Skip to main content

Mass Spectrometry-Based Chemoproteomic Approaches

  • Protocol
  • First Online:
Chemical Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 803))

Abstract

The term “chemical proteomics” refers to a research area at the interface of chemistry, biochemistry, and cell biology that focuses on studying the mechanism of action of bioactive small molecule compounds, which comprises the mapping of their target proteins and their impact on protein expression and posttranslational modifications in target cells or tissues of interest on a proteome-wide level. For this purpose, a large arsenal of approaches has emerged in recent years, many of which employing quantitative mass spectrometry. This review briefly summarizes major experiment types employed in current chemical proteomics research.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Bantscheff, M., Scholten, A., and Heck, A. J. (2009) Revealing promiscuous drug-target interactions by chemical proteomics, Drug Discov Today 14, 1021–1029.

    Article  PubMed  CAS  Google Scholar 

  2. Carlson, S. M., and White, F. M. (2010) Using Small Molecules and Chemical Genetics To Interrogate Signaling Networks, ACS Chem Biol 6(1):75–85.

    Article  PubMed  Google Scholar 

  3. Cravatt, B. F., Wright, A. T., and Kozarich, J. W. (2008) Activity-based protein profiling: from enzyme chemistry to proteomic chemistry, Annu Rev Biochem 77, 383–414.

    Article  PubMed  CAS  Google Scholar 

  4. Kruse, U., Bantscheff, M., Drewes, G., and Hopf, C. (2008) Chemical and pathway proteomics: powerful tools for oncology drug discovery and personalized health care, Mol Cell Proteomics 7, 1887–1901.

    Article  PubMed  CAS  Google Scholar 

  5. Lolli, G., Thaler, F., Valsasina, B., Roletto, F., Knapp, S., Uggeri, M., Bachi, A., Matafora, V., Storici, P., Stewart, A., Kalisz, H. M., and Isacchi, A. (2003) Inhibitor affinity chromatography: profiling the specific reactivity of the proteome with immobilized molecules, Proteomics 3, 1287–1298.

    Article  PubMed  CAS  Google Scholar 

  6. Sadaghiani, A. M., Verhelst, S. H., and Bogyo, M. (2007) Tagging and detection strategies for activity-based proteomics, Curr Opin Chem Biol 11, 20–28.

    Article  PubMed  CAS  Google Scholar 

  7. Yamamoto, K., Yamazaki, A., Takeuchi, M., and Tanaka, A. (2006) A versatile method of identifying specific binding proteins on affinity resins, Anal Biochem 352, 15–23.

    Article  PubMed  CAS  Google Scholar 

  8. Rix, U., and Superti-Furga, G. (2009) Target profiling of small molecules by chemical proteomics, Nat Chem Biol 5, 616–624.

    Article  PubMed  CAS  Google Scholar 

  9. Cohen, A. A., Geva-Zatorsky, N., Eden, E., Frenkel-Morgenstern, M., Issaeva, I., Sigal, A., Milo, R., Cohen-Saidon, C., Liron, Y., Kam, Z., Cohen, L., Danon, T., Perzov, N., and Alon, U. (2008) Dynamic proteomics of individual cancer cells in response to a drug, Science 322, 1511–1516.

    Article  PubMed  CAS  Google Scholar 

  10. Lee, A. Y., Paweletz, C. P., Pollock, R. M., Settlage, R. E., Cruz, J. C., Secrist, J. P., Miller, T. A., Stanton, M. G., Kral, A. M., Ozerova, N. D., Meng, F., Yates, N. A., Richon, V., and Hendrickson, R. C. (2008) Quantitative analysis of histone deacetylase-1 selective histone modifications by differential mass spectrometry, J Proteome Res 7, 5177–5186.

    Article  PubMed  CAS  Google Scholar 

  11. Liang, X., Hajivandi, M., Veach, D., Wisniewski, D., Clarkson, B., Resh, M. D., and Pope, R. M. (2006) Quantification of change in phosphorylation of BCR-ABL kinase and its substrates in response to Imatinib treatment in human chronic myelogenous leukemia cells, Proteomics 6, 4554–4564.

    Article  PubMed  CAS  Google Scholar 

  12. Song, D., Chaerkady, R., Tan, A. C., Garcia-Garcia, E., Nalli, A., Suarez-Gauthier, A., Lopez-Rios, F., Zhang, X. F., Solomon, A., Tong, J., Read, M., Fritz, C., Jimeno, A., Pandey, A., and Hidalgo, M. (2008) Antitumor activity and molecular effects of the novel heat shock protein 90 inhibitor, IPI-504, in pancreatic cancer, Mol Cancer Ther 7, 3275–3284.

    Article  PubMed  CAS  Google Scholar 

  13. Brehmer, D., Godl, K., Zech, B., Wissing, J., and Daub, H. (2004) Proteome-wide identification of cellular targets affected by bisindolylmaleimide-type protein kinase C inhibitors, Mol Cell Proteomics 3, 490–500.

    Article  PubMed  CAS  Google Scholar 

  14. Bantscheff, M., Schirle, M., Sweetman, G., Rick, J., and Kuster, B. (2007) Quantitative mass spectrometry in proteomics: a critical review, Anal Bioanal Chem 389, 1017–1031.

    Article  PubMed  CAS  Google Scholar 

  15. Domon, B., and Aebersold, R. (2010) Options and considerations when selecting a quantitative proteomics strategy, Nat Biotechnol 28, 710–721.

    Article  PubMed  CAS  Google Scholar 

  16. Mallick, P., and Kuster, B. (2010) Proteomics: a pragmatic perspective, Nat Biotechnol 28, 695–709.

    Article  PubMed  CAS  Google Scholar 

  17. Schirle, M., Heurtier, M. A., and Kuster, B. (2003) Profiling core proteomes of human cell lines by one-dimensional PAGE and liquid chromatography-tandem mass spectrometry, Mol Cell Proteomics 2, 1297–1305.

    Article  PubMed  CAS  Google Scholar 

  18. Sui, J., Zhang, J., Tan, T. L., Ching, C. B., and Chen, W. N. (2008) Comparative proteomics analysis of vascular smooth muscle cells incubated with S- and R-enantiomers of atenolol using iTRAQ-coupled two-dimensional LC-MS/MS, Mol Cell Proteomics 7, 1007–1018.

    Article  PubMed  CAS  Google Scholar 

  19. Zhang, J., Sui, J., Ching, C. B., and Chen, W. N. (2008) Protein profile in neuroblastoma cells incubated with S- and R-enantiomers of ibuprofen by iTRAQ-coupled 2-D LC-MS/MS analysis: possible action of induced proteins on Alzheimer’s disease, Proteomics 8, 1595–1607.

    Article  PubMed  CAS  Google Scholar 

  20. Yamanaka, H., Yakabe, Y., Saito, K., Sekijima, M., and Shirai, T. (2007) Quantitative proteomic analysis of rat liver for carcinogenicity prediction in a 28-day repeated dose study, Proteomics 7, 781–795.

    Article  PubMed  CAS  Google Scholar 

  21. Mackeen, M. M., Kramer, H. B., Chang, K. H., Coleman, M. L., Hopkinson, R. J., Schofield, C. J., and Kessler, B. M. (2010) Small-molecule-based inhibition of histone demethylation in cells assessed by quantitative mass spectrometry, J Proteome Res 9, 4082–4092.

    Article  PubMed  CAS  Google Scholar 

  22. Pan, C., Olsen, J. V., Daub, H., and Mann, M. (2009) Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics, Mol Cell Proteomics 8, 2796–2808.

    Article  PubMed  CAS  Google Scholar 

  23. Li, J., Rix, U., Fang, B., Bai, Y., Edwards, A., Colinge, J., Bennett, K. L., Gao, J., Song, L., Eschrich, S., Superti-Furga, G., Koomen, J., and Haura, E. B. (2010) A chemical and phosphoproteomic characterization of dasatinib action in lung cancer, Nat Chem Biol 6, 291–299.

    Article  PubMed  CAS  Google Scholar 

  24. Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., and Mann, M. (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics, Mol Cell Proteomics 1, 376–386.

    Article  CAS  Google Scholar 

  25. Choudhary, C., Kumar, C., Gnad, F., Nielsen, M. L., Rehman, M., Walther, T. C., Olsen, J. V., and Mann, M. (2009) Lysine acetylation targets protein complexes and co-regulates major cellular functions, Science 325, 834–840.

    Article  PubMed  CAS  Google Scholar 

  26. Hall, S. E. (2006) Chemoproteomics-driven drug discovery: addressing high attrition rates, Drug Discov Today 11, 495–502.

    Article  PubMed  CAS  Google Scholar 

  27. Nomura, D. K., Dix, M. M., and Cravatt, B. F. (2010) Activity-based protein profiling for biochemical pathway discovery in cancer, Nat Rev Cancer 10, 630–638.

    Article  PubMed  CAS  Google Scholar 

  28. Liu, Y., Patricelli, M. P., and Cravatt, B. F. (1999) Activity-based protein profiling: the serine hydrolases, Proc Natl Acad Sci USA 96, 14694–14699.

    Article  PubMed  CAS  Google Scholar 

  29. Kato, D., Boatright, K. M., Berger, A. B., Nazif, T., Blum, G., Ryan, C., Chehade, K. A., Salvesen, G. S., and Bogyo, M. (2005) Activity-based probes that target diverse cysteine protease families, Nat Chem Biol 1, 33–38.

    Article  PubMed  CAS  Google Scholar 

  30. Saghatelian, A., Jessani, N., Joseph, A., Humphrey, M., and Cravatt, B. F. (2004) Activity-based probes for the proteomic profiling of metalloproteases, Proc Natl Acad Sci USA 101, 10000–10005.

    Article  PubMed  CAS  Google Scholar 

  31. Patricelli, M. P., Szardenings, A. K., Liyanage, M., Nomanbhoy, T. K., Wu, M., Weissig, H., Aban, A., Chun, D., Tanner, S., and Kozarich, J. W. (2007) Functional interrogation of the kinome using nucleotide acyl phosphates, Biochemistry 46, 350–358.

    Article  PubMed  CAS  Google Scholar 

  32. Yee, M. C., Fas, S. C., Stohlmeyer, M. M., Wandless, T. J., and Cimprich, K. A. (2005) A cell-permeable, activity-based probe for protein and lipid kinases, J Biol Chem 280, 29053–29059.

    Article  PubMed  CAS  Google Scholar 

  33. Kumar, S., Zhou, B., Liang, F., Wang, W. Q., Huang, Z., and Zhang, Z. Y. (2004) Activity-based probes for protein tyrosine phosphatases, Proc Natl Acad Sci USA 101, 7943–7948.

    Article  PubMed  CAS  Google Scholar 

  34. Salisbury, C. M., and Cravatt, B. F. (2007) Activity-based probes for proteomic profiling of histone deacetylase complexes, Proc Natl Acad Sci USA 104, 1171–1176.

    Article  PubMed  CAS  Google Scholar 

  35. Vocadlo, D. J., and Bertozzi, C. R. (2004) A strategy for functional proteomic analysis of glycosidase activity from cell lysates, Angew Chem Int Ed Engl 43, 5338–5342.

    Article  PubMed  CAS  Google Scholar 

  36. Bachovchin, D. A., Brown, S. J., Rosen, H., and Cravatt, B. F. (2009) Identification of selective inhibitors of uncharacterized enzymes by high-throughput screening with fluorescent activity-based probes, Nat Biotechnol 27, 387–394.

    Article  PubMed  CAS  Google Scholar 

  37. Bachovchin, D. A., Ji, T., Li, W., Simon, G. M., Blankman, J. L., Adibekian, A., Hoover, H., Niessen, S., and Cravatt, B. F. (2010) Superfamily-wide portrait of serine hydrolase inhibition achieved by library-versus-library screening, Proc Natl Acad Sci USA 107, 20941–20946.

    Article  PubMed  CAS  Google Scholar 

  38. Wright, A. T., and Cravatt, B. F. (2007) Chemical proteomic probes for profiling cytochrome p450 activities and drug interactions in vivo, Chem Biol 14, 1043–1051.

    Article  PubMed  CAS  Google Scholar 

  39. Speers, A. E., Adam, G. C., and Cravatt, B. F. (2003) Activity-based protein profiling in vivo using a copper(i)-catalyzed azide-alkyne [3  +  2] cycloaddition, J Am Chem Soc 125, 4686–4687.

    Article  PubMed  CAS  Google Scholar 

  40. Speers, A. E., and Cravatt, B. F. (2004) Profiling enzyme activities in vivo using click chemistry methods, Chem Biol 11, 535–546.

    Article  PubMed  CAS  Google Scholar 

  41. Koster, H., Little, D. P., Luan, P., Muller, R., Siddiqi, S. M., Marappan, S., and Yip, P. (2007) Capture compound mass spectrometry: a technology for the investigation of small molecule protein interactions, Assay Drug Dev Technol 5, 381–390.

    Article  PubMed  Google Scholar 

  42. Luo, Y., Blex, C., Baessler, O., Glinski, M., Dreger, M., Sefkow, M., and Koster, H. (2009) The cAMP capture compound mass spectrometry as a novel tool for targeting cAMP-binding proteins: from protein kinase A to potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channels, Mol Cell Proteomics 8, 2843–2856.

    Article  PubMed  CAS  Google Scholar 

  43. Fischer, J. J., Graebner Baessler, O. Y., Dalhoff, C., Michaelis, S., Schrey, A. K., Ungewiss, J., Andrich, K., Jeske, D., Kroll, F., Glinski, M., Sefkow, M., Dreger, M., and Koester, H. (2010) Comprehensive identification of staurosporine-binding kinases in the hepatocyte cell line HepG2 using Capture Compound Mass Spectrometry (CCMS), J Proteome Res 9, 806–817.

    Article  PubMed  CAS  Google Scholar 

  44. Dalhoff, C., Huben, M., Lenz, T., Poot, P., Nordhoff, E., Koster, H., and Weinhold, E. (2010) Synthesis of S-adenosyl-L-homocysteine capture compounds for selective photoinduced isolation of methyltransferases, Chembiochem 11, 256–265.

    Article  PubMed  CAS  Google Scholar 

  45. Oda, Y., Owa, T., Sato, T., Boucher, B., Daniels, S., Yamanaka, H., Shinohara, Y., Yokoi, A., Kuromitsu, J., and Nagasu, T. (2003) Quantitative chemical proteomics for identifying candidate drug targets, Anal Chem 75, 2159–2165.

    Article  PubMed  CAS  Google Scholar 

  46. 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., and Drewes, G. (2007) Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors, Nat Biotechnol 25, 1035–1044.

    Article  PubMed  CAS  Google Scholar 

  47. Brehmer, D., Greff, Z., Godl, K., Blencke, S., Kurtenbach, A., Weber, M., Muller, S., Klebl, B., Cotten, M., Keri, G., Wissing, J., and Daub, H. (2005) Cellular targets of gefitinib, Cancer Res 65, 379–382.

    PubMed  CAS  Google Scholar 

  48. Daub, H., Olsen, J. V., Bairlein, M., Gnad, F., Oppermann, F. S., Korner, R., Greff, Z., Keri, G., Stemmann, O., and Mann, M. (2008) Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle, Mol Cell 31, 438–448.

    Article  PubMed  CAS  Google Scholar 

  49. Godl, K., Gruss, O. J., Eickhoff, J., Wissing, J., Blencke, S., Weber, M., Degen, H., Brehmer, D., Orfi, L., Horvath, Z., Keri, G., Muller, S., Cotten, M., Ullrich, A., and Daub, H. (2005) Proteomic characterization of the angiogenesis inhibitor SU6668 reveals multiple impacts on cellular kinase signaling, Cancer Res 65, 6919–6926.

    Article  PubMed  CAS  Google Scholar 

  50. Remsing Rix, L. L., Rix, U., Colinge, J., Hantschel, O., Bennett, K. L., Stranzl, T., Muller, A., Baumgartner, C., Valent, P., Augustin, M., Till, J. H., and Superti-Furga, G. (2009) Global target profile of the kinase inhibitor bosutinib in primary chronic myeloid leukemia cells, Leukemia 23, 477–485.

    Article  PubMed  CAS  Google Scholar 

  51. Rix, U., Hantschel, O., Durnberger, G., Remsing Rix, L. L., Planyavsky, M., Fernbach, N. V., Kaupe, I., Bennett, K. L., Valent, P., Colinge, J., Kocher, T., and Superti-Furga, G. (2007) Chemical proteomic profiles of the BCR-ABL inhibitors imatinib, nilotinib, and dasatinib reveal novel kinase and nonkinase targets, Blood 110, 4055–4063.

    Article  PubMed  CAS  Google Scholar 

  52. Graves, P. R., Kwiek, J. J., Fadden, P., Ray, R., Hardeman, K., Coley, A. M., Foley, M., and Haystead, T. A. (2002) Discovery of novel targets of quinoline drugs in the human purine binding proteome, Mol Pharmacol 62, 1364–1372.

    Article  PubMed  CAS  Google Scholar 

  53. Gharbi, S. I., Zvelebil, M. J., Shuttleworth, S. J., Hancox, T., Saghir, N., Timms, J. F., and Waterfield, M. D. (2007) Exploring the specificity of the PI3K family inhibitor LY294002, Biochem J 404, 15–21.

    Article  PubMed  CAS  Google Scholar 

  54. Krugmann, S., Anderson, K. E., Ridley, S. H., Risso, N., McGregor, A., Coadwell, J., Davidson, K., Eguinoa, A., Ellson, C. D., Lipp, P., Manifava, M., Ktistakis, N., Painter, G., Thuring, J. W., Cooper, M. A., Lim, Z. Y., Holmes, A. B., Dove, S. K., Michell, R. H., Grewal, A., Nazarian, A., Erdjument-Bromage, H., Tempst, P., Stephens, L. R., and Hawkins, P. T. (2002) Identification of ARAP3, a novel PI3K effector regulating both Arf and Rho GTPases, by selective capture on phosphoinositide affinity matrices, Mol Cell 9, 95–108.

    Article  PubMed  CAS  Google Scholar 

  55. Hanke, S. E., Bertinetti, D., Badel, A., Schweinsberg, S., Genieser, H. G., and Herberg, F. W. (2010) Cyclic nucleotides as affinity tools: phosphorothioate cAMP analogues address specific PKA subproteomes, Nat Biotechnol 28(4):294–301.

    Article  PubMed  Google Scholar 

  56. Scholten, A., Poh, M. K., van Veen, T. A., van Breukelen, B., Vos, M. A., and Heck, A. J. (2006) Analysis of the cGMP/cAMP interactome using a chemical proteomics approach in mammalian heart tissue validates sphingosine kinase type 1-interacting protein as a genuine and highly abundant AKAP, J Proteome Res 5, 1435–1447.

    Article  PubMed  CAS  Google Scholar 

  57. Bantscheff, M., Hopf, C., Savitski, M. M., Dittmann, A., Grandi, P., Michon, A. M., Schlegl, J., Abraham, Y., Becher, I., Bergamini, G., Boesche, M., Delling, M., Dumpelfeld, B., Eberhard, D., Huthmacher, C., Mathieson, T., Poeckel, D., Reader, V., Strunk, K., Sweetman, G., Kruse, U., Neubauer, G., Ramsden, N. G., and Drewes, G. (2011) Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes, Nat Biotechnol 29, 255–265.

    Google Scholar 

  58. Hanke, S., and Mann, M. (2009) The phosphotyrosine interactome of the insulin receptor family and its substrates IRS-1 and IRS-2, Mol Cell Proteomics 8, 519–534.

    Article  PubMed  CAS  Google Scholar 

  59. Schulze, W. X., Deng, L., and Mann, M. (2005) Phosphotyrosine interactome of the ErbB-receptor kinase family, Mol Syst Biol 1, 2005 0008.

    PubMed  Google Scholar 

  60. Vermeulen, M., Eberl, H. C., Matarese, F., Marks, H., Denissov, S., Butter, F., Lee, K. K., Olsen, J. V., Hyman, A. A., Stunnenberg, H. G., and Mann, M. (2010) Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers, Cell 142, 967–980.

    Article  PubMed  CAS  Google Scholar 

  61. Borawski, J., Troke, P., Puyang, X., Gibaja, V., Zhao, S., Mickanin, C., Leighton-Davies, J., Wilson, C. J., Myer, V., Cornellataracido, I., Baryza, J., Tallarico, J., Joberty, G., Bantscheff, M., Schirle, M., Bouwmeester, T., Mathy, J. E., Lin, K., Compton, T., Labow, M., Wiedmann, B., and Gaither, L. A. (2009) Class III phosphatidylinositol 4-kinase alpha and beta are novel host factor regulators of hepatitis C virus replication, J Virol 83, 10058–10074.

    Article  PubMed  CAS  Google Scholar 

  62. Fleischer, T. C., Murphy, B. R., Flick, J. S., Terry-Lorenzo, R. T., Gao, Z. H., Davis, T., McKinnon, R., Ostanin, K., Willardsen, J. A., and Boniface, J. J. (2010) Chemical proteomics identifies Nampt as the target of CB30865, an orphan cytotoxic compound, Chem Biol 17, 659–664.

    Article  PubMed  CAS  Google Scholar 

  63. Huang, S. M., Mishina, Y. M., Liu, S., Cheung, A., Stegmeier, F., Michaud, G. A., Charlat, O., Wiellette, E., Zhang, Y., Wiessner, S., Hild, M., Shi, X., Wilson, C. J., Mickanin, C., Myer, V., Fazal, A., Tomlinson, R., Serluca, F., Shao, W., Cheng, H., Shultz, M., Rau, C., Schirle, M., Schlegl, J., Ghidelli, S., Fawell, S., Lu, C., Curtis, D., Kirschner, M. W., Lengauer, C., Finan, P. M., Tallarico, J. A., Bouwmeester, T., Porter, J. A., Bauer, A., and Cong, F. (2009) Tankyrase inhibition stabilizes axin and antagonizes Wnt signalling, Nature 461, 614–620.

    Article  PubMed  CAS  Google Scholar 

  64. Raijmakers, R., Dadvar, P., Pelletier, S., Gouw, J., Rumpel, K., and Heck, A. J. (2010) Target profiling of a small library of phosphodiesterase 5 (PDE5) inhibitors using chemical proteomics, ChemMedChem 5, 1927–1936.

    Article  PubMed  CAS  Google Scholar 

  65. Oppermann, F. S., Gnad, F., Olsen, J. V., Hornberger, R., Greff, Z., Keri, G., Mann, M., and Daub, H. (2009) Large-scale proteomics analysis of the human kinome, Mol Cell Proteomics 8, 1751–1764.

    Article  PubMed  CAS  Google Scholar 

  66. Trinkle-Mulcahy, L., Boulon, S., Lam, Y. W., Urcia, R., Boisvert, F. M., Vandermoere, F., Morrice, N. A., Swift, S., Rothbauer, U., Leonhardt, H., and Lamond, A. (2008) Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes, J Cell Biol 183, 223–239.

    Article  PubMed  CAS  Google Scholar 

  67. 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., and Pappin, D. J. (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents, Mol Cell Proteomics 3, 1154–1169.

    Article  PubMed  CAS  Google Scholar 

  68. 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., and Carr, S. A. (2009) Identifying the proteins to which small-molecule probes and drugs bind in cells, Proc Natl Acad Sci USA 106, 4617–4622.

    Article  PubMed  CAS  Google Scholar 

  69. Day, E., Waters, B., Spiegel, K., Alnadaf, T., Manley, P. W., Buchdunger, E., Walker, C., and Jarai, G. (2008) Inhibition of collagen-induced discoidin domain receptor 1 and 2 activation by imatinib, nilotinib and dasatinib, Eur J Pharmacol 599, 44–53.

    Article  PubMed  CAS  Google Scholar 

  70. Winger, J. A., Hantschel, O., Superti-Furga, G., and Kuriyan, J. (2009) The structure of the leukemia drug imatinib bound to human quinone reductase 2 (NQO2), BMC Struct Biol 9, 7.

    Article  PubMed  Google Scholar 

  71. Sharma, K., Weber, C., Bairlein, M., Greff, Z., Keri, G., Cox, J., Olsen, J. V., and Daub, H. (2009) Proteomics strategy for quantitative protein interaction profiling in cell extracts, Nat Methods 6, 741–744.

    Article  PubMed  CAS  Google Scholar 

  72. Breitkopf, S. B., Oppermann, F. S., Keri, G., Grammel, M., and Daub, H. (2010) Proteomics analysis of cellular imatinib targets and their candidate downstream effectors, J Proteome Res 9, 6033–6043.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Marcus Bantscheff .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Bantscheff, M. (2012). Mass Spectrometry-Based Chemoproteomic Approaches. In: Drewes, G., Bantscheff, M. (eds) Chemical Proteomics. Methods in Molecular Biology, vol 803. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-364-6_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-364-6_1

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-363-9

  • Online ISBN: 978-1-61779-364-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics