Evaluation of Chemical Derivatisation Methods for Protein Identification using MALDI MS/MS

  • Janice L. Joss
  • Mark P. Molloy
  • Lyn A. Hinds
  • Elizabeth M. Deane
Article

DOI: 10.1007/s10989-006-9026-3

Cite this article as:
Joss, J., Molloy, M., Hinds, L. et al. Int J Pept Res Ther (2006) 12: 225. doi:10.1007/s10989-006-9026-3

In proteomic studies, assigning protein identity from organisms whose genomes are yet to be completely sequenced remains a challenging task. For these organisms, protein identification is typically based on cross species matching of amino acid sequence obtained from collision induced dissociation (CID) of peptides using mass spectrometry. The most direct approach of de novo sequencing is slow and often difficult, due to the complexity of the resultant CID spectra. For MALDI-MS, this problem has been addressed by using chemical derivatisation to direct peptide fragmentation, thereby simplifying CID spectra and facilitating de novo interpretation. In this study, milk whey proteins from the tammar wallaby (Macropus eugenii) were used to evaluate three chemical derivatisation methods compatible with MALDI MS/MS. These methods included (i) guanidination and sulfonation using chemically-assisted fragmentation (CAF), (ii) guanidination and sulfonation using 4-sulfophenyl isothiocyanate (SPITC) and (iii) derivatising the epsilon-amino group of lysine residues with Lys Tag 4H. Derivatisation with CAF and SPITC resulted in more protein identification than Lys Tag 4H. Sulfonation using SPITC was the preferred method due to the low cost per experiment, the reactivity with both lysine and arginine terminated peptides and the resultant simplified MS/MS spectra.

Keywords

cross species matching de novo sequencing MALDI MS/MS guanidination sulfonation 

Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • Janice L. Joss
    • 1
  • Mark P. Molloy
    • 2
  • Lyn A. Hinds
    • 3
  • Elizabeth M. Deane
    • 1
    • 4
  1. 1.Division of Environmental and Life Sciences, Department of Biological ScienceMacquarie UniversitySydneyAustralia
  2. 2.Australian Proteome Analysis FacilityMacquarie UniversitySydneyAustralia
  3. 3.CSIRO, Division of EntomologyCanberraAustralia
  4. 4.Division of Environmental and Life Sciences, Department of Biological ScienceMacquarie UniversitySydneyAustralia

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