Skip to main content
SpringerLink
Log in

Identification of the Candida albicans Immunome During Systemic Infection by Mass Spectrometry

  • Protocol
Book cover Host-Pathogen Interactions

Part of the book series: Methods in Molecular Biology ((MIMB,volume 470))

Abstract

Over the past two decades, mass spectrometry (MS) has ceased to be a fairly exotic technique banished from the protein scientists’ mind to become a seminal tool for deciphering the information encoded in the genomes of many biological species. Clues to this shift in the modus operandi for characterizing their proteomes stem from the progressive availability of full genome sequences and well-annotated protein databases of many model (micro)organisms, the development both of soft ionization methods for large biomolecules (peptides and proteins) and of innovative instrumentation designs, and the introduction of sophisticated search algorithms able to correlate MS information with sequence databases, to name but a few. Here we integrate the typical MS-based strategy for identifying proteins of Candida albicans, an opportunistic fungal pathogen of humans, which have proved to be present during systemic infection and targeted by the immune system as a consequence of its interaction with the host (i.e., the C. albicans immunome).

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

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Wilkins, M. R., Sanchez, J. C., Gooley, A. A., Appel, R. D., Humphery-Smith, I., Hochstrasser, D. F., and Williams, K. L. (1996) Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol. Genet. Eng Rev. 13, 19–50.

    CAS  PubMed  Google Scholar 

  2. Wasinger, V. C., Cordwell, S. J., Cerpa-Poljak, A., Yan, J. X., Gooley, A. A., Wilkins, M. R., Duncan, M. W., Harris, R., Williams, K. L., and Humphery-Smith, I. (1995) Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium. Electrophoresis 16, 1090–1094.

    Article  CAS  PubMed  Google Scholar 

  3. Pitarch, A., Nombela, C., and Gil, C. (2006) Candida albicans biology and pathogenicity: insights from proteomics. Methods Biochem. Anal. 49, 285–330.

    CAS  PubMed  Google Scholar 

  4. Pitarch, A., Nombela, C., and Gil, C. (2006) Contributions of proteomics to diagnosis, treatment, and prevention of candidiasis. Methods Biochem. Anal. 49, 331–361.

    CAS  PubMed  Google Scholar 

  5. Jones, T., Federspiel, N. A., Chibana, H., Dungan, J., Kalman, S., Magee, B. B., Newport, G., Thorstenson, Y. R., Agabian, N., Magee, P. T., Davis, R. W., and Scherer, S. (2004) The diploid genome sequence of Candida albicans. Proc. Natl. Acad. Sci. U.S.A. 101, 7329–7334.

    Article  CAS  PubMed  Google Scholar 

  6. Goffeau, A., Barrell, B. G., Bussey, H., Davis, R. W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J. D., Jacq, C., Johnston, M., Louis, E. J., Mewes, H. W., Murakami, Y., Philippsen, P., Tettelin, H., and Oliver, S. G. (1996) Life with 6000 genes. Science 274, 563–546.

    Article  Google Scholar 

  7. d’Enfert, C., Goyard, S., Rodriguez-Arnaveilhe, S., Frangeul, L., Jones, L., Tekaia, F., Bader, O., Albrecht, A., Castillo, L., Dominguez, A., Ernst, J. F., Fradin, C., Gaillardin, C., Garcia-Sanchez, S., de Groot, P., Hube, B., Klis, F. M., Krishnamurthy, S., Kunze, D., Lopez, M. C., Mavor, A., Martin, N., Moszer, I., Onesime, D., Perez, M. J., Sentandreu, R., Valentin, E., and Brown, A. J. (2005) CandidaDB: a genome database for Candida albicans pathogenomics. Nucleic Acids Res. 33, D353–D357.

    Article  PubMed  Google Scholar 

  8. Arnaud, M. B., Costanzo, M. C., Skrzypek, M. S., Shah, P., Binkley, G., Lane, C., Miyasato, S. R., and Sherlock, G. (2007) Sequence resources at the Candida Genome Database. Nucleic Acids Res. 35, D452–D456.

    Article  CAS  PubMed  Google Scholar 

  9. Csank, C., Costanzo, M. C., Hirschman, J., Hodges, P., Kranz, J. E., Mangan, M., O’Neill, K., Robertson, L. S., Skrzypek, M. S., Brooks, J., and Garrels, J. I. (2002) Three yeast proteome databases: YPD, PombePD, and CalPD (MycoPathPD). Methods Enzymol. 350, 347–373.

    Article  CAS  PubMed  Google Scholar 

  10. Pitarch, A., Sanchez, M., Nombela, C., and Gil, C. (2003) Analysis of the Candida albicans proteome. II. Protein information technology on the Net (update 2002). J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 787, 129–148.

    Article  CAS  PubMed  Google Scholar 

  11. Nash, R., Weng, S., Hitz, B., Balakrishnan, R., Christie, K. R., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hirschman, J. E., Hong, E. L., Livstone, M. S., Oughtred, R., Park, J., Skrzypek, M., Theesfeld, C. L., Binkley, G., Dong, Q., Lane, C., Miyasato, S., Sethuraman, A., Schroeder, M., Dolinski, K., Botstein, D., and Cherry, J. M. (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res. 35, D468–D471.

    Article  CAS  PubMed  Google Scholar 

  12. Tanaka, K., Waki, H., Ido, Y. (1988). Protein and polymer analyses up to m/z 100,000 by laser ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 2, 151.

    Article  CAS  Google Scholar 

  13. Karas, M. and Hillenkamp, F. (1988) Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem. 60, 2299–2301.

    Article  CAS  PubMed  Google Scholar 

  14. Fenn, J. B., Mann, M., Meng, C. K., Wong, S. F., and Whitehouse, C. M. (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246, 64–71.

    Article  CAS  PubMed  Google Scholar 

  15. Palagi, P. M., Hernandez, P., Walther, D., and Appel, R. D. (2006) Proteome informatics I: bioinformatics tools for processing experimental data. Proteomics 6, 5435–5444.

    Article  CAS  PubMed  Google Scholar 

  16. Shadforth, I., Crowther, D., and Bessant, C. (2005) Protein and peptide identification algorithms using MS for use in high-throughput, automated pipelines. Proteomics 5, 4082–4095.

    Article  CAS  PubMed  Google Scholar 

  17. Pitarch, A., Sanchez, M., Nombela, C., and Gil, C. (2003) Analysis of the Candida albicans proteome. I. Strategies and applications. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 787, 101–128.

    Article  CAS  PubMed  Google Scholar 

  18. Graves, P. R. and Haystead, T. A. (2002) Molecular biologist’s guide to proteomics. Microbiol. Mol. Biol. Rev. 66, 39–63.

    Article  CAS  PubMed  Google Scholar 

  19. Annan, R. S. and Carr, S. A. (1997) The essential role of mass spectrometry in characterizing protein structure: mapping posttranslational modifications. J. Protein Chem. 16, 391–402.

    Article  CAS  PubMed  Google Scholar 

  20. Mann, M., Hendrickson, R. C., and Pandey, A. (2001) Analysis of proteins and proteomes by mass spectrometry. Annu. Rev. Biochem. 70, 437–473.

    Article  CAS  PubMed  Google Scholar 

  21. Domon, B. and Aebersold, R. (2006) Mass spectrometry and protein analysis. Science 312, 212–217.

    Article  CAS  PubMed  Google Scholar 

  22. Aebersold, R. and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198–207.

    Article  CAS  PubMed  Google Scholar 

  23. Baldwin, M. A. (2005) Mass spectrometers for the analysis of biomolecules. Methods Enzymol. 402, 3–48.

    Article  CAS  PubMed  Google Scholar 

  24. Mann, M., Hendrickson, R. C., and Pandey, A. (2001) Analysis of proteins and proteomes by mass spectrometry. Annu. Rev. Biochem. 70, 437–473.

    Article  CAS  PubMed  Google Scholar 

  25. Pitarch, A., Abian, J., Carrascal, M., Sanchez, M., Nombela, C., and Gil, C. (2004) Proteomics-based identification of novel Candida albicans antigens for diagnosis of systemic candidiasis in patients with underlying hematological malignancies. Proteomics 4, 3084–3106.

    Article  CAS  PubMed  Google Scholar 

  26. Pardo, M., Ward, M., Pitarch, A., Sanchez, M., Nombela, C., Blackstock, W., and Gil, C. (2000) Cross-species identification of novel Candida albicans immunogenic proteins by combination of two-dimensional polyacrylamide gel electrophoresis and mass spectrometry. Electrophoresis 21, 2651–2659.

    Article  CAS  PubMed  Google Scholar 

  27. Shevchenko, A., Jensen, O. N., Podtelejnikov, A. V., Sagliocco, F., Wilm, M., Vorm, O., Mortensen, P., Shevchenko, A., Boucherie, H., and Mann, M. (1996) Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels. Proc. Natl. Acad. Sci. U.S.A. 93, 14440–14445.

    Article  CAS  PubMed  Google Scholar 

  28. Masuoka, J., Glee, P. M., and Hazen, K. C. (1998) Preparative isoelectric focusing and preparative electrophoresis of hydrophobic Candida albicans cell wall proteins with in-line transfer to polyvinylidene difluoride membranes for sequencing. Electrophoresis 19, 675–678.

    Article  CAS  PubMed  Google Scholar 

  29. Washburn, M. P., Wolters, D., and Yates, J. R., III (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242–247.

    Article  CAS  PubMed  Google Scholar 

  30. Pitarch, A., Jimenez, A., Nombela, C., and Gil, C. (2006) Decoding serological response to Candida cell wall immunome into novel diagnostic, prognostic, and therapeutic candidates for systemic candidiasis by proteomic and bioinformatic analyses. Mol. Cell Proteomics 5, 79–96.

    CAS  PubMed  Google Scholar 

  31. Wilson, R. A., Curwen, R. S., Braschi, S., Hall, S. L., Coulson, P. S., and Ashton, P. D. (2004) From genomes to vaccines via the proteome. Mem. Inst. Oswaldo Cruz 99, 45–50.

    Article  CAS  PubMed  Google Scholar 

  32. Sette, A., Fleri, W., Peters, B., Sathiamurthy, M., Bui, H. H., and Wilson, S. (2005) A roadmap for the immunomics of category A-C pathogens. Immunity 22, 155–161.

    Article  CAS  PubMed  Google Scholar 

  33. Pitarch, A., Molero, G., Monteoliva, L., Thomas, D. P., López-Ribot, J. L., Nombela, C., and Gil, C. (2007) Proteomics in Candida species, in Candida: Comparative and Functional Genomics. (d’Enfert, C. and Hube, B., eds), Caister Academic Press, UK, pp. 169–194.

    Google Scholar 

  34. Thomas, D. P., Pitarch, A., Monteoliva, L., Gil, C., and Lopez-Ribot, J. L. (2006) Proteomics to study Candida albicans biology and pathogenicity. Infect. Disord. Drug Targets 6, 335–341.

    Article  CAS  PubMed  Google Scholar 

  35. Wilm, M., Shevchenko, A., Houthaeve, T., Breit, S., Schweigerer, L., Fotsis, T., and Mann, M. (1996) Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry. Nature 379, 466–469.

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  37. McCormack, A. L., Schieltz, D. M., Goode, B., Yang, S., Barnes, G., Drubin, D., and Yates, J. R., III (1997) Direct analysis and identification of proteins in mixtures by LC/MS/MS and database searching at the low-femtomole level. Anal. Chem. 69, 767–776.

    Article  CAS  PubMed  Google Scholar 

  38. Gharahdaghi, F., Weinberg, C. R., Meagher, D. A., Imai, B. S., and Mische, S. M. (1999) Mass spectrometric identification of proteins from silver-stained polyacrylamide gel: a method for the removal of silver ions to enhance sensitivity. Electrophoresis 20, 601–605.

    Article  CAS  PubMed  Google Scholar 

  39. Yates, J. R., Speicher, S., Griffin, P. R., and Hunkapiller, T. (1993) Peptide mass maps: a highly informative approach to protein identification. Anal. Biochem. 214, 397–408.

    Article  CAS  PubMed  Google Scholar 

  40. James, P., Quadroni, M., Carafoli, E., and Gonnet, G. (1993) Protein identification by mass profile fingerprinting. Biochem. Biophys. Res. Commun. 195, 58–64.

    Article  CAS  PubMed  Google Scholar 

  41. Thiede, B., Hohenwarter, W., Krah, A., Mattow, J., Schmid, M., Schmidt, F., and Jungblut, P. R. (2005) Peptide mass fingerprinting. Methods 35, 237–247.

    Article  CAS  PubMed  Google Scholar 

  42. Marvin, L. F., Roberts, M. A., and Fay, L. B. (2003) Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in clinical chemistry. Clin. Chim. Acta 337, 11–21.

    Article  CAS  PubMed  Google Scholar 

  43. Rappsilber, J., Moniatte, M., Nielsen, M. L., Podtelejnikov, A. V., Mann, M. (2003). Experiencies and perspectives of MALDI MS and MS/MS in proteomic research. Int. J. Mass Spectrom. 226, 223–237.

    Article  CAS  Google Scholar 

  44. Jensen, O. N., Podtelejnikov, A., and Mann, M. (1996) Delayed extraction improves specificity in database searches by matrix-assisted laser desorption/ionization peptide maps. Rapid Commun. Mass Spectrom. 10, 1371–1378.

    Article  CAS  PubMed  Google Scholar 

  45. Wysocki, V. H., Resing, K. A., Zhang, Q., and Cheng, G. (2005) Mass spectrometry of peptides and proteins. Methods 35, 211–222.

    Article  CAS  PubMed  Google Scholar 

  46. Medzihradszky, K. F. (2005) Peptide sequence analysis. Methods Enzymol. 402, 209–244.

    Article  CAS  PubMed  Google Scholar 

  47. Wilm, M. and Mann, M. (1996) Analytical properties of the nanoelectrospray ion source. Anal. Chem. 68, 1–8.

    Article  CAS  PubMed  Google Scholar 

  48. Jonscher, K. R. and Yates, J. R. (1997) The quadrupole ion trap mass spectrometer–a small solution to a big challenge. Anal.Biochem. 244, 1–15.

    Article  CAS  PubMed  Google Scholar 

  49. Biemann, K. (1992) Mass spectrometry of peptides and proteins. Annu. Rev. Biochem. 61, 977–1010.

    Article  CAS  PubMed  Google Scholar 

  50. Cook, K. D. (2002) ASMS members John Fenn and Koichi Tanaka share Nobel: the world learns our “secret.” American Society for Mass Spectrometry. J. Am. Soc. Mass Spectrom. 13, 1359.

    Article  CAS  PubMed  Google Scholar 

  51. Cooks, R. G., Rockwood, A. L. (1991) The “Thomson”: A suggested unit for mass spectroscopy. Rapid Commun. Mass Spectrom. 5, 93.

    CAS  Google Scholar 

  52. Graves, P. R. and Haystead, A. J. (2003) Proteomics and molecular biologist, in Handbook of Proteomic Methods (Conn, P. M., ed), The Humana Press Inc., Totowa, NJ, pp. 3–16.

    Google Scholar 

  53. Strupat, K. (2005) Molecular weight determination of peptides and proteins by ESI and MALDI. Methods Enzymol. 405, 1–36.

    Article  CAS  PubMed  Google Scholar 

  54. Syka, J. E., Coon, J. J., Schroeder, M. J., Shabanowitz, J., and Hunt, D. F. (2004) Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 101, 9528–9533.

    Article  CAS  PubMed  Google Scholar 

  55. Zubarev, R. A., Horn, D. M., Fridriksson, E. K., Kelleher, N. L., Kruger, N. A., Lewis, M. A., Carpenter, B. K., and McLafferty, F. W. (2000) Electron capture dissociation for structural characterization of multiply charged protein cations. Anal. Chem. 72, 563–573.

    Article  CAS  PubMed  Google Scholar 

  56. Whitelegge, J., Halgand, F., Souda, P., and Zabrouskov, V. (2006) Top-down mass spectrometry of integral membrane proteins. Expert. Rev. Proteomics 3, 585–596.

    Article  CAS  PubMed  Google Scholar 

  57. Kelleher, N. L. (2004) Top-down proteomics. Anal. Chem. 76, 197A–203A.

    Article  PubMed  Google Scholar 

  58. Sze, S. K., Ge, Y., Oh, H., and McLafferty, F. W. (2002) Top-down mass spectrometry of a 29-kDa protein for characterization of any posttranslational modification to within one residue. Proc. Natl. Acad. Sci. U.S.A. 99, 1774–1779.

    Article  CAS  PubMed  Google Scholar 

  59. Taylor, G. K., Kim, Y. B., Forbes, A. J., Meng, F., McCarthy, R., and Kelleher, N. L. (2003) Web and database software for identification of intact proteins using “top down” mass spectrometry. Anal. Chem. 75, 4081–4086.

    Article  CAS  PubMed  Google Scholar 

  60. Swanson, S. K. and Washburn, M. P. (2005) The continuing evolution of shotgun proteomics. Drug Discov. Today 10, 719–725.

    Article  CAS  PubMed  Google Scholar 

  61. McDonald, W. H. and Yates, J. R. (2003) Shotgun proteomics: integrating technologies to answer biological questions. Curr. Opin. Mol. Ther. 5, 302–309.

    CAS  PubMed  Google Scholar 

  62. Westermeier, R. and Naven, T. (eds.) (2002) Proteomics in Practice: A Laboratory Manual of Proteome Analysis. Wiley-VCH, Weinheim, Germany.

    Google Scholar 

  63. Vorm, O., Roepstorff, P., and Mann, M. (1994) Improved resolution and very high sensitivity in MALDI-TOF of matrix surfaces made by fast evaporation. Anal. Chem. 66, 3281–3287.

    Article  CAS  Google Scholar 

  64. Kussmann, M., Lassing, U., Sturmer, C. A., Przybylski, M., and Roepstorff, P. (1997) Matrix-assisted laser desorption/ionization mass spectrometric peptide mapping of the neural cell adhesion protein neurolin purified by sodium dodecyl sulfate polyacrylamide gel electrophoresis or acidic precipitation. J. Mass Spectrom. 32, 483–493.

    Article  CAS  PubMed  Google Scholar 

  65. Schuerenberg, M., Luebbert, C., Eickhoff, H., Kalkum, M., Lehrach, H., and Nordhoff, E. (2000) Prestructured MALDI-MS sample supports. Anal. Chem. 72, 3436–3442.

    Article  CAS  PubMed  Google Scholar 

  66. Cornish, T. J. and Cotter, R. J. (1994) A curved field reflectron time-of-flight mass spectrometer for the simultaneous focusing of metastable ions. Rapid Commun. Mass Spectrom. 8, 781–785.

    Article  CAS  PubMed  Google Scholar 

  67. Vestal, M. L., Juhasz, P., and Martín, S. A. (1995) Delayed extraction matrix-assisted laser desorption time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 9, 1044–1050.

    Article  CAS  Google Scholar 

  68. Jensen, O. N., Wilm, M., Shevchenko, A., Mann, M. (1999) Sample preparation methods for mass spectrometric peptide mapping directly from 2-DE gels. Methods Mol. Biol. 112, 513–530.

    CAS  PubMed  Google Scholar 

  69. Kaufmann, R., Spengler, B., and Lutzenkirchen, F. (1993) Mass spectrometric sequencing of linear peptides by product-ion analysis in a reflectron time-of-flight mass spectrometer using matrix-assisted laser desorption ionization. Rapid Commun. Mass Spectrom. 7, 902–910.

    Article  CAS  PubMed  Google Scholar 

  70. Mann, M. and Wilm, M. (1994) Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal.Chem. 66, 4390–4399.

    Article  CAS  PubMed  Google Scholar 

  71. Jensen, O. N., Wilm, M., Shevchenko, A., Mann, M. (1999) Peptide sequencing of 2-DE gel-isolated proteins by nanoelectrospray tandem mass spectrometry. Methods Mol. Biol. 112, 571–588.

    CAS  PubMed  Google Scholar 

  72. Pitarch, A., Nombela, C., and Gil, C. (2008) Collection of proteins secreted from yeast protoplasts in active cell wall regeneration. Methods Mol. Biol. 425, 241–263.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Microbiology II, Faculty of Pharmacy, Complutense University of Madrid, Madrid, Spain

    Aida Pitarch, César Nombela & Concha Gil

Authors
  1. Aida Pitarch
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. César Nombela
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Concha Gil
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Fraunhofer Institute for Interfacial Engineering and Biotechnology, Nobelstrasse 12, 70569 Stuttgart, Germany

    Steffen Rupp  & Kai Sohn  & 

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

Pitarch, A., Nombela, C., Gil, C. (2009). Identification of the Candida albicans Immunome During Systemic Infection by Mass Spectrometry. In: Rupp, S., Sohn, K. (eds) Host-Pathogen Interactions. Methods in Molecular Biology, vol 470. Humana Press. https://doi.org/10.1007/978-1-59745-204-5_15

Download citation

  • DOI: https://doi.org/10.1007/978-1-59745-204-5_15

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-886-7

  • Online ISBN: 978-1-59745-204-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation