Abstract
Recombinant protein pharmaceuticals have revolutionized the treatment of a variety of medical ailments, including cancer, autoimmune diseases, and hemostatic disorders. Proteins manufactured with eukaryotic expression systems may be complex and heterogeneous because of posttranslational modifications (PTMs) and differential proteolytic processing. At one time, detailed characterization and definition of the protein structure were difficult, and the manufacturing process defined the product. If process changes were made, clinical trials were required to demonstrate product equivalence prior to regulatory agency acceptance of the product manufactured by the modified process. To adopt new manufacturing processes in a timely manner, the biopharmaceutical industry and regulatory agencies have worked together over the last few years to develop new guidance documents based on knowledge gained from industry experience in the manufacture and clinical testing of protein pharmaceuticals (1,2). Manufacturers of protein pharmaceuticals consistently strive to deliver the highest quality product in a cost-efficient manner. This can be accomplished through optimization of the production process and incorporation of new technologies to enhance product purity and yield. Process improvements may include a change of the host cell line, enhancement of the cell culture medium or cell culture management, or modifications to the purification process. In some cases, an additional manufacturing site is brought online to augment production capacity.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Food and Drug Administration. (2003) Guidance for industry, comparability protocols-protein drug products and biological products-chemistry, manufacturing, and controls information, draft guidance. Available at http://www.fda.gov/cber/guidelines.htm.
ICH. (2003) ICH Q5E, Comparability of biotechnological/biological products, note for guidance on biotechnological/biological products subject to changes in their manufacturing process (CPMP/ICH/5721/03). Available at http://www.hc-sc.gc.ca/hpfb-dgpsa/tpd-dpt/q5e_step2_notice_e.html.
Kelleher, N. L., Lin, H. Y., Valaskovic, G. A., Aaserud, D. J., Fridriksson, E. K., and McLafferty, F. W. (1999) Top down versus bottom up protein characterization by tandem high-resolution mass spectrometry. J. Am. Chem. Soc. 121, 806–812.
VerBerkmoes, N. C., Bundy, J. L., Hauser, L., Asano, K. G., Razumovskaya, J., Larimer, F., et al. (2002) Integrating “top-down” and “bottom-up” mass spectrometric approaches for proteomic analysis of Shewanella oneidensis. J. Proteome Res. 1, 239–252.
Nemeth-Cawley, J. F., Tangarone, B. S., and Rouse, J. C. (2003) “Top Down” characterization is a complementary technique to peptide sequencing for identifying protein species in complex mixtures. J. Proteome Res. 2, 495–505.
Balogh, M. P. (2004) Debating resolution and mass accuracy. LCGC North America 22, 118–130.
McLafferty, F. W. (2001) Tandem mass spectrometric analysis of complex biological mixtures. Int. J. Mass Spectrom. 212, 81–87.
Ge, Y., Lawhorn, B. G., El Naggar, M., Strauss, E., Park, J. H., Begley, T. P., and McLafferty, F. W. (2002) Top down characterization of larger proteins (45 kDa) by electron capture dissociation mass spectrometry. J. Am. Chem. Soc. 124, 672–678.
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. USA 99, 1774–1779.
Sze, S. K., Ge, Y., Oh, H., and McLafferty, F. W. (2003) Plasma electron capture dissociation for the characterization of large proteins by top down mass spectrometry. Anal. Chem. 75, 1599–1603.
Shi, S. D., Hemling, M. E., Carr, S. A., Horn, D. M., Lindh, I., and McLafferty, F. W. (2001) Phosphopeptide/phosphoprotein mapping by electron capture dissociation mass spectrometry. Anal. Chem. 73, 19–22.
Ge, Y., El Naggar, M., Sze, S. K., Oh, H. B., Begley, T. P., McLafferty, F. W., et al. (2003) Top down characterization of secreted proteins from Mycobacterium tuberculosis by electron capture dissociation mass spectrometry. J. Am. Soc. Mass. Spectrom. 14, 253–261.
Ge, Y., Lawhorn, B. G., El Naggar, M., Sze, S. K., Begley, T. P., and McLafferty, F. W. (2003) Detection of four oxidation sites in viral prolyl-4-hydroxylase by top-down mass spectrometry. Protein Sci. 12, 2320–2326.
Pesavento, J. J., Kim, Y.-B., Taylor, G. K., and Kelleher, N. L. (2004) Shotgun annotation of histone modifications: a new approach for streamlined characterization of proteins by top down mass spectrometry. J. Am. Chem. Soc. 126, 3386–3387.
Horn, D. M., Ge, Y., and McLafferty, F. W. (2000) Activated ion electron capture dissociation for mass spectral sequencing of larger (42 kDa) proteins. Anal. Chem. 72, 4778–4784.
Zubarev, R. A. (2003) Reactions of polypeptide ions with electrons in the gas phase. Mass Spectrom. Rev. 22, 57–77.
Forbes, A. J., Mazur, M. T., Patel, H. M., Walsh, C. T., and Kelleher, N. L. (2001) Toward efficient analysis of >70 kDa proteins with 100% sequence coverage. Proteomics 1, 927–933.
Reid, G. E. and McLuckey, S. A. (2002) “Top down” protein characterization via tandem mass spectrometry. J. Mass Spectrom. 37, 663–675.
Stephenson, J. L., McLuckey, S. A., Reid, G. E., Wells, J. M., and Bundy, J. L. (2002) Ion/ion chemistry as a top-down approach for protein analysis. Curr. Opin. Biotechnol. 13, 57–64.
Hogan, J. M. and McLuckey, S. A. (2003) Charge state dependent collision-induced dissociation of native and reduced porcine elastase. J. Mass Spectrom. 38, 245–256.
Amunugama, R., Hogan, J. M., Newton, K. A., and McLuckey, S. A. (2004) Whole protein dissociation in a quadrupole ion trap: identification of an a priori unknown modified protein. Anal. Chem. 76, 720–727.
Reid, G. E., Stephenson, J. L., Jr., and McLuckey, S. A. (2002) Tandem mass spectrometry of ribonuclease A and B: N-linked glycosylation site analysis of whole protein ions. Anal. Chem. 74, 577–583.
Hogan, J. M., Pitteri, S. J., and McLuckey, S. A. (2003) Phosphorylation site identification via ion trap tandem mass spectrometry of whole protein and peptide ions: bovine alpha-crystallin A chain. Anal. Chem. 75, 6509–6516.
Blackburn, R. K. and Moseley, M. A., III. (1999) Quadrupole time-of-flight mass spectrometry: a powerful new tool for protein identification and characterization. Am. Pharm. Rev. 2, 49–59.
Morris, H. R., Paxton, T., Dell, A., Langhorne, J., Berg, M., Bordoli, R. S., et al. (1996) High sensitivity collisionally-activated decomposition tandem mass spectrometry on a novel quadrupole/orthogonal-acceleration time-of-flight mass spectrometer. Rapid Commun. Mass Spectrom. 10, 889–896.
Nemeth-Cawley, J. F. and Rouse, J. C. (2002) Identification and sequencing analysis of intact proteins via collision-induced dissociation and quadrupole time-of-flight mass spectrometry. J. Mass Spectrom. 37, 270–282.
Thevis, M., Ogorzalek Loo, R. R., and Loo, J. A. (2003) Mass spectrometric characterization of transferrins and their fragments derived by reduction of disulfide bonds. J. Am. Soc. Mass Spectrom. 14, 635–647.
Ferrige, A. G., Seddon, M. J., Green, B. N., Jarvis, S. A., and Skilling, J. (1992) Disentangling electrospray spectra with maximum entropy. Rapid Comm. Mass Spectrom. 6, 707–711.
Green, B. N., Hutton, T., and Vinogradov, S. N. Analysis of complex protein and glycoprotein mixtures by electrospray ionization mass spectrometry with maximum entropy processing, in Protein and Peptide Analysis by Mass Spectrometry (Chapman, J. R., ed.), Humana, Totowa, NJ, 1996, pp. 279–294.
Rouse, J. C., Marzilli, L. A., Johnson, K. A., McClellan, J. E., and Czupryn, M. J. “Top down” glycoprotein characterization by high resolution mass spectrometry and its application to biopharmaceutical development. Well Characterized Biopharmaceuticals 2004: 8th Symposium on the Interface of Regulatory and Analytical Sciences for Biotechnology Health Products, Washington DC, 2004.
Sandberg, H., Almstedt, A., Brandt, J., Castro, V. M., Gray, E., Holmquist, L., et al. (2001) Structural and functional characterization of B-domain deleted recombinant factor VIII. Semin. Hematol. 38(2 Suppl. 4), 4–12.
Czupryn, M. Current analytical methodologies: application to comparability assessment of recombinant clotting factors. PDA/IABS Conference, State of the art analytical methods for the characterisation of biological therapeutic products and assessment of comparability, Bethesda, MD, 2003.
Mehndiratta, P., Grunder, B. C., Marzilli, L. A., McClellan, J. E., Tangarone, B. S., Porter, T. J., and Rouse, J. C. LC/MS characterization of recombinant monoclonal antibodies at the pre-development stage. Sixth International Symposium on Mass Spectrometry in the Health and Life Sciences: Molecular and Cellular Proteomics, San Francisco, CA, 2003.
Bond, M., Jankowski, M., Patel, H., Karnik, S., Strang, A., Xu, B., et al. (1998) Biochemical characterization of recombinant factor IX. Semin. Hematol. 35(2 Suppl. 2), 11–17.
DiScipio, R. G., Kurachi, K., and Davie, E. W. (1978) Activation of human factor IX (Christmas factor). J Clin. Invest. 61, 1528–1538.
Fujikawa, K., Legaz, M. E., Kato, H., and Davie, E. W. (1974) The mechanism of activation of bovine factor IX (Christmas factor) by bovine factor XIa (activated plasma thromboplastin antecedent). Biochemistry 13, 4508–4516.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Humana Press Inc.
About this protocol
Cite this protocol
Rouse, J.C., McClellan, J.E., Patel, H.K., Jankowski, M.A., Porter, T.J. (2005). Top-Down Characterization of Protein Pharmaceuticals by Liquid Chromatography/Mass Spectrometry. In: Smales, C.M., James, D.C. (eds) Therapeutic Proteins. Methods in Molecular Biology™, vol 308. Humana Press. https://doi.org/10.1385/1-59259-922-2:435
Download citation
DOI: https://doi.org/10.1385/1-59259-922-2:435
Publisher Name: Humana Press
Print ISBN: 978-1-58829-390-9
Online ISBN: 978-1-59259-922-6
eBook Packages: Springer Protocols