Skip to main content
SpringerLink
Log in

Mass Discrimination in High-Mass MALDI-MS

  • Research Article
  • Published:
Journal of The American Society for Mass Spectrometry

Abstract

In high-mass matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), the accessible m/z range is limited by the detector used. Therefore, special high-mass detectors based on ion conversion dynodes (ICDs) have been developed. Recently, we have found that mass bias may exist when such ICD detectors are used [Weidmann et al., Anal. Chem. 85(6), 3425–3432 (2013)]. In this contribution, the mass-dependent response of an ICD detector was systematically studied, the response factors for proteins with molecular weights from 35.9 to 129.9 kDa were determined, and the reasons for mass bias were identified. Compared with commonly employed microchannel plate detectors, we found that the mass discrimination is less pronounced, although ions with higher masses are weakly favored when using an ICD detector. The relative response was found to depend on the laser power used for MALDI; low-mass ions are discriminated against with higher laser power. The effect of mutual ion suppression in dependence of the proteins used and their molar ratio is shown. Mixtures consisting of protein oligomers that only differ in mass show less mass discrimination than mixtures consisting of different proteins with similar masses. Furthermore, mass discrimination increases for molar ratios far from 1. Finally, we present clear guidelines that help to choose the experimental parameters such that the response measured matches the actual molar fraction as closely as possible.

á…Ÿ

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Figure 1
Figure 2
Figure 3
Figure 4

Similar content being viewed by others

References

  1. Beavis, R.C., Chait, B.T.: Rapid, sensitive analysis of protein mixtures by mass-spectrometry. Proc. Natl. Acad. Sci. U.S.A. 87(17), 6873–6877 (1990)

    Google Scholar 

  2. Bahr, U., Deppe, A., Karas, M., Hillenkamp, F., Giessmann, U.: Mass spectrometry of synthetic polymers by UV-matrix-assisted laser desorption/ionization. Anal. Chem. 64(22), 2866–2869 (1992)

    Article  CAS  Google Scholar 

  3. Montaudo, G., Montaudo, M.S., Puglisi, C., Samperi, F.: Characterization of polymers by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: Molecular weight estimates in samples of varying polydispersity. Rapid Commun. Mass Spectrom. 9(5), 453–460 (1995)

    Article  CAS  Google Scholar 

  4. Montaudo, G., Montaudo, M.S., Puglisi, C., Samperi, F.: Characterization of polymers by matrix-assisted laser-desorption ionization-time of flight mass-spectrometry. End group determination and molecular-weight estimates in poly(ethylene glycols). Macromolecules 28(13), 4562–4569 (1995)

    Article  CAS  Google Scholar 

  5. Martin, K., Spickermann, J., Räder, H.J., Müllen, K.: Why does matrix-assisted laser desorption/ionization time-of-flight mass spectrometry give incorrect results for broad polymer distributions? Rapid Commun. Mass Spectrom. 10(12), 1471–1474 (1996)

    Article  CAS  Google Scholar 

  6. Schriemer, D.C., Li, L.: Mass discrimination in the analysis of polydisperse polymers by MALDI time-of-flight mass spectrometry. 1. Sample preparation and desorption/ionization issues. Anal. Chem. 69(20), 4169–4175 (1997)

    Article  CAS  Google Scholar 

  7. Schriemer, D.C., Li, L.: Mass discrimination in the analysis of polydisperse polymers by MALDI time-of-flight mass spectrometry. 2. Instrumental issues. Anal. Chem. 69(20), 4176–4183 (1997)

    Article  CAS  Google Scholar 

  8. Shimada, K., Lusenkova, M.A., Sato, K., Saito, T., Matsuyama, S., Nakahara, H., Kinugasa, S.: Evaluation of mass discrimination effects in the quantitative analysis of polydisperse polymers by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using uniform oligostyrenes. Rapid Commun. Mass Spectrom. 15(4), 277–282 (2001)

    Article  CAS  Google Scholar 

  9. Shimada, K., Nagahata, R., Kawabata, S.-I., Matsuyama, S., Saito, T., Kinugasa, S.: Evaluation of the quantitativeness of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using an equimolar mixture of uniform poly(ethylene glycol) oligomers. J. Mass Spectrom. 38(9), 948–954 (2003)

    Article  CAS  Google Scholar 

  10. Pieles, U., Zürcher, W., Schär, M., Moser, H.E.: Matrix-assisted laser desorption ionization time-of-flight mass-spectrometry: A powerful tool for the mass and sequence analysis of natural and modified oligonucleotides. Nucleic Acids Res. 21(14), 3191–3196 (1993)

    Article  CAS  Google Scholar 

  11. Roskey, M.T., Juhasz, P., Smirnov, I.P., Takach, E.J., Martin, S.A., Haff, L.A.: DNA sequencing by delayed extraction matrix-assisted laser desorption/ionization time of flight mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 93(10), 4724–4729 (1996)

    Google Scholar 

  12. Shaler, T.A., Tan, Y., Wickham, J.N., Wu, K.J., Becker, C.H.: Analysis of enzymatic DNA-sequencing reactions by matrix-assisted laser-desorption ionization time-of-flight mass-spectrometry. Rapid Commun. Mass Spectrom. 9(10), 942–947 (1995)

    Article  CAS  Google Scholar 

  13. Chen, X., Westphall, M.S., Smith, L.M.: Mass spectrometric analysis of DNA mixtures: Instrumental effects responsible for decreased sensitivity with increasing mass. Anal. Chem. 75(21), 5944–5952 (2003)

    Article  CAS  Google Scholar 

  14. Farmer, T.B., Caprioli, R.M.: Assessing the multimeric states of proteins: Studies using laser desorption mass spectrometry. Biol. Mass Spectrom. 20(12), 796–800 (1991)

    Article  CAS  Google Scholar 

  15. Farmer, T.B., Caprioli, R.M.: Determination of protein–protein interactions by matrix-assisted laser desorption/ionization mass spectrometry. J. Mass Spectrom. 33(8), 697–704 (1998)

    Article  CAS  Google Scholar 

  16. Mädler, S., Seitz, M., Robinson, J., Zenobi, R.: Does chemical cross-linking with NHS esters reflect the chemical equilibrium of protein–protein noncovalent interactions in solution? J. Am. Soc. Mass Spectrom. 21(10), 1775–1783 (2010)

    Article  Google Scholar 

  17. Gabelica, V., Galic, N., Rosu, F., Houssier, C., De Pauw, E.: Influence of response factors on determining equilibrium association constants of noncovalent complexes by electrospray ionization mass spectrometry. J. Mass Spectrom. 38(5), 491–501 (2003)

    Article  CAS  Google Scholar 

  18. Weidmann, S., Barylyuk, K., Nespovitaya, N., Mädler, S., Zenobi, R.: A new, modular mass calibrant for high-mass MALDI-MS. Anal. Chem. 85(6), 3425–3432 (2013)

    Article  CAS  Google Scholar 

  19. Farmer, T.B., Caprioli, R.M.: Mass discrimination in matrix-assisted laser-desorption ionization time-of-flight mass-spectrometry: A study using cross-linked oligomeric complexes. J. Mass Spectrom. 30(9), 1245–1254 (1995)

    Article  CAS  Google Scholar 

  20. Wiza, J.L.: Microchannel plate detectors. Nucl. Inst. Methods 162(1–3), 587–601 (1979)

    Google Scholar 

  21. Beuhler, R.J., Friedman, L.: Threshold studies of secondary-electron emission induced by macro-ion impact on solid-surfaces. Nucl. Inst. Methods 170(1–3), 309–315 (1980)

    Google Scholar 

  22. Geno, P.W., Macfarlane, R.D.: Secondary electron emission induced by impact of low-velocity molecular ions on a microchannel plate. Int. J. Mass Spectrom. Ion Process. 92, 195–210 (1989)

    Article  CAS  Google Scholar 

  23. Brunelle, A., Chaurand, P., Della-Negra, S., Le Beyec, Y., Baptista, G.B.: Surface secondary-electron and secondary-ion emission induced by large molecular ion impacts. Int. J. Mass Spectrom. Ion Process. 126, 65–73 (1993)

    Article  CAS  Google Scholar 

  24. Coeck, S., Beck, M., Delauré, B., Golovko, V.V., Herbane, M., Lindroth, A., Kopecky, S., Kozlov, V.Y., Kraev, I.S., Phalet, T., Severijns, N.: Microchannel plate response to high-intensity ion bunches. Nucl. Inst. Methods A 557(2), 516–522 (2006)

    Article  CAS  Google Scholar 

  25. Frank, M., Labov, S.E., Westmacott, G., Benner, W.H.: Energy-sensitive cryogenic detectors for high-mass biomolecule mass spectrometry. Mass Spectrom. Rev. 18(3–4), 155–186 (1999)

    Google Scholar 

  26. Kraus, H.: Cryogenic detectors and their application to mass spectrometry. Int. J. Mass Spectrom. 215(1–3), 45–58 (2002)

    Google Scholar 

  27. Park, J., Qin, H., Scalf, M., Hilger, R.T., Westphall, M.S., Smith, L.M., Blick, R.H.: A mechanical nanomembrane detector for time-of-flight mass spectrometry. Nano Lett. 11(9), 3681–3684 (2011)

    Article  CAS  Google Scholar 

  28. Wenzel, R.J., Röhling, U., Nazabal, A., Hillenkamp, F.: A detector device for high mass ion detection, a method for analyzing ions of high mass and a device for selection between ion detectors. Internat. Patent WO2009086642-A1, July 16 (2009).

  29. Winograd, N.: The magic of cluster SIMS. Anal. Chem. 77(7), 142 A–149 A (2005)

    Article  CAS  Google Scholar 

  30. Fletcher, J.S., Lockyer, N.P., Vickerman, J.C.: Developments in molecular SIMS depth profiling and 3D imaging of biological systems using polyatomic primary ions. Mass Spectrom. Rev. 30(1), 142–174 (2011)

    Article  CAS  Google Scholar 

  31. Chen, F., Gerber, S., Heuser, K., Korkhov, V.M., Lizak, C., Mireku, S., Locher, K.P., Zenobi, R.: High-mass matrix-assisted laser desorption ionization-mass spectrometry of integral membrane proteins and their complexes. Anal. Chem. 85(7), 3483–3488 (2013)

    Article  CAS  Google Scholar 

  32. Wetzel, S.K., Settanni, G., Kenig, M., Binz, H.K., Plückthun, A.: Folding and unfolding mechanism of highly stable full-consensus ankyrin repeat proteins. J. Mol. Biol. 376(1), 241–257 (2008)

    Article  CAS  Google Scholar 

  33. Binz, H.K., Stumpp, M.T., Forrer, P., Amstutz, P., Plückthun, A.: Designing repeat proteins: Well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins. J. Mol. Biol. 332(2), 489–503 (2003)

    Article  CAS  Google Scholar 

  34. Forrer, P., Binz, H.K., Stumpp, M.T., Plückthun, A.: Consensus design of repeat proteins. ChemBioChem 5(2), 183–189 (2004)

    Article  CAS  Google Scholar 

  35. Boeri Erba, E., Barylyuk, K., Yang, Y., Zenobi, R.: Quantifying protein–protein interactions within noncovalent complexes using electrospray ionization mass spectrometry. Anal. Chem. 83(24), 9251–9259 (2011)

    Article  CAS  Google Scholar 

  36. Dreisewerd, K.: The desorption process in MALDI. Chem. Rev. 103(2), 395–425 (2003)

    Article  CAS  Google Scholar 

  37. Knochenmuss, R.: Ion formation mechanisms in UV-MALDI. Analyst 131(9), 966–986 (2006)

    Article  CAS  Google Scholar 

  38. Aksenov, A.A., Bier, M.E.: The analysis of polystyrene and polystyrene aggregates into the mega dalton mass range by cryodetection MALDI TOF MS. J. Am. Soc. Mass Spectrom. 19(2), 219–230 (2008)

    Article  CAS  Google Scholar 

  39. Zenobi, R.: Ionization processes and detection in MALDI-MS of polymers. In: Li, L. (ed.) MALDI Mass Spectrometry for Synthetic Polymer Analysis, pp. 9–26. John Wiley and Sons, Inc, Hoboken, NJ (2009)

    Chapter  Google Scholar 

  40. Ingendoh, A., Karas, M., Hillenkamp, F., Giessmann, U.: Factors affecting the resolution in matrix-assisted laser desorption-ionization mass spectrometry. Int. J. Mass Spectrom. Ion Process. 131, 345–354 (1994)

    Article  CAS  Google Scholar 

  41. Knochenmuss, R., Zenobi, R.: MALDI ionization: The role of in-plume processes. Chem. Rev. 103(2), 441–452 (2003)

    Article  CAS  Google Scholar 

  42. Kaltashov, I.A., Mohimen, A.: Estimates of protein surface areas in solution by electrospray ionization mass spectrometry. Anal. Chem. 77(16), 5370–5379 (2005)

    Article  CAS  Google Scholar 

  43. Spurlino, J.C., Lu, G.-Y., Quiocho, F.A.: The 2.3-Å resolution structure of the maltose- or maltodextrin-binding protein, a primary receptor of bacterial active transport and chemotaxis. J. Biol. Chem. 266(8), 5202–5219 (1991)

    CAS  Google Scholar 

  44. Binz, H.K., Amstutz, P., Kohl, A., Stumpp, M.T., Briand, C., Forrer, P., Grütter, M.G., Plückthun, A.: High-affinity binders selected from designed ankyrin repeat protein libraries. Nat. Biotechnol. 22(5), 575–582 (2004)

    Article  CAS  Google Scholar 

  45. Kohl, A., Binz, H.K., Forrer, P., Stumpp, M.T., Plückthun, A., Grütter, M.G.: Designed to be stable: Crystal structure of a consensus ankyrin repeat protein. Proc. Natl. Acad. Sci. U.S.A. 100(4), 1700–1705 (2003)

    Google Scholar 

  46. Prajapati, R.S., Indu, S., Varadarajan, R.: Identification and thermodynamic characterization of molten globule states of periplasmic binding proteins. Biochemistry 46(36), 10339–10352 (2007)

    Article  CAS  Google Scholar 

  47. Mädler, S., Barylyuk, K., Boeri Erba, E., Nieckarz, R.J., Zenobi, R.: Compelling advantages of negative ion mode detection in high-mass MALDI-MS for homomeric protein complexes. J. Am. Soc. Mass Spectrom. 23(2), 213–224 (2012)

    Article  Google Scholar 

Download references

Acknowledgments

The authors thank the SystemsX.ch initiative (CINA grant) and the Swiss National Science Foundation (grant no. 200020–124663) for their financial support. G.M. was supported by a Swiss Government Excellence Scholarship (2011–2013). The authors also thank Stefanie Mädler (currently at York University, Toronto, Canada) and Nadezhda Nespovitaya (ETH Zürich, Switzerland) for their help with the design and synthesis of the MBP3 polyproteins, and the Plückthun Lab (University of Zürich, Switzerland) for the generous gift of the DARPin samples.

Author information

Authors and Affiliations

  1. Department of Chemistry and Applied Biosciences, ETH (Swiss Federal Institute of Technology) Zürich, CH-8093, Zürich, Switzerland

    Simon Weidmann, Gediminas Mikutis, Konstantin Barylyuk & Renato Zenobi

Authors
  1. Simon Weidmann
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Gediminas Mikutis
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Konstantin Barylyuk
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Renato Zenobi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Renato Zenobi.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Weidmann, S., Mikutis, G., Barylyuk, K. et al. Mass Discrimination in High-Mass MALDI-MS. J. Am. Soc. Mass Spectrom. 24, 1396–1404 (2013). https://doi.org/10.1007/s13361-013-0686-x

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13361-013-0686-x

Key words

Search

Navigation