Application of Selected Reaction Monitoring to Highly Multiplexed Targeted Quantitative Proteomics: A Replacement for Western Blot Analysis

76 Pages·2013·1.056 MB·English

by  Michael Kinter, Caroline S. Kinter (auth.)

SPRINGER BRIEFS IN SYSTEMS BIOLOGY
Michael Kinter · Caroline S. Kinter
Application of Selected
Reaction Monitoring
to Highly Multiplexed
Targeted Quantitative
Proteomics
123
SpringerBriefs in Systems Biology
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Michael Kinter (cid:129) Caroline S. Kinter
Application of Selected
Reaction Monitoring
to Highly Multiplexed
Targeted Quantitative
Proteomics
A Replacement for Western Blot Analysis
Michael Kinter Caroline S. Kinter
Oklahoma Medical Research Foundation Oklahoma Medical Research Foundation
Oklahoma City , OK , USA Oklahoma City , OK , USA
ISSN 2193-4746 ISSN 2193-4754 (electronic)
ISBN 978-1-4614-8665-7 ISBN 978-1-4614-8666-4 (eBook)
DOI 10.1007/978-1-4614-8666-4
Springer New York Heidelberg Dordrecht London
Library of Congress Control Number: 2013947406
© The Authors 2013
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For Lauren and Courtney

Preface
The original experiment in the fi eld of proteomics identifi ed proteins contained in
SDS-PAGE gel bands by digesting those proteins with the enzyme trypsin and
sequencing the resulting peptides by collision-induced dissociation in a tandem
mass spectrometer. Although the reasons for selecting any particular gel band for
identifi cation varied, a common reason was because a change had been seen in the
abundance of that band under different experimental conditions. While these exper-
iments were certainly quantitative proteomics, the quantitative information came
from the gel through the pattern of protein staining that was seen. In 2000, we wrote
one of the fi rst books describing this identifi cation experiment on a practical level.
The goal of this book is to describe a new type of quantitative proteomics experi-
ment called selected reaction monitoring that has seen growing use over the past
several years. The selected reaction monitoring experiment leverages several devel-
opments in the fi elds of genomics, information technology, and mass spectrometry.
The result is a robust and powerful method to measure the abundance of a protein in
complex samples, with high specifi city and sensitivity.
Oklahoma City, OK, USA Michael Kinter
Oklahoma City, OK, USA Caroline S. Kinter
vii

Acknowledgments
There are three groups of people that contributed to the ideas and work presented in
this volume. The Proteomics group in the Department of Cell Biology in the Lerner
Research Institute of the Cleveland Clinic carried out the experiments that laid the
groundwork for the current methods in the course of an extensive series of identifi -
cation experiments and a modest number of quantitative experiments—Belinda
Willard, Suma Kaveti, Andrew Keightley, Heather Hargett, Cristian Ruse, James
Conway, Lemin Zheng, Assem Ziady, and Dongmei Zhang. More recently, our
group in the Free Radical Biology and Aging Research Program at the Oklahoma
Medical Research Foundation has now taken the targeted quantitative proteomics
work and made it a routine, highly productive tool for our research program—Jolyn
Fernandes, Clair Crewe, Paul Rindler, Halee Patel, Jillian Lundie, Alex Weddle,
Aaron McLain, Melinda West, and Luke Szweda. In both institutions we have been
fortunate to collaborate with a large group of scientists with outstanding research
programs and challenging analytical problems that were an exceptional driving
force throughout the refi nement of these approaches. In addition, we would like to
acknowledge Michael MacCoss at the University of Washington School of
Medicine. His lunchtime presentation sponsored by ThermoScientifi c in June 2008
at the Annual Meeting of the American Society for Mass Spectrometry conveyed
both the excitement and opportunity of using selected reaction monitoring in
this way.
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