Skip to main content
SpringerLink
Log in

MALDI-TOF mass spectrometry in protein chemistry

  • Chapter
Proteomics in Functional Genomics

Part of the book series: EXS ((EXS,volume 88))

Summary

Mass spectrometry has in the last decade been accepted as a key analytical technique in protein chemistry. It is now the preferred technique for identification of proteins separated by one-or two-dimensional polyacrylamide gel electrophoresis, i.e. in proteome analysis. It is the dominating technique for determination of posttranslational modifications in proteins. The two ionization techniques presently widely used in protein studies are matrix-assisted laser desorption/ionization (MALDI) in combination with time-of-flight (TOF) mass analyzers and electrospray ionization (ESI) in combination with a variety of mass analyzers. In this chapter the principles and performance of MALDI-TOF mass spectrometry will be described as well as the application of this technique to a variety of applications.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
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

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Wilkins MR, Pasquali C, Appel RD, Ou K, Golaz O, Sanchez J-C, Jan ix, Gouley AA, Humphrey-Smith I, Williams KL et al (1996) From proteins to proteomers: large-scale protein identification by two-dimensional electrophoresis and amino acid analysis. Bio/Technology 14: 61–65

    Article  PubMed  CAS  Google Scholar 

  2. Karas M, Hillenkamp F (1988) Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal Chem 60: 2299–2301

    Article  PubMed  CAS  Google Scholar 

  3. Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM (1989) Electrospray ionization for the mass spectrometry of large biomolecules. Science 246: 64–71

    Article  PubMed  CAS  Google Scholar 

  4. Vestal ML, Juhasz P, Martin SA (1995) Delayedextraction matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry. Rapid Comm Mass Spectrom 9: 1044–1050

    Article  CAS  Google Scholar 

  5. Kussmann M, Nordhoff E, Nielsen HR, Larsen M, Haebel S, Mirgorodskaya E, Jensen C, Roepstorff P (1997) Sample preparation in MALDI-MS designed for various peptide and protein analytes. J Mass Spectrom 32: 593–601

    Article  CAS  Google Scholar 

  6. Vorm O, Roepstorff P, Mann M (1994) Improved resolution and very high sensitivity in MALDI-TOF of matrix surfaces made by fast evaporation. Anal Chem 66: 3281–3287

    Article  CAS  Google Scholar 

  7. Jespersen S, Niessen WM, Tjaden UR, GreefJ vd, Litborn E, Lindberg U, Roeraade J (1994) Attomole detection of proteins by matrix assisted lasr desorption/ionization mass spectrometry with the use of picoliter vials. Rapid Comm. Mass Spectrom 8: 581–584

    CAS  Google Scholar 

  8. Gobom J, Nordhoff E, Mirgorodskaya E, Ekman R, Roepstorff P (1999) A sample purification and preparation technique based on nano-scale RP-columns for the sensitive analysis of complex peptide mixtures by MALDI-MS. J Mass Spectrom 34: 105–116

    Article  PubMed  CAS  Google Scholar 

  9. Cohen S, Chait BT (1996) Influence of matrix solution conditions on the MALDI-MS analysis of peptides and proteins. Anal Chem 68: 31–37

    Article  PubMed  CAS  Google Scholar 

  10. Kussmann M, Lassing U, Stiirmer CAO, Przybylski M, Roepstorff P (1997) MALDI mass spectrometric peptide mapping of hte neural cell adhesion protein neurolin purified by sodium dodecyl sulfate polyacrylamide gel electrophoresis or acidic precipitation. J Mass Spectrom 32: 483–493

    Article  PubMed  CAS  Google Scholar 

  11. Spengler B, Kirsch D, Kaufmann R, Jaeger E (1992) Peptide sequencing by matrix assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom 6: 105–108

    Article  PubMed  CAS  Google Scholar 

  12. Reiber DC, Grower TA, Brown RS (1998) Identifying proteins and matrix-assisted laser desorption/ionization in source fragmentation data combined with databasesearching. Anal Chem 70: 673–683

    Article  PubMed  CAS  Google Scholar 

  13. Reiber DC, Brown RS, Weinberger S, Kenny J, Bailey JC (1998) Unknown peptide sequencing using matrix assisted laser desorption/ionization and in-source decay. Anal Chem 70: 1214–1222

    Article  PubMed  CAS  Google Scholar 

  14. Patterson DH, Tarr GE, Regnier FE, Martin SA (1995) C-terminal ladder sequencing via matrix-assisted laser desorption/ionization mass spectrometry coupled with carboxypeptidase Y time-dependent and concentration-dependent digestions. Anal Chem 67: 3971–3978

    Article  PubMed  CAS  Google Scholar 

  15. Chait BT, Wang R, Beavis RC, Kent SBH (1993) Protein ladder sequencing. Science 262: 89–92

    Article  PubMed  CAS  Google Scholar 

  16. Vorm O, Roepstorff P (1994) Peptide sequence information derived by partial acid hydrolysis and matrix assisted laser desorption ionization mass spectrometry. Biol Mass Spectrom 23: 734–740

    Article  PubMed  CAS  Google Scholar 

  17. Zubarev RA, Chivanov VD, Hakansson P, Sundqvist BUR (1994) Peptide sequencing by partial acid hydrolysis and high resolution plasma desorption mass spectrometry. Rapid Commun Mass Spectrom 8: 906–912

    Article  PubMed  CAS  Google Scholar 

  18. Mirgorodskaya E, Hassan H, Wandall HH, Clausen H, Roepstorff P (1999) Partial vapor phase hydrolysis of peptide bonds: an effective method for mass spectrometric determination of 0-glycosylated sites in glycopeptides. Anal Biochem 269: 54–65

    Article  PubMed  CAS  Google Scholar 

  19. Gobom J, Mirgorodskaya E, Nordhoff E, Roepstorff P (1998) Mass spectrometric peptide mapping using a new chemical method for sequence specific cleavage of proteins. Proc. 46th ASMS Conference of Mass Spectrometry and Allied Topics, Orlando, Florida, 30 May— 4 June

    Google Scholar 

  20. O’Farrell PH (1975) High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250: 4007–4021

    PubMed  Google Scholar 

  21. Klose J (1975) Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik 26: 231

    PubMed  CAS  Google Scholar 

  22. Fey SJ, Nawrocki A, Larsen MR, Gorg A, Roepstorff P, Skews GN, Williams R, Larsen PM (1997) Proteome analysis of Saccharomyces cerevisiae: A methodological outline. Electrophoresis 18: 1361–1372

    Article  PubMed  CAS  Google Scholar 

  23. Celis JE, Ratz GP, Madsen P, Gesser B, Lauridsen JB, Kwee S, Rasmussen HH, Nielsen HV, Cruger D, Basse B et al (1989) Comprehensive, human cellular protein databases and their implication for the study of genome organization and function. FEBS Lett 244: 247–254

    Article  PubMed  CAS  Google Scholar 

  24. Henzel WJ, Billeci TM, Stults JT, Wong SC (1993) Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc Natl Acad Sci USA 90: 5011–5015

    Article  PubMed  CAS  Google Scholar 

  25. Mann M, Hojrup P, Roepstorff P (1993) Use of mass spectrometric molecular weight in-formation to identify proteins in sequence databases. Biol Mass Spectrom 22: 338–345

    Article  PubMed  CAS  Google Scholar 

  26. Pappin DJC HØjrup P, Bleasby AJ (1993) Protein identification by peptide mass fingerprinting. Curr Biol 3: 327–332

    Article  PubMed  CAS  Google Scholar 

  27. James P, Quadroni M, Carafoli E, Gonnet G (1993) Protein identification by mass profile fingerprinting, Biochem Biophys Res Commun 195: 58–64

    Article  PubMed  CAS  Google Scholar 

  28. Yates JR, Speicher S, Griffin PR, Hunkapiller T (1993) Peptide mass maps: a highly informative approach to protein identification. Anal Biochem 214: 397–408

    Article  PubMed  CAS  Google Scholar 

  29. Engl JK, McCormack AL, Yates JR (1994) An approach to correlate tandem mass spectra of peptides with amino acid sequences in protein databases. J Am Soc Mass Spectrom 5: 976–989

    Article  Google Scholar 

  30. Mann M, Wilm MS (1994) Error tolerant identification of peptides in sequence databases by peptide sequence tags. Anal Chem 66: 4390–4399

    Article  PubMed  CAS  Google Scholar 

  31. Gevaert K, Demol H, Skylyarova T, Vandekerckhove J, Houthave T (1998) A peptide concentration and purification method for protein characterization in the subpicomole range using matrix assisted laser desorption/ionization-post source decay (MALDI-PSD) sequencing. Electrophoresis 19: 909–917

    Article  PubMed  CAS  Google Scholar 

  32. Patterson SD, Aebersold R (1995) Mass spectrometric approaches for the identification of gel-separated proteins. Electrophoresis 16: 1791–1814

    Article  PubMed  CAS  Google Scholar 

  33. Shevchenko A, Jensen ON, Podtelejnikov AV, Sagliocco F, Wilm M, Vorm O, Mortensen P, Shevchenko A, Boucherie H, Mann M (1996) Linking genome and proteome by mass spectrometry: large scale identification of yeast proteins from two dimensional gels. Proc Natl Acad Sci USA 93: 14440–14445

    Article  PubMed  CAS  Google Scholar 

  34. Dongre A, Eng J, Yates JR (1997) Emerging tandem-mass-spectrometry techniques for the rapid identification of proteins. Trends Biotechnol 15: 418–425

    Article  PubMed  CAS  Google Scholar 

  35. Patterson SD (ed) (1998) Paper symposium. Mass spectrometry in electrophoresis. Electrophoresis 19: 883–1054

    Article  Google Scholar 

  36. Fey SJ, Nawrocki A, Larsen MR, Gorg A, Roepstorff P, Skews GN, Williams R, Mose Larsen P (1997) Proteome analysis of Saccharomyces cerevisiae: a methodological outline. Electrophoresis 18: 1361–1372

    Article  PubMed  CAS  Google Scholar 

  37. Mann M (1996) A shortcut to interesting human genes: peptide sequence tags, ESTs and computers. Trends Biol Sci 21: 494–495

    Article  CAS  Google Scholar 

  38. Wilm M, Shevchenko A, Houthaeve T, Breit S, Schweigerer L, Fotsis T, Mann M (1996) Femtomole sequencing of proteins from polyacrylamide gels by nanoelectrospray mass spectrometry. Nature 379: 466–469

    Article  PubMed  CAS  Google Scholar 

  39. Shevchenko A, Wilm M, Mann M (1997) Peptide sequencing by mass spectrometry for homology searches and cloning of genes. J Protein Chem 16: 481–490

    Article  PubMed  CAS  Google Scholar 

  40. Roepstorff P, Hojrup P (1993) A general strategy for the use of mass spectrometric molecular weight information in protein purification and sequence determination. In: Methods in Protein Sequence Analysis: K Imahori, F Sakiyama (eds) Plenum Press, New York, 149–156

    Google Scholar 

  41. Andersen JS, Svensson B, Roepstorff P (1996) Electrospray ionization and matrix-assisted laser desorption/ionization mass spectrometry: powerful analytical tools in recombinant protein chemistry. Nature Biotechnol 14: 449–457

    Article  CAS  Google Scholar 

  42. Burlingame AL, Carr SA (eds) (1996) Mass spectrometry in biological sciences. Humana Press, Totowa, NY

    Google Scholar 

  43. Andersen JS, Sogaard M, Svensson B, Roepstorff P (1994) Localization of an 0-glycosylated site in recombinant barley a-amylase 1 produced in yeast and correction of the amino acid sequence using matrix assisted laser desorption ionization. Biol Mass Spectrom 23: 547–554

    Article  PubMed  CAS  Google Scholar 

  44. Brody S, Andersen JS, Kannagara CG, Melgaard M, Roepstorff P, von Wettstein D (1995) Characterization of different spectral forms of glutamate 1-semialdehyde amino transferase by mass spectrometry. Biochemistry 34: 15918–15924

    Article  PubMed  CAS  Google Scholar 

  45. Juge N, Andersen JS, Tull D, Roepstorff P, Svensson B (1996) Overexpression, purification, and characterization of recombinant barley a-amylases 1 and 2 secreted by the methylotrophic yest Pichia pastoris. Protein Expression and Purification 8: 204–214

    Article  PubMed  CAS  Google Scholar 

  46. Kristensen AK, Schou C, Roepstorff P (1997) Determination of isoforms, N-linked glycan structure and disulfide bond linkages of the major cat allergen Fel d 1 by a mass spectrometric approach. Biol Chem 378: 899–908

    Article  PubMed  CAS  Google Scholar 

  47. Rahbek-Nielsen H, Roepstorff P, Reischl H, Wozny M, Koll H, Haselbeck A (1997) Glycopeptide profiling of human urinary erythropoietin by matrix-assisted laser desorption ionization mass spectrometry. J Mass Spectrom 32: 948–958

    Article  PubMed  CAS  Google Scholar 

  48. Strupat K, Karas K, Hillenkamp F, Eckerskorn C, Lottspeich F (1994) Matrix assisted laser desorption/ionization mass spectrometry of proteins electroblotted after polyacrylamide gel electrophoresis. Anal Chem 66: 464–470

    Article  CAS  Google Scholar 

  49. Haebel S, Jensen C, Andersen SO, Roepstorff P (1995) Isoforms of a cuticular protein from larvae of the meal beetle, Tenebrio molitor, studied by mass spectrometry in combination with Edman degradation and 2D-PAGE. Protein Sci 4: 394–404

    Article  PubMed  CAS  Google Scholar 

  50. Jensen C, Haebel S, Andersen SO, Roepstorff P (1997) Towards monitoring of protein purification by matrix-assisted laser desorption ionization mass spectrometry. Int J Mass Spectrom Ion Proc 160: 339–356

    Article  CAS  Google Scholar 

  51. Cohen S, Chait B (1997) Mass spectrometry of whole proteins eluted from sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels. Anal Biochem 247: 257–267

    Article  PubMed  CAS  Google Scholar 

  52. Vorm O, Roepstorff P (1996) Detection bias gating for improved detector response and calibration in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Mass Spectrom 31: 351–358

    Article  CAS  Google Scholar 

  53. Jensen ON, Larsen MR, Roepstorff P (1998) Mass spectrometric identification and micro-characterization of proteins from electrophoretic gels: strategies and applications. Proteins: Structure, Function and Genetics 999: 74–89

    Article  Google Scholar 

  54. Oda Y, Chait B (1998) Purification and identification of phosphopeptides. Proc. 46th ASMS Conference of Mass Spectrometry and Allied Topics, Orlando, Florida, 30 May— 4 June

    Google Scholar 

  55. Burlingame AL (1996) Characterization of protein glycosylation by mass spectrometry. Curr Opin Biotechnol 7: 4–10

    Article  PubMed  CAS  Google Scholar 

  56. Mertz E, Sareneva T, Haebel S, Julkunen I, Roepstorff P (1996) Mass spectrometric characterization of glycosylated interferon-gamma variants separated by gel electrophoresis. Electrophoresis 17: 925–931

    Article  Google Scholar 

  57. Martz E, Sareneva T, Julkunen I, Roepstorff P (1996) Does matrix-assisted laser desorption/ionization mass spectrometry allow analysis of carbohydrate heterogeneity in glycoproteins? A study of natural human interferon-gamma. J Mass Spectrom 31: 1109–1118

    Article  Google Scholar 

  58. Olsen EHN, Rahbek-Nielsen H, Thogersen IB, Roepstorff P, Enghild JJ (1998) Post-translational modifications of human inter-a-inhibitor: identification of glycans and disulfide bridges in heavy chains 1 and 2. Biochemistry 37: 408–416

    Article  PubMed  CAS  Google Scholar 

  59. Ploug M, Rahbek-Nielsen H, Nielsen PF, Reopstorff P, Dario K (1998) Glycosylation profile of a recombinant urokinase-type plasminogen activator receptor expressed in Chinese hamster ovary cells. J Biol Chem 273: 13933–13943

    Article  PubMed  CAS  Google Scholar 

  60. Krogh TN, Mirgorodskaya E, Mertz E, Hojrup P, Roepstorff P (1996) Characterization of protein glycosylation by post source decay and exoglycosidase digestion. Proc. 44th ASMS Conference of Mass Spectrometry and Allied Topics, Portland, Oregon, 12–16 May, 1336

    Google Scholar 

  61. Ens W, Standing K, Chernushevitc IV (eds) (1998) New methods for the study of biomolecular complexes. Kluver Academic Publishers, Dordrecht

    Google Scholar 

  62. Roepstorff P (1997) Mass spectrometry in protein studies from genome to function. Curr Opin Biotech 8: 6–13

    Article  PubMed  CAS  Google Scholar 

  63. Strupat K, Hillenkamp F (1998) Analysis of quaternary protein ensembles by matrix assisted laser desorption/ionization mass spectrometry. J Am Chem Soc 119: 1046–1052

    Google Scholar 

  64. Suckau D, Mak M, Przybylski M (1992) Protein surface-topology probing by selective chemical modification and mass spectrometric mapping. Proc Natl Acad Sci USA 89: 5630–5634

    Article  PubMed  CAS  Google Scholar 

  65. Ellison D, Hinton J, Hubbard SJ, Beinon RJ (1995) Limited proteolysis of native proteins: the interaction between avidin and proteinase K. Prot Sci 4: 1337–1345

    Article  CAS  Google Scholar 

  66. Ploug M, Rahbek-Nielsen H, Ellis V, Roepstorff P, Dane K (1995) Chemical modification of the urokinase-type plasminogen activator and its receptor using tetranitromethane. Evidence for the involvement of specific tyrosine residues in both molecules during receptor-ligand interaction. Biochemistry 34: 12524–12534

    Article  PubMed  CAS  Google Scholar 

  67. Nordhoff E, Roepstorff P (1998) New methods for protein foot-printing using MALDI-MS. Proccedings of the 46th ASMS Conference on Mass Spectrometry and Allied Topics, Orlando, Florida, 30 May— 4 June

    Google Scholar 

  68. Kussmann M, Bennett KL, Sorensen P, Godswon M, Bjoerk P, Roepstorff P (1998) Studying protein-protein interactions by protein cross-linking and differential MALDI mass spectrometric peptide mapping. Proceedings of the 44th ASMS Conference on Mass Spectrometry and Allied Topics, Orlando, Florida 30 May— 4 June

    Google Scholar 

  69. Zhao Y, Muir TW, Kent SBH, Tischer T, Scardina JM, Chait BT (1996) Mapping protein-protein interactions by affinity-directed mass spectrometry. Proc Natl Acad Sci USA 93: 4020–4024

    Article  PubMed  CAS  Google Scholar 

  70. Schriemer DC, Li L (1996) Combining avidin-biotin chemistry with matrix-assisted laser desorption/ionization mass spectrometry. Anal Chem 68: 3382–3387

    Article  PubMed  CAS  Google Scholar 

  71. Girault S, Sagan S, Bolbach G, Lavielle S, Chassaing G (1996) The use of photolabeled peptides to localize the substance-P-binding site in the human neurokin-1 tachykinin receptor. Eur J Biochem 240: 215–222

    Article  PubMed  CAS  Google Scholar 

  72. Nelson RW, Krone JR, Bieber AL, Williams P (1995) Mass spectrometric immunoassay. Anal Chem 67: 1153–1158

    Article  PubMed  CAS  Google Scholar 

  73. Krone JR, Nelson RW, Dogruel D, Williams P (1997) BIA/MS: interfacing biomolecular interaction analysis with mass spectrometry. Anal Chem 69: 4363–4368

    Article  PubMed  Google Scholar 

  74. Sonksen CP, Nordhoff E, Jansson O, Malmqvist M, Roepstorff P (1998) Combining MALDI mass spectrometry and biomolecular interaction analysis using surface plasmon resonance. Anal Chem 70: 2731–2736

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Molecular Biology, Odense University, Odense M, DK-5230, Denmark

    Peter Roepstorff

Authors
  1. Peter Roepstorff
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Laboratoire de Chimie des Substances Naturelles URA C.N.R.S. No. 401, Muséum National d’Histoire Naturelle, 63, rue Buffon, F-75005, Paris, France

    P. Jollès

  2. Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77, Stockholm, Sweden

    H. Jörnvall

Rights and permissions

Reprints and permissions

Copyright information

© 2000 Springer Basel AG

About this chapter

Cite this chapter

Roepstorff, P. (2000). MALDI-TOF mass spectrometry in protein chemistry. In: Jollès, P., Jörnvall, H. (eds) Proteomics in Functional Genomics. EXS, vol 88. Birkhäuser, Basel. https://doi.org/10.1007/978-3-0348-8458-7_6

Download citation

  • DOI: https://doi.org/10.1007/978-3-0348-8458-7_6

  • Publisher Name: Birkhäuser, Basel

  • Print ISBN: 978-3-0348-9576-7

  • Online ISBN: 978-3-0348-8458-7

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation