ABSTRACT
From Proteomics to Protein-Based Biomarkers: A Toolbox of Opportunity
Dale H. Patterson, Ph.D.
Director, World Wide Application Support

Overcoming the challenges presented to us in our endeavors to identify and characterize
proteins in complex media requires advanced analytical tools and workflows. Applied
Biosystems has a complete set of tools designed to meet the sensitivity, dynamic range,
precision and specificity requirements and has proven itself a leader in pioneering
workflows for each challenge. This talk will briefly overview AB’s proteomics portfolio
including the 4800 MALDI TOF/TOFÔ Analyzer, the QStar® Elite Hybrid LC/MS/MS
System, the 3200/4000 Q Trap® LC/MS/MS Systems and the Tempo™ Systems,

highlighting the specific proteomics tasks for which each was built. Examples for protein
identification, intact protein analysis and post-translational analysis will be shown.

As proteomics itself has matured, as well as the tools that drive the field, many
researchers have set their sites on a different end point, the discovery of individual or
panels of protein-based biomarkers. This field demands not only the depth of coverage,
speed and specificity of proteomics, but also accurate and precise quantification (both
relative and absolute). Trying to tackle biomarker research with one tool and/or in one
experiment has proven unfruitful causing the pioneers in the field to take a step back and
really think about the various stages, their unique needs and the analytical solutions that
best fit each bin. Hence, the field of biomarker research has been sub-segmented into
discovery, verification and validation. This part of the talk will show how Applied
Biosystems’ toolbox addresses the needs across these segments. The 4800 MALDI
TOF/TOF™ Analyzer or the QStar® Elite Hybrid LC/MS/MS System combined with our
novel multiplex-enabled iTRAQ™ Reagents afford simultaneous protein ID and
quantification required for the biomarker discovery segment when one is searching for
putative markers of disease, efficacy or toxicity. This combination of tools yields
unparalleled depth of coverage and precision of quantification that is so critical to this
stage of the process. Once a putative panel of markers is found, the next challenge is to
verify the specificity of these markers over a larger population set. Taking advantage of
the unique capability of the combination of a hybrid triple quadrupole linear ion trap
instrument and using our patented MRM Initiated Detection and Sequencing (MIDAS)
workflow, this putative panel of biomarkers can easily and rapidly be reduced to the most
likely set for the validation stage. This last stage requires absolute quantification and
very high throughput. Examples of how iTRAQ™ Reagents used in combination with
the Q Trap® Systems for this stage will also be presented.



Biography
Dale H. Patterson, Ph.D.
Director, World Wide Application Support
Proteomics and Small Molecule Division
Applied Biosystems
500 Old Connecticut Path
Framingham, MA 01701 USA

Dr. Patterson received his undergraduate degree in chemistry from the University of
North Carolina at Chapel Hill and his Ph.D. from Purdue University in analytical
chemistry. Holding a variety of positions at Applied Biosystems in his 13-year career,
including roles in research and development, the Applied Biosystems Proteomics
Research Center and product/product line management, Dr. Patterson has focused on the
application of advanced analytical tools to meet the challenges of proteomics and
biomarker discovery. Dr. Patterson has 21 peer-reviewed publications and 5 issued
patents to his name.

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