Skip to main content
SpringerLink
Log in

Cell Culture Tracking by Multivariate Analysis of Raw LCMS Data

  • Published:
Applied Biochemistry and Biotechnology Aims and scope Submit manuscript

Abstract

Liquid chromatography mass spectrometry (LCMS) is a powerful technique that could serve to rapidly characterize cell culture protein expression profile and be used as a process monitoring and control tool. However, this application is often hampered by both the sample proteome and the LCMS signal complexities as well as the variability of this signal. To alleviate this problem, culture samples are usually extensively fractionated and pretreated before being analyzed by top-end instruments. Such an approach precludes LCMS usage for routine on-line or at-line application. In this work, by applying multivariate analysis (MA) directly on raw LCMS signals, we were able to extract relevant information from cell culture samples that were simply lyzed. By using the recombinant adenovirus production process as a model, we were able to follow the accumulation of the three major proteins produced, identified their accumulation dynamics, and draw useful conclusions from these results. The combination of LCMS and MA provides a simple, rapid, and precise means to monitor cell culture.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig.1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10
Fig. 11

Similar content being viewed by others

References

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

    Article  CAS  Google Scholar 

  2. Walther, T. C., & Mann, M. (2010). Mass spectrometry-based proteomics in cell biology. The Journal of Cell Biology, 190, 491–500.

    Article  CAS  Google Scholar 

  3. Pan, S., Chen, R., Aebersold, R., & Brentnall, T. A. (2011). Mass spectrometry based glycoproteomics—from a proteomics perspective. Molecular & Cellular Proteomics, 10(R110), 003251.

    Google Scholar 

  4. Li, M., Zhou, Z., Nie, H., Bai, Y., & Liu, H. (2011). Recent advances of chromatography and mass spectrometry in lipidomics. Analytical and Bioanalytical Chemistry, 399, 243–249.

    Article  CAS  Google Scholar 

  5. Roux, A., Lison, D., Junot, C., & Heilier, J. F. (2011). Applications of liquid chromatography coupled to mass spectrometry-based metabolomics in clinical chemistry and toxicology: a review. Clinical Biochemistry, 44, 119–135.

    Article  CAS  Google Scholar 

  6. Choudhary, C., & Mann, M. (2010). Decoding signalling networks by mass spectrometry-based proteomics. Nature Reviews Molecular Cell Biology, 11, 427–439.

    Article  CAS  Google Scholar 

  7. Cheng, K. W., Wong, C. C., Wang, M., He, Q. Y., & Chen, F. (2010). Identification and characterization of molecular targets of natural products by mass spectrometry. Mass Spectrometry Reviews, 29, 126–155.

    CAS  Google Scholar 

  8. Street, J. M., & Dear, J. W. (2010). The application of mass-spectrometry-based protein biomarker discovery to theragnostics. British Journal of Clinical Pharmacology, 69, 367–378.

    Article  CAS  Google Scholar 

  9. Michaud, F. T., Garnier, A., Lemieux, L., & Duchesne, C. (2009). Multivariate analysis of single quadrupole LC-MS spectra for routine characterization and quantification of intact proteins. Proteomics, 9, 512–520.

    Article  CAS  Google Scholar 

  10. Datta, S., & Pihur, V. (2010). Feature selection and machine learning with mass spectrometry data. Methods in Molecular Biology, 593, 205–229.

    Article  CAS  Google Scholar 

  11. Mostacci, E., Truntzer, C., Cardot, H., & Ducoroy, P. (2010). Multivariate denoising methods combining wavelets and principal component analysis for mass spectrometry data. Proteomics, 10, 2564–2572.

    Article  CAS  Google Scholar 

  12. Backstrom, D., Moberg, M., Sjoberg, P. J., Bergquist, J., & Danielsson, R. (2007). Multivariate comparison between peptide mass fingerprints obtained by liquid chromatography-electrospray ionization-mass spectrometry with different trypsin digestion procedures. Journal of Chromatography. A, 1171, 69–79.

    Article  Google Scholar 

  13. Boccard, J., Grata, E., Thiocone, A., Gauvrit, J. Y., Lantéri, P., Carrupt, P. A., et al. (2006). Multivariate data analysis of rapid LC-TOF/MS experiments from Arabidopsis thaliana stressed by wounding. Chemometrics and Intelligent Laboratory, 86(2), 189–197.

    Article  Google Scholar 

  14. Idborg, H., Edlund, P. O., & Jacobsson, S. P. (2004). Multivariate approaches for efficient detection of potential metabolites from liquid chromatography/mass spectrometry data. Rapid Communications in Mass Spectrometry, 18, 944–954.

    Article  CAS  Google Scholar 

  15. Jonsson, P., Gullberg, J., Nordstrõm, A., Kusano, M., Kowalczyk, M., Sjõstrõm, M., et al. (2004). A strategy for identifying differences in large series of metabolomic samples analyzed by GC/MS. Analytical Chemistry, 76, 1738–1745.

    Article  CAS  Google Scholar 

  16. Woolley, J. F., & Al-Rubeai, M. (2009). The application of SELDI-TOF mass spectrometry to mammalian cell culture. Biotechnology Advances, 27, 177–184.

    Article  CAS  Google Scholar 

  17. Garnier, A., Cote, J., Nadeau, I., Kamen, A., & Massie, B. (1994). Scale-up of the adenovirus expression system for the production of recombinant protein in human 293 S cells. Cytotechnology, 15, 145–155.

    Article  CAS  Google Scholar 

  18. Gilbert, P.-A., Garnier, A., Jacob, D., & Kamen, A. (2000). On-line measurement of green fluorescent protein (GFP) fluorescence for the monitoring of recombinant adenovirus production. Biotechnology Letters, 22, 561–567.

    Article  CAS  Google Scholar 

  19. Graham, F. L., Smiley, J., Russell, W. C., & Nairn, R. (1977). Characteristics of a human cell line transformed by DNA from human adenovirus type 5. Journal of General Virology, 36, 59–74.

    Article  CAS  Google Scholar 

  20. Klyushnichenko, V., Bernier, A., Kamen, A., & Harmsen, E. (2001). Improved high-performance liquid chromatographic method in the analysis of adenovirus particles. Journal of Chromatography B: Biomedical Sciences and Applications, 755, 27–36.

    Article  CAS  Google Scholar 

  21. Maizel, J. V., White, D. O., & Scharff, M. D. (1968). The polypeptides of adenovirus. I. Evidence for multiple protein components in the virion and a comparison of types 2, 7A, and 12. Virology, 36, 115–125.

    Article  CAS  Google Scholar 

  22. Yu, H., & MacGregor, J. F. (2003). Multivariate image analysis and regression for prediction of coating content and distribution in the production of snack foods. Chemometrics and Intelligent Laboratory, 67, 125.

    Article  CAS  Google Scholar 

  23. Trygg, J., Holmes, E., & Lundstedt, T. (2007). Chemometrics in metabonomics. Journal of Proteome Research, 6, 469–479.

    Article  CAS  Google Scholar 

  24. Wold, S., Sjõstrõm, M., & Eriksson, L. (2001). PLS-regression: a basic tool of chemometrics. Chemometrics and Intelligent Laboratory, 58, 109–130.

    Article  CAS  Google Scholar 

  25. Wold, S. (1978). Cross-validatory estimation of the number of components in factor and principal components models. Technometrics, 20, 397–405.

    Google Scholar 

  26. Chong, I. G., & Jun, C. H. (2005). Performance of some variable selection methods when multicollinearity is present. Chemometrics and Intelligent Laboratory, 78, 103.

    Article  CAS  Google Scholar 

  27. Lindberg, W., Persson, J. A., & Wold, S. (1983). Partial least squares method for spectrofluorimetric analysis of mixtures of humic acid and ligninsulfonate. Analytical Chemistry, 55, 648.

    Article  Google Scholar 

  28. Lehmberg, E., Traina, J. A., Chakel, J. A., Chang, R. J., Parkman, M., McCaman, M. T., et al. (1999). Reversed-phase high-performance liquid chromatographic assay for the adenovirus type 5 proteome. Journal of Chromatography B: Biomedical Sciences and Applications, 732, 411–423.

    Article  CAS  Google Scholar 

  29. Blanche, F., Monegier, B., Faucher, D., Duchesne, M., Audhuy, F., Barbot, A., et al. (2001). Polypeptide composition of an adenovirus type 5 used in cancer gene therapy. Journal of Chromatography. A, 921, 39–48.

    Article  CAS  Google Scholar 

  30. Mirza, U. A., Liu, Y. H., Tang, J. T., Porter, F., Bondoc, L., Chen, G., et al. (2000). Extraction and characterization of adenovirus proteins from sodium dodecylsulfate polyacrylamide gel electrophoresis by matrix-assisted laser desorption/ionization mass spectrometry. Journal of the American Society for Mass Spectrometry, 11, 356–361.

    Article  CAS  Google Scholar 

  31. Stewart, P. L., & Burnett, R. M. (1993). Difference imaging of adenovirus: bridging the resolution gap between X-ray crystallography and electron microscopy. EMBO Journal, 12, 2589–2599.

    CAS  Google Scholar 

Download references

Acknowledgment

This work was supported by NSERC and PROTEO, a FQRNT research center.

Author information

Authors and Affiliations

  1. Feldan Inc., 4975 Rideau Street, Québec, QC, Canada, G2E 5H5

    François-Thomas Michaud

  2. Département Génie Chimique, Université Laval, 1065 Ave. de la Médecine, Québec, QC, Canada, G1V 0A6

    Pierre Claver Havugimana, Carl Duchesne & Alain Garnier

  3. Département de Biologie Médicale, Hôpital du Saint-Sacrement, 1050 chemin Ste-Foy, Québec, QC, Canada, G1S 4L8

    François Sanschagrin

  4. Institut de Recherche en Biotechnologie (IRB), Conseil National de Recherche du Canada (CNRC), Montréal, Québec, Canada, H4P 2R2

    Alice Bernier

  5. Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 Ave. de la Médecine, Québec, QC, Canada, G1V 0A6

    Roger C. Lévesque

Authors
  1. François-Thomas Michaud
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Pierre Claver Havugimana
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Carl Duchesne
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. François Sanschagrin
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Alice Bernier
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Roger C. Lévesque
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Alain Garnier
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Alain Garnier.

Additional information

Both François-Thomas Michaud and Pierre Claver Havugimana contributed equally to this work.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Michaud, FT., Havugimana, P.C., Duchesne, C. et al. Cell Culture Tracking by Multivariate Analysis of Raw LCMS Data. Appl Biochem Biotechnol 167, 474–488 (2012). https://doi.org/10.1007/s12010-012-9661-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12010-012-9661-4

Keywords

Search

Navigation