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100% protein sequence coverage: a modern form of surrealism in proteomics

  • Review Article
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Abstract

This review intends not only to discuss the current possibilities to gain 100% sequence coverage for proteins, but also to point out the critical limits to such an attempt. The aim of 100% sequence coverage, as the review title already implies, seems to be rather surreal if the complexity and dynamic range of a proteome is taken into consideration. Nevertheless, established bottom-up shotgun approaches are able to roughly identify a complete proteome as exemplary shown by yeast. However, this proceeding ignores more or less the fact that a protein is present as various protein species. The unambiguous identification of protein species requires 100% sequence coverage. Furthermore, the separation of the proteome must be performed on the protein species and not on the peptide level. Therefore, top-down is a good strategy for protein species analysis. Classical 2D-electrophoresis followed by an enzymatic or chemical cleavage, which is a combination of top-down and bottom-up, is another interesting approach. Moreover, the review summarizes further top-down and bottom-up combinations and to which extent middle-down improves the identification of protein species. The attention is also focused on cleavage strategies other than trypsin, as 100% sequence coverage in bottom-up experiments is only obtainable with a combination of cleavage reagents.

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Acknowledgments

We would like to thank the Cluster of Excellence “Macromolecular Complexes” at the Goethe-University Frankfurt for the financial support and our colleagues Thorsten W. Jaskolla, Stavroula Markoutsa and Dorota Urbanek.

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  1. Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany

    Bjoern Meyer, Dimitrios G. Papasotiriou & Michael Karas

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  1. Bjoern Meyer
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  2. Dimitrios G. Papasotiriou
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  3. Michael Karas
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Correspondence to Bjoern Meyer.

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Meyer, B., Papasotiriou, D.G. & Karas, M. 100% protein sequence coverage: a modern form of surrealism in proteomics. Amino Acids 41, 291–310 (2011). https://doi.org/10.1007/s00726-010-0680-6

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