Table Of ContentGuodong Chen Editor
Characterization
of Protein
Therapeutics using
Mass Spectrometry
Characterization of Protein Therapeutics
using Mass Spectrometry
Guodong Chen
Editor
Characterization of Protein
Therapeutics using Mass
Spectrometry
1 3
Editor
Guodong Chen
Bioanalytical and Discovery Analytical Sciences
Bristol-Myers Squibb
Princeton, NJ
USA
ISBN 978-1-4419-7861-5 ISBN 978-1-4419-7862-2 (eBook)
DOI 10.1007/978-1-4419-7862-2
Springer New York Heidelberg Dordrecht London
Library of Congress Control Number: 2013938173
© Springer Science+Business Media New York 2013
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Preface
Since the introduction of the first recombinant DNA-derived protein insulin in the
1980s, protein therapeutics market has shown a steady growth. Their high efficacy,
safety, and ability to treat life-threatening diseases such as cancer, inflammation,
and genetic disorders have revolutionized modern medicine. This is primarily
due to advances in recombinant DNA technology that have provided the means
to produce therapeutic proteins. However, there are significant challenges in
characterizing protein therapeutics, including heterogeneity associated with post-
translational modifications, protein conformational dynamics upon modifications,
and the complexity in analysis due to the presence of biological matrices. Mass
spectrometry (MS) is one of the most highly utilized analytical techniques in the
characterization of protein therapeutics because of its unique analytical sensitivity,
selectivity, and specificity. Advances in ionization methods including electrospray
ionization and matrix-assisted laser desorption ionization, the improvement of MS
instrumentation, and the growth in the data processing have greatly contributed to
wide applications of MS in biopharmaceutical research and development.
I am delighted to bring together the work of contributors from academia and
industry in highlighting current analytical approaches and industry practices for
the characterization of protein therapeutics using MS. The book begins with an
overview on protein MS (Chap. 1), followed by descriptions of quantitative analysis
of therapeutic peptides and proteins in biological matrices (Chaps. 2, 3). Structural
characterization of protein therapeutics is discussed in Chaps. 4–6 with the focus
on modifications of protein therapeutics from discovery to development. A unique
class of protein therapeutics, antibody–drug conjugates, is also described in detail
(Chap. 7). The remaining chapters (Chaps. 8–10) cover emerging MS techniques
for the characterization of protein therapeutics, including hydrogen/deuterium
exchange MS, fast photochemical oxidation of proteins, and ion mobility MS.
I would like to acknowledge the special efforts and patience of all the authors,
who have made significant contributions to this book.
Guodong Chen
v
Contents
1 Introduction to Protein Mass Spectrometry ..................... 1
Ismael Cotte-Rodriguez, Zhixin Miao, Yun Zhang and Hao Chen
2 Quantitative Analysis of Therapeutic and Endogenous Peptides
using LC/MS/MS Methods ................................... 59
Erin E. Chambers
3 The Development and Implementation of LC/MS-Based
Bioanalytical Methods for the Quantification of Protein
Therapeutics in Drug Discovery .............................. 95
Timothy V. Olah, Asoka Ranasinghe, Hongwei Zhang,
Richard L. Wong, John Mehl, Dieter M. Drexler, James Smalley,
Steven Wu, Bogdan Sleczka, Yongxin Zhu, Yulia Benitex,
Eric Shields and Baomin Xin
4 Post-Translationally Modified Proteins: Glycosylation
and Disulfide Bond Formation ................................ 117
Anthony Tsarbopoulos and Fotini N. Bazoti
5 Mass Spectrometric Characterization in Protein
Therapeutics Discovery ..................................... 163
Jingjie Mo, Adrienne A. Tymiak and Guodong Chen
6 Molecular Variants Characterization in Protein
Therapeutics Development ................................... 207
Richard Ludwig, Jacob Bongers, Li Tao, Yunping Huang, Jinmei Fu,
Wei Wu, Peiran Liu, Hangtian Song and Reb Russell
7 Mass Spectrometry of Antibody–Drug Conjugates in Plasma
and Tissue in Drug Development .............................. 279
Surinder Kaur, Keyang Xu, Ola Saad, Luna Liu, Tim Slattery
and Randall Dere
vii
viii Contents
8 Hydrogen/Deuterium Exchange Mass Spectrometry
for Protein Higher-Order Structure Characterization ............ 305
Hui Wei, Adrienne A. Tymiak and Guodong Chen
9 Fast Photochemical Oxidation of Proteins for Structural
Characterization ........................................... 343
Lisa M. Jones
10 Applications of Ion Mobility Mass Spectrometry
for Characterization of Protein Therapeutics ................... 371
Weibin Chen and Asish Chakraborty
Index ......................................................... 403
Contributors
Fotini N. Bazoti The Goulandris Natural History Museum, Kifissia, Greece
Yulia Benitex Bristol-Myers Squibb, Wallingford, CT, USA
Jacob Bongers Bristol-Myers Squibb, East Syracuse, NY, USA
Asish Chakraborty Waters Corporation, Milford, MA, USA
Erin E. Chambers Waters Corporation, Milford, MA, USA
Guodong Chen Bristol-Myers Squibb, Princeton, NJ, USA
Hao Chen Ohio University, Athens, OH, USA
Weibin Chen Waters Corporation, Milford, MA, USA
Ismael Cotte-Rodriguez Procter & Gamble, Loveland, OH , USA
Randall Dere Genentech, South San Francisco, CA, USA
Dieter M. Drexler Bristol-Myers Squibb, Wallingford, CT, USA
Jinmei Fu Bristol-Myers Squibb, East Syracuse, NY, USA
Yunping Huang Bristol-Myers Squibb, Hopewell, NJ, USA
Lisa M. Jones Indiana University-Purdue University, Indianapolis, IN, USA
Surinder Kaur Genentech, South San Francisco, CA, USA
Luna Liu Genentech, South San Francisco, CA, USA
Peiran Liu Bristol-Myers Squibb, Hopewell, NJ, USA
Richard Ludwig Bristol-Myers Squibb, Hopewell, NJ, USA
John Mehl Bristol-Myers Squibb, Princeton, NJ, USA
Zhixin Miao Ohio University, Athens, OH, USA
Jingjie Mo Bristol-Myers Squibb, Princeton, NJ, USA
Timothy V. Olah Bristol-Myers Squibb, Princeton, NJ, USA
ix
x Contributors
Asoka Ranasinghe Bristol-Myers Squibb, Princeton, NJ, USA
Reb Russell Bristol-Myers Squibb, Bloomsbury, NJ, USA
Ola Saad Genentech, South San Francisco, CA, USA
Eric Shields Bristol-Myers Squibb, Bloomsbury, NJ, USA
Tim Slattery Genentech, South San Francisco, CA, USA
Bogdan Sleczka Bristol-Myers Squibb, Princeton, NJ, USA
James Smalley Bristol-Myers Squibb, Hopewell, NJ, USA
Hangtian Song Bristol-Myers Squibb, East Syracuse, NY, USA
Li Tao Bristol-Myers Squibb, Hopewell, NJ, USA
Anthony Tsarbopoulos University of Athens Medical School, Athens, Greece
Adrienne A. Tymiak Bristol-Myers Squibb, Princeton, NJ, USA
Hui Wei Bristol-Myers Squibb, Princeton, NJ, USA
Richard L. Wong Bristol-Myers Squibb, Hopewell, NJ, USA
Steven Wu Bristol-Myers Squibb, Princeton, NJ, USA
Wei Wu Bristol-Myers Squibb, Bloomsbury, NJ, USA
Baomin Xin Bristol-Myers Squibb, Hopewell, NJ, USA
Keyang Xu Genentech, South San Francisco, CA, USA
Hongwei Zhang Bristol-Myers Squibb, Hopewell, NJ, USA
Yun Zhang Ohio University, Athens, OH, USA
Yongxin Zhu Bristol-Myers Squibb, Princeton, NJ, USA
Chapter 1
Introduction to Protein Mass Spectrometry
Ismael Cotte-Rodriguez, Zhixin Miao, Yun Zhang and Hao Chen
1.1 Introduction
Proteins fulfill a plethora of biochemical functions within every living organism,
and mass spectrometry (MS) has become one of the most powerful and popu-
lar modern physical–chemical methods to study the complexities of proteins. In
particular, the invention of matrix-assisted laser desorption/ionization (MALDI)
[1] and electrospray ionization (ESI) technologies [2, 3] allows one to measure
protein molecular weights and sequences, and to probe conformations and post-
translational modifications of proteins. In addition, the mass range of species ame-
nable for MS analysis has increased, enabling the transfer of ionized non-covalent
species with masses well over one million (e.g., 1.5 MDa 24-Mer flavoprotein
vanillyl-alcohol oxidase (VAO) from Penicillium simplicissimum [4] into the gas
phase). These advances moved MS into the range of intact protein oligomers and
functional machineries.
This chapter serves as an introduction to protein MS. As it is a broad topic with
a vast literature coverage [5–17], we first introduce spray- and laser-based protein
ionization techniques used for protein ionization, beginning with an introduc-
tion on the historical development of protein ionization methods, followed by the
description of several methods including their principles, strengths, and analytical
applications. In addition, we also survey various ion activation methods used for
protein/peptide structure analysis (viz. tandem mass spectrometry), including col-
lision-, photon-, surface-, and electron-based ion dissociation strategies.
I. Cotte-Rodriguez
Procter & Gamble, Cincinnati, OH, USA
Z. Miao · Y. Zhang · H. Chen (*)
Department of Chemistry and Biochemistry, Ohio University, 391 Clippinger Laboratory 100
University Terrace, 45701 Athens, OH, USA
e-mail: [email protected]
G. Chen (ed.), Characterization of Protein Therapeutics using Mass Spectrometry, 1
DOI: 10.1007/978-1-4419-7862-2_1, © Springer Science+Business Media New York 2013
