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Proteome Bioinformatics pp 123–135Cite as

Cross Species Proteomics

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Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 604))

Abstract

Proteomics has advanced in leaps and bounds over the past couple of decades. However, the continuing dependency of mass spectrometry-based protein identification on the searching of spectra against protein sequence databases limits many proteomics experiments. If there is no sequenced genome for a given species, then cross species proteomics is required, attempting to identify proteins across the species boundary, typically using the sequenced genome of a closely related species. Unlike sequence searching for homologues, the proteomics equivalent is confounded by small differences in amino acid sequences, leading to large differences in peptide masses; this renders mass matching of peptides and their product ions difficult. Therefore, the phylogenetic distance between the two species and the attendant level of conservation between the homologous proteins play a huge part in determining the extent of protein identification that is possible across the species boundary. In this chapter, we review the cross species challenge itself, as well as various approaches taken to deal with it and the success met with in past studies. This is followed by recommendations of best practice and suggestions to researchers facing this challenge as well as a final section predicting developments, which may help improve cross species proteomics in the future.

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Abbreviations

PMF:

Peptide mass fingerprint

ESI:

Electrospray ionisation

MALDI:

Matrix assisted laser desorption/ionisation

MS:

Mass spectrometry

m/z :

Mass to charge

PTM:

Post translational modification

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Acknowledgments

James Wright acknowledges NERC (NER/S/R/2005/13607) for his PhD funding.

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Authors and Affiliations

  1. Department Veterinary Preclinical Sciences, University of Liverpool, Crown Street, Liverpool, UK

    J. C. Wright & R. J. Beynon

  2. Faculty of Life Sciences, University of Manchester, Manchester, UK

    J. C. Wright & S. J. Hubbard

Authors
  1. J. C. Wright
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  2. R. J. Beynon
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  3. S. J. Hubbard
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Correspondence to S. J. Hubbard .

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Editors and Affiliations

  1. Fac. Life Sciences, University of Manchester, Oxford Rd., Manchester, M13 9PT, United Kingdom

    Simon J. Hubbard

  2. Fac. Veterinary Science, University of Liverpool, Liverpool, L69 7ZJ, United Kingdom

    Andrew R. Jones

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Wright, J.C., Beynon, R.J., Hubbard, S.J. (2010). Cross Species Proteomics. In: Hubbard, S., Jones, A. (eds) Proteome Bioinformatics. Methods in Molecular Biology™, vol 604. Humana Press. https://doi.org/10.1007/978-1-60761-444-9_9

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  • DOI: https://doi.org/10.1007/978-1-60761-444-9_9

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