Mass spectrometry for monitoring protease reactions

  • H. Schlüter
  • D. Hildebrand
  • C. Gallin
  • A. Schulz
  • J. Thiemann
  • M. Trusch
Review

Abstract

More than 560 genes are annotated as proteases in the human genome. About half of the genes are not or are only marginally characterized. Over the past decade, mass spectrometry has become the basis for proteomics, especially for protein identification, performed in a high-throughput manner. This development was also very fruitful for exploring the complex systems associated with protease functions, as briefly reviewed here. Mass spectrometry is an ideal tool for monitoring protease reactions, as will be highlighted in this review.

Keywords

Bioanalytical methods Enzymes Mass spectrometry 

References

  1. 1.
    Müller J, Schwann T (1836) Arch Anat Physiol Med 90–138Google Scholar
  2. 2.
    Mackman N, Tilley RE, Key NS (2007) Arterioscler Thromb Vasc Biol 27:1687–1693CrossRefGoogle Scholar
  3. 3.
    Alao JP (2007) Mol Cancer 6:24CrossRefGoogle Scholar
  4. 4.
    Bowerman B, Kurz T (2006) Development 133:773–784CrossRefGoogle Scholar
  5. 5.
    Rushton I (2007) Nurs Stand 21:68–72Google Scholar
  6. 6.
    Siegel RM (2006) Nat Rev Immunol 6:308–317CrossRefGoogle Scholar
  7. 7.
    Lopez-Otin C, Matrisian LM (2007) Nat Rev Cancer 7:800–808CrossRefGoogle Scholar
  8. 8.
    Lane DA, Philippou H, Huntington JA (2005) Blood 106:2605–2612CrossRefGoogle Scholar
  9. 9.
    Yanagisawa M, Kurihara H, Kimura S, Tomobe Y, Kobayashi M, Mitsui Y, Yazaki Y, Goto K, Masaki T (1988) Nature 332:411–415CrossRefGoogle Scholar
  10. 10.
    Yorimitsu K, Moroi K, Inagaki N, Saito T, Masuda Y, Masaki T, Seino S, Kimura S (1995) Biochem Biophys Res Commun 208:721–727CrossRefGoogle Scholar
  11. 11.
    Schlüter H (2007) In: Hicks MG, Kettner C (eds) Experimental standard conditions of enzyme characterizations. Logos, BerlinGoogle Scholar
  12. 12.
    Cohen N, Kudryashova E, Kramerova I, Anderson LV, Beckmann JS, Bushby K, Spencer MJ (2006) Proteomics 6:6075–6084CrossRefGoogle Scholar
  13. 13.
    Lleo A (2008) Curr Top Med Chem 8:9–16CrossRefGoogle Scholar
  14. 14.
    Carragher NO, Frame MC (2002) Int J Biochem Cell Biol 34:1539–1543CrossRefGoogle Scholar
  15. 15.
    Overall CM, Blobel CP (2007) Nat Rev Mol Cell Biol 8:245–257CrossRefGoogle Scholar
  16. 16.
    Schilling O, Overall CM (2007) Curr Opin Chem Biol 11:36–45CrossRefGoogle Scholar
  17. 17.
    auf dem Keller U, Doucet A, Overall CM (2007) Biol Chem 388:1159–1162CrossRefGoogle Scholar
  18. 18.
    Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM (1989) Science 246:64–71CrossRefGoogle Scholar
  19. 19.
    Karas M, Hillenkamp F (1988) Anal Chem 60:2299–2301CrossRefGoogle Scholar
  20. 20.
    Aebersold R, Mann M (2003) Nature 422:198–207CrossRefGoogle Scholar
  21. 21.
    Link AJ, Eng J, Schieltz DM, Carmack E, Mize GJ, Morris DR, Garvik BM, Yates JRI (1999) Nat Biotechnol 17:676–682CrossRefGoogle Scholar
  22. 22.
    Swanson S, Washburn M (2005) Drug Discov Today 10:719–725CrossRefGoogle Scholar
  23. 23.
    Gevaert K, Vandekerckhove J (2000) Electrophoresis 21:1145–1154CrossRefGoogle Scholar
  24. 24.
    Rykl J, Thiemann J, Kurzawski S, Pohl T, Gobom J, Zidek W, Schluter H (2006) J Hypertens 24:1797–1807CrossRefGoogle Scholar
  25. 25.
    Overall CM, Tam EM, Kappelhoff R, Connor A, Ewart T, Morrison CJ, Puente X, Lopez-Otin C, Seth A (2004) Biol Chem 385:493–504CrossRefGoogle Scholar
  26. 26.
    Jeffery DA, Bogyo M (2003) Curr Opin Biotechnol 14:87–95CrossRefGoogle Scholar
  27. 27.
    Cravatt BF, Wright AT, Kozarich JW (2008) Annu Rev Biochem 77:383–414Google Scholar
  28. 28.
    Thimon V, Belghazi M, Labas V, Dacheux JL, Gatti JL (2008) Anal Biochem 375:382–384CrossRefGoogle Scholar
  29. 29.
    Matthews DJ, Wells JA (1993) Science 260:1113–1117CrossRefGoogle Scholar
  30. 30.
    Deng SJ, Bickett DM, Mitchell JL, Lambert MH, Blackburn RK, Carter HL 3rd, Neugebauer J, Pahel G, Weiner MP, Moss ML (2000) J Biol Chem 275:31422–31427CrossRefGoogle Scholar
  31. 31.
    Turk BE, Huang LL, Piro ET, Cantley LC (2001) Nat Biotechnol 19:661–667CrossRefGoogle Scholar
  32. 32.
    Lopez-Otin C, Overall CM (2002) Nat Rev Mol Cell Biol 3:509–519CrossRefGoogle Scholar
  33. 33.
    Overall CM (2001) Methods Mol Biol 151:79–120Google Scholar
  34. 34.
    Puente XS, Sanchez LM, Overall CM, Lopez-Otin C (2003) Nat Rev Genet 4:544–558CrossRefGoogle Scholar
  35. 35.
    Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R (1999) Nat Biotechnol 17:994–999CrossRefGoogle Scholar
  36. 36.
    DeSouza L, Diehl G, Rodrigues MJ, Guo J, Romaschin AD, Colgan TJ, Siu KW (2005) J Proteome Res 4:377–386CrossRefGoogle Scholar
  37. 37.
    Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M (2002) Mol Cell Proteomics 1:376–386CrossRefGoogle Scholar
  38. 38.
    Tam EM, Morrison CJ, Wu YI, Stack MS, Overall CM (2004) Proc Natl Acad Sci USA 101:6917–6922CrossRefGoogle Scholar
  39. 39.
    Dean RA, Overall CM (2007) Mol Cell Proteomics 6:611–623CrossRefGoogle Scholar
  40. 40.
    Enoksson M, Li J, Ivancic MM, Timmer JC, Wildfang E, Eroshkin A, Salvesen GS, Tao WA (2007) J Proteome Res 6:2850–2858CrossRefGoogle Scholar
  41. 41.
    Neher SB, Villen J, Oakes EC, Bakalarski CE, Sauer RT, Gygi SP, Baker TA (2006) Mol Cell 22:193–204CrossRefGoogle Scholar
  42. 42.
    Gevaert K, Van Damme J, Goethals M, Thomas GR, Hoorelbeke B, Demol H, Martens L, Puype M, Staes A, Vandekerckhove J (2002) Mol Cell Proteomics 1:896–903CrossRefGoogle Scholar
  43. 43.
    Gevaert K, Goethals M, Martens L, Van Damme J, Staes A, Thomas GR, Vandekerckhove J (2003) Nat Biotechnol 21:566–569CrossRefGoogle Scholar
  44. 44.
    Van Damme P, Martens L, Van Damme J, Hugelier K, Staes A, Vandekerckhove J, Gevaert K (2005) Nat Methods 2:771–777CrossRefGoogle Scholar
  45. 45.
    Van Damme P, Vandekerckhove J, Gevaert K (2008) Biol Chem 389(4):371–381Google Scholar
  46. 46.
    Greis KD (2007) Mass Spectrom Rev 26:324–339CrossRefGoogle Scholar
  47. 47.
    Liesener A, Karst U (2005) Anal Bioanal Chem 382:1451–1464CrossRefGoogle Scholar
  48. 48.
    Tipton KF (1992) Enzyme assays, a practical approach. IRL, OxfordGoogle Scholar
  49. 49.
    Schlüter H, Jankowski J, Thiemann J, Rykl J, Kurzawski S, Runge D (2004) Determination of enzyme activities by mass spectrometry. Logos, BerlinGoogle Scholar
  50. 50.
    Ahmed S, Thiemann J, Kurzawski S, Rykl J, Jankowski J, Wittmann-Liebold B, Pohl T, Schlüter H (2005) J Electrophoresis 49:1–6CrossRefGoogle Scholar
  51. 51.
    Hermant B, Bibert S, Concord E, Dublet B, Weidenhaupt M, Vernet T, Gulino-Debrac D (2003) J Biol Chem 278:14002–14012CrossRefGoogle Scholar
  52. 52.
    Hess JL, Porsch EA, Shertz CA, Boyle MD (2007) J Microbiol Methods 70:284–291CrossRefGoogle Scholar
  53. 53.
    Burlet-Schiltz O, Claverol S, Gairin JE, Monsarrat B (2005) Methods Enzymol 405:264–300CrossRefGoogle Scholar
  54. 54.
    Nussbaum AK, Dick TP, Keilholz W, Schirle M, Stevanovic S, Dietz K, Heinemeyer W, Groll M, Wolf DH, Huber R, Rammensee HG, Schild H (1998) Proc Natl Acad Sci USA 95:12504–12509CrossRefGoogle Scholar
  55. 55.
    Wenzel T, Eckerskorn C, Lottspeich F, Baumeister W (1994) FEBS Lett 349:205–209CrossRefGoogle Scholar
  56. 56.
    Ehring B, Meyer T, Eckerskorn C, Lottspeich F, Tampé R (1996) Eur J Biochem 235:404–415CrossRefGoogle Scholar
  57. 57.
    Peters B, Janek K, Kuckelkorn U, Holzhutter HG (2002) J Mol Biol 318:847–862CrossRefGoogle Scholar
  58. 58.
    Takeshita H, Desiderio DM, Fridland G (1986) Biomed Chromatogr 1:126–139CrossRefGoogle Scholar
  59. 59.
    Nilsson CL, Karlsson G, Bergquist J, Westman A, Ekman R (1998) Peptides 19:781–789CrossRefGoogle Scholar
  60. 60.
    Silberring J, Li YM, Hjerten S (1994) Biochem Soc Trans 22:136–140Google Scholar
  61. 61.
    Chu LH, Choy WY, Tsai SN, Rao Z, Ngai SM (2006) Protein Sci 15:699–709CrossRefGoogle Scholar
  62. 62.
    Dahlmann B, Ruppert T, Kuehn L, Merforth S, Kloetzel P (2000) J Mol Biol 303:643–653CrossRefGoogle Scholar
  63. 63.
    Bungert D, Heinzle E, Tholey A (2004) Anal Biochem 326:167–175CrossRefGoogle Scholar
  64. 64.
    Tholey A, Zabet-Moghaddam M, Heinzle E (2006) Anal Chem 78:291–297CrossRefGoogle Scholar
  65. 65.
    John H, Hierer J, Haas O, Forssmann W (2007) Anal Biochem 362:117–125CrossRefGoogle Scholar
  66. 66.
    Tamvakopoulos C (2007) Mass Spectrom Rev 26:389–402CrossRefGoogle Scholar
  67. 67.
    Anderson L, Hunter CL (2006) Mol Cell Proteomics 5:573–588Google Scholar
  68. 68.
    Barnidge DR, Goodmanson MK, Klee GG, Muddiman DC (2004) J Proteome Res 3:644–652CrossRefGoogle Scholar
  69. 69.
    Kuhn E, Wu J, Karl J, Liao H, Zolg W, Guild B (2004) Proteomics 4:1175–1186CrossRefGoogle Scholar
  70. 70.
    Barr JR, Moura H, Boyer AE, Woolfitt AR, Kalb SR, Pavlopoulos A, McWilliams LG, Schmidt JG, Martinez RA, Ashley DL (2005) Emerg Infect Dis 11:1578–1583Google Scholar
  71. 71.
    Andre M, Karas M (2007) Anal Bioanal Chem 389:1047–1053CrossRefGoogle Scholar
  72. 72.
    Cañas B, Piñeiro C, Calvo E, López-Ferrer D, Gallardo J (2007) J Chromatogr A 1153:235–258CrossRefGoogle Scholar
  73. 73.
    Wang Y, Zagorevski DV, Stenken JA (2008) Anal Chem 80:2050–2057CrossRefGoogle Scholar
  74. 74.
    Villanueva J, Nazarian A, Lawlor K, Yi SS, Robbins RJ, Tempst P (2008) Mol Cell Proteomics 7:509–518Google Scholar
  75. 75.
    Schlüter H, Jankowski J, Rykl J, Thiemann J, Belgardt S, Zidek W, Wittmann B, Pohl T (2003) Anal Bioanal Chem 377:1102–1107CrossRefGoogle Scholar
  76. 76.
    Schlüter H, Rykl J, Thiemann J, Kurzawski S, Gobom J, Tepel M, Zidek W, Linscheid M (2007) Anal Chem 79:1251–1255CrossRefGoogle Scholar
  77. 77.
    Liotta LA, Petricoin EF (2006) J Clin Invest 116:26–30CrossRefGoogle Scholar
  78. 78.
    Tammen H, Peck A, Budde P, Zucht HD (2007) Expert Rev Mol Diagn 7:605–613CrossRefGoogle Scholar
  79. 79.
    Villanueva J, Shaffer DR, Philip J, Chaparro CA, Erdjument-Bromage H, Olshen AB, Fleisher M, Lilja H, Brogi E, Boyd J, Sanchez-Carbayo M, Holland EC, Cordon-Cardo C, Scher HI, Tempst P (2006) J Clin Invest 116:271–284CrossRefGoogle Scholar
  80. 80.
    Findeisen P, Post S, Wenz F, Neumaier M (2007) Clin Chem 53:1864–1866CrossRefGoogle Scholar
  81. 81.
    Findeisen P, Peccerella T, Post S, Wenz F, Neumaier M (2008) Rapid Commun Mass Spectrom 22:1223–1229CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • H. Schlüter
    • 1
  • D. Hildebrand
    • 1
  • C. Gallin
    • 1
  • A. Schulz
    • 1
  • J. Thiemann
    • 2
  • M. Trusch
    • 1
  1. 1.Charite - Core Facility Protein AnalysisBerlinGermany
  2. 2.Agilent TechnologiesWaldbronnGermany

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