Armstrong, J.D.; Choudhary, J.S.; Grant, S.G. Targeted tandem affinity purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins. Mol. Syst. Biol., 2009, 5, 269.
174. Frias, M.A.; Thoreen, C.C.; Jaffe, J.D.; Schroder, W.; Sculley, T.; Carr, S.A.; Sabatini, D.M. mSin1 is necessary for Akt/PKB phosphorylation, and its isoforms define three distinct mTORC2s. Curr. Biol., 2006, 16, 1865-1870.
175. Jacinto, E.; Facchinetti, V.; Liu, D.; Soto, N.; Wei, S.; Jung, S.Y.; Huang, Q.; Qin, J.; Su, B. SIN1/MIP1 maintains rictor-mTOR complex integrity and regulates Akt phosphorylation and substrate specificity. Cell, 2006, 127, 125-137.
176. Wang, L.; Harris, T.E.; Roth, R.A.; Lawrence Jr, J.C. PRAS40 regulates mTORC1 kinase activity by functioning as a direct inhibitor of substrate binding. J. Biol. Chem., 2007, 282, 20036-20044.
177. Sancak, Y.; Thoreen, C.C.; Peterson, T.R.; Lindquist, R.A.; Kang, S.A.; Spooner, E.; Carr, S.A.; Sabatini, D.M. PRAS40 is an insulinregulated inhibitor of the mTORC1 protein kinase. Mol. cell, 2007, 25, 903-915.
178. Van der Haar, E.; Lee, S.I.; Bandhakavi, S.; Griffin, T.J.; Kim, D.H. Insulin signalling to mTOR mediated by the Akt/PKB substrate PRAS40. Nat. Cell Biol., 2007, 9, 316-23.
179. Faivre, S.; Kroemer, G.; Raymond, E. Current development of mTOR inhibitors as anticancer agents. Nat. Rev. Drug Discov., 2006, 5, 671-688.
180. Remy, I.; Michnick, S.W. Visualization of biochemical networks in living cells. Proc. Natl. Acad. Sci. USA, 2001, 98, 7678-7683.
181. MacDonald, M.L.; Lamerdin, J.; Owens, S.; Keon, B.H.; Bilter, G.K.; Shang, Z.; Huang, Z.; Yu, H.; Dias, J.; Minami, T.; Michnick, S.W.; Westwick, J.K. Identifying off-target effects and hidden phenotypes of drugs in human cells. Nat. Cell Biol., 2006, 2, 329-337.
182. Keshamouni, V.G.; Michailidis, G.; Grasso, C.S.; Anthwal, S.; Strahler, J.R.; Walker, A.; Arenberg, D.A.; Reddy, R.C.; Akulapalli, S.; Thannickal, V.J.; Standiford, T.J.; Andrews, P.C.; Omenn, G.S. Differential protein expression profiling by iTRAQ 2DLC-MS/MS of lung cancer cells undergoing epithelialmesenchymal transition reveals a migratory/invasive phenotype. J. Proteome Res., 2006, 5, 1143-1154.
183. Keshamouni, V.G.; Jagtap, P.; Michailidis, G.; Strahler, J.R.; Kuick, R.; Reka, A.K.; Papoulias, P.; Krishnapuram, R.; Srirangam, A.; Standiford, T.J.; Andrews, P.C.; Omenn, G.S. Temporal quantitative proteomics by iTRAQ 2D-LC-MS/MS and corresponding mRNA expression analysis identify posttranscriptional modulation of actin-cytoskeleton regulators during TGF-beta-Induced epithelial-mesenchymal transition. J. Proteome Res., 2009, 8, 35-47.
184. Choe, L.; D'Ascenzo, M.; Relkin, N.R.; Pappin, D.; Ross, P.; Williamson, B.; Guertin, S.; Pribil, P.; Lee, K.H. 8-plex quantitation of changes in cerebrospinal fluid protein expression in subjects undergoing intravenous immunoglobulin treatment for Alzheimer's disease. Proteomics, 2007, 7, 3651-3660.
185. Kassie, F.; Anderson, L.B.; Higgins, L.A.; Pan, Y.; Matise, I.; Negia, M.; Upadhyaya, P.; Wang, M.; Hecht, S.S. Chemopreventive agents modulate the protein expression profile of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone plus benzo[a]pyrene-induced lung tumors in A/J mice. Carcinogenesis, 2008, 29, 610-619.
186. Bonvin, A.M. Flexible protein-protein docking. Curr. Opin. Struct. Biol., 2006, 16, 194-200.
187. Hu, Z.; Mellor, J.; Wu, J.; Kanehisa, M.; Stuart, J.M.; DeLisi, C. Towards zoomable multidimensional maps of the cell. Nat. Biotechnol., 2007, 25, 547-554.
188. Hu, Z.; Hung, J.H.; Wang, Y.; Chang, Y.C.; Huang, C.L.; Huyck, M.; DeLisi, C. VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. Nucleic Acids Res., 2009, 37, W115-121.
189. Mayburd, A.L.; Martlínez, A.; Sackett, D.; Liu, H.; Shih, J.; Tauler, J.; Avis, I.; Mulshine, J.L. Ingenuity network-assisted transcription profiling: Identification of a new pharmacologic mechanism for MK886. Clin. Cancer Res., 2006, 12, 1820-1827.
190. Li, X.; Hansen, P.A.; Xi, L.; Chandraratna, R.A.S.; Burant, C.F. Distinct mechanisms of glucose lowering by specific agonists for peroxisomal proliferator activated receptor gamma and retinoic acid X receptors. J. Biol. Chem., 2005, 280, 38317-38327.
191. An, E.; Lu, X.; Flippin, J.; Devaney, J.M.; Halligan, B.; Hoffman, E.P.; Strunnikova, N.; Csaky, K.; Hathout, Y. Secreted proteome profiling in human RPE cell cultures derived from donors with age related macular degeneration and age matched healthy donors. J. Proteome Res., 2006, 5, 2599-2610.
192. Wu, J.; Liu, W.; Bemis, A.; Wang, E.; Qiu, Y.; Morris, E.A.; Flannery, C.R.; Yang, Z. Comparative proteomic characterization of articular cartilage tissue from normal donors and patients with osteoarthritis. Arthritis Rheum., 2007, 56, 3675-3684.
193. Zhu, S.; Wurdak, H.; Wang, Y.; Galkin, A.; Tao, H.; Li, J.; Lyssiotis, C.A.; Yan, F.; Tu, B.P.; Miraglia, L.; Walker, J.; Sun, F.; Orth, A.; Schultz, P.G.; Wu, X. A genomic screen identifies TYRO3 as a MITF regulator in melanoma. Proc. Natl. Acad. Sci. USA, 2009, 106, 17025-17030.
194. Prokai, L.; Stevens Jr, S.M.; Rauniyar, N.; Nguyen, V. Rapid label free identification of estrogen-induced differential protein expression in vivo from mouse brain and uterine tissue. J. Proteome Res., 2009, 8, 3862-3871.
195. Merrick, B.A. The plasma proteome, adductome and idiosyncratic toxicity in toxicoproteomics research. Brief. Funct. Genomic Proteomic, 2008, 7, 35-49.
196. Gao, Y.; Holland, R.D.; Yu, L.R. Quantitative proteomics for drug toxicity. Brief. Funct. Genomic Proteomic, 2009, 8, 158-166.
197. Arrell, D.K.; Niederlnder, N.J.; Perez-Terzic, C.; Chung, S.; Behfar, A.; Terzic, A. Pharmacoproteomics: advancing the efficacy and safety of regenerative therapeutics. Clin. Pharmacol. Ther., 2007, 82, 316-319.
198. Jain, K.K. Role of pharmacoproteomics in the development of personalized medicine. Pharmacogenomics., 2004, 5, 331-336.
199. Wulfkuhle, J.D.; Edmiston, K.H.; Liotta, L.A.; Petricoin, E.F. Technology Insight: pharmacoproteomics for cancer-promises of patient-tailored medicine using protein microarrays. Nat. Clin. Pract. Oncol., 2006, 3, 256-268.
200. Jia, J.; Zhu, F.; Ma, X.; Cao, Z.; Li, Y.; Chen, Y.Z. Mechanisms of drug combinations: interaction and network perspectives. Nat. Rev. Drug Discov., 2009, 8, 111-128.
201. Szakács, G.; Paterson, J.K.; Ludwig, J.A.; Booth-Genthe, C.; Gottesman, M.M. Targeting multidrug resistance in cancer. Nat. Rev. Drug Discov., 2006, 5, 219-234.
202. Mimeault, M.; Hauke, R.; Batra, S.K. Recent advances on the molecular mechanisms involved in the drug resistance of cancer cells and novel targeting therapies. Clin. Pharmacol. Ther., 2008, 83, 673-691.