Skip to main content

Phage Proteomics: Applications of Mass Spectrometry

  • Protocol

Part of the Methods in Molecular Biology™ book series (MIMB,volume 502)

Abstract

Current techniques in mass spectrometry (MS) allow sensitive and accurate identification of proteins thanks to the in silico availability of these protein sequences within databases.

This chapter provides a short overview of MS techniques used in the identification of phage structural proteins and focuses on an electron spray peptide ionization (ESI-MS/MS) approach to identify the phage structural proteome in a comprehensive and systematic ways. Such analyses provide an experimental examination of structural proteins and confirm genome-based gene predictions.

Key Words

  • Structural proteome
  • mass spectrometry
  • whole-phage shotgun proteomics
  • bacteriophage

This is a preview of subscription content, access via your institution.

Buying options

Protocol
USD   49.95
Price excludes VAT (USA)
  • DOI: 10.1007/978-1-60327-565-1_14
  • Chapter length: 13 pages
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
eBook
USD   149.00
Price excludes VAT (USA)
  • ISBN: 978-1-60327-565-1
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Softcover Book
USD   199.99
Price excludes VAT (USA)
Hardcover Book
USD   279.99
Price excludes VAT (USA)
Fig. 14.1

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Nakayama, K., Kanaya, S., Ohnishi, M., Terawaki, Y. and Hayashi, T. (1999) The complete nucleotide sequence of \(\phi\mathrm{CTX}\), a cytotoxin-converting phage of Pseudomonas aeruginosa: implications for phage evolution and horizontal gene transfer via bacteriophages. Mol Microbiol., 31, 399–419.

    CAS  CrossRef  PubMed  Google Scholar 

  2. Loessner, M.J., Inman, R.B., Lauer, P. and Calendar, R. (2000) Complete nucleotide sequence, molecular analysis and genome structure of bacteriophage A118 of Listeria monocytogenes: implications for phage evolution. Mol Microbiol., 35, 324–340.

    CAS  CrossRef  PubMed  Google Scholar 

  3. Zimmer, M., Sattelberger, E., Inman, R.B., Calendar, R. and Loessner, M.J. (2003) Genome and proteome of Listeria monocytogenes phage PSA: an unusual case for programmed \(+\) 1 translational frameshifting in structural protein synthesis. Mol Microbiol., 50, 303–317.

    CAS  CrossRef  PubMed  Google Scholar 

  4. Roberts, M.D., Martin, N.L. and Kropinski, A.M. (2004) The genome and proteome of coliphage T1. Virology, 318, 245–266.

    CAS  CrossRef  PubMed  Google Scholar 

  5. Chibani-Chennoufi, S., Canchaya, C., Bruttin, A. and Brüssow, H. (2004) Comparative genomics of the T4-Like Escherichia coli phage JS98: implications for the evolution of T4 phages. J Bacteriol., 186, 8276–8286.

    CAS  CrossRef  PubMed  Google Scholar 

  6. Scholl, D., Kieleczawa, J., Kemp, P., Rush, J., Richardson, C.C., Merril, C., Adhya, S. and Molineux, I.J. (2004) Genomic analysis of bacteriophages SP6 and K1–5, an estranged subgroup of the T7 supergroup. J Mol Biol., 335, 1151–1171.

    CAS  CrossRef  PubMed  Google Scholar 

  7. Levesque, C., Duplessis, M., Labonte, J., Labrie, S., Fremaux, C., Tremblay, D. and Moineau, S. (2005) Genomic organization and molecular analysis of virulent bacteriophage 2972 infecting an exopolysaccharide-producing Streptococcus thermophilus strain. Appl Environ Microbiol., 71, 4057–4068.

    CAS  CrossRef  PubMed  Google Scholar 

  8. Byrne, M. and Kropinski, A.M. (2005) The genome of the Pseudomonas aeruginosa generalized transducing bacteriophage F116. Gene, 346, 187–194.

    CAS  CrossRef  PubMed  Google Scholar 

  9. Bukovska, G., Klucar, L., Vlcek, C., Adamovic, J., Turna, J. and Timko, J. (2006) Complete nucleotide sequence and genome analysis of bacteriophage BFK20–a lytic phage of the industrial producer Brevibacterium flavum. Virology, 348, 57–71.

    CAS  CrossRef  PubMed  Google Scholar 

  10. Lavigne, R., Noben, J.P., Hertveldt, K., Ceyssens, P-J., Briers, Y., Dumont, D., Roucourt, B., Krylov, V.N., Mesyanzhinov, V.V., Robben, J. and Volckaert, G. (2006) The structural proteome of Pseudomonas aeruginosa bacteriophage \(\phi\mathrm{KMV}\). Microbiology, 152(Pt 2), 529–534.

    CAS  CrossRef  PubMed  Google Scholar 

  11. Ceyssens, P-J., Lavigne, R., Chibeu, A., Mattheus, W., Hertveldt, K., Robben, J. en Volckaert, G (2006) Genomic analysis of Pseudomonas aeruginosa phages LKD16 and LKA1: Establishment of the \(\phi\mathrm{KMV}\) subgroup within the T7 supergroup. J. Bacteriology, 188(19), 6924–6931.

    CAS  CrossRef  Google Scholar 

  12. Rees, J.C. and Voorhees, K.J. (2005) Simultaneous detection of two bacterial pathogens using bacteriophage amplification coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom., 19, 2757–2761.

    CAS  CrossRef  PubMed  Google Scholar 

  13. Dumont, D., Noben, J.P., Raus, J., Stinissen, P. and Robben, J. (2004) Proteomic analysis of cerebrospinal fluid from multiple sclerosis patients. Proteomics, 4, 2117–2124.

    CAS  CrossRef  PubMed  Google Scholar 

  14. Shevchenko, A., Wilm, M., Vorm, O. and Mann M. (1996) Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal Chem., 68, 850–858.

    CAS  CrossRef  PubMed  Google Scholar 

  15. Steen, H. and Mann, M.(2004) The ABC’s (and XYZ’s) of peptide sequencing. Nat Rev Mol Cell Biol., 5, 699–711.

    CAS  CrossRef  PubMed  Google Scholar 

  16. Taylor, J.A. and Johnson, R.S. (1997) Sequence database searches via de novo peptide sequencing by tandem mass spectrometry. Rapid Commun Mass Spectrom., 11, 1067–1075.

    CAS  CrossRef  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and Permissions

Copyright information

© 2009 Humana Press, a part of Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Lavigne, R., Ceyssens, PJ., Robben, J. (2009). Phage Proteomics: Applications of Mass Spectrometry. In: Clokie, M.R., Kropinski, A.M. (eds) Bacteriophages. Methods in Molecular Biology™, vol 502. Humana Press. https://doi.org/10.1007/978-1-60327-565-1_14

Download citation

  • DOI: https://doi.org/10.1007/978-1-60327-565-1_14

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60327-564-4

  • Online ISBN: 978-1-60327-565-1

  • eBook Packages: Springer Protocols