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Monday, May 19

7:00 - 6:00 pm Registration Open

7:30 Morning Coffee

8:10 Opening Plenary Introduction

8:20 Molecular Targets & Diagnostics: Critical Role of Sample Preparation in Discovery
James L. Wittliff, Ph. D., M. D. hc, FACB, Professor of Biochemistry & Molecular Biology, James Graham Brown Cancer Center, University of Louisville
Clinically relevant genomic and proteomic test development using human tissue specimens requires specialized collection, handling and cryopreservation methods for generating reliable analyses. Although global gene expression assays of intact cancer biopsies are utilized to distinguish patterns, validation of mRNA expression of specific gene sets by techniques such as quantitative PCR is essential using well characterized samples. Non-distructive procurement of pure cell populations from frozen and formalin-fixed, paraffin-embedded tissues by Laser Capture Microdissection and optimized methods for RNA and protein analyses enhance identification of candidate molecular targets for development of drugs and diagnostics. These approaches must be complemented by well annotated records of patient characteristics, tissue pathology and clinical outcome

View a Life Science webcast w/ James L Wittliff from last year's GOT Summit conference

9:00 Opportunities and Obstacles in Proteomic Analysis of Biofluids
Sunny Tam, Ph.D., Research Associate Professor, University of Massachusetts Medical School
Proteomic analyses of biofluids, such as plasma or amniotic fluid, traditionally have the same obstacles due to the presence of abundant proteins and large dynamic range of protein concentration. Recent fractionation reagents have helped in the isolation of abundant proteins to allow the examination of lower abundant proteins. We have examined plasma from a diabetic rat model and important clinical diseases after adequatefractionation schemes. The proteomic finding from gel based and iTRAQ based studies have yielded interesting observations after bioinformatics analysis. Furthermore, the biological significances of the differential protein expression have been validated with traditional biochemical methods.

9:40 Grand Opening Coffee Break in the Exhibit Hall


10:25 Chairperson’s Remarks

10:30 Protein Quantification and Separation before 2D Electrophoresis Using Label Free Intrinsic Imaging
Judit Nagy, Ph.D., Proteomics Facility Director, Institute of Biomedical Engineering, Imperial College London
One of the most commonly used protein separation techniques in proteomics is two dimensional gel electrophoresis (2DE). Although 2DE is cheap to set up and gives a visual profile of complex protein mixtures, it has many drawbacks. It is not quantitative, it can be laborious, it cannot separate the complete protein set and the reproducibility is low. All these factors result in increased sample replicates needed in the discovery of biologically relevant protein changes. To avoid running low quality samples on 2D gels and wasting valuable materials and time, samples are first analysed and quality checked using deltaDOT’s Peregrine system.

Protein detection is based on Label Free Intrinsic Imaging (LFII™) developed by deltaDOT. This work-flow not only allows to speed up and improve the 2DE gel outputs but also gives the opportunity to verify and quantitate proteins which are identified from the 2D gels by mass spectrometry.

11:00 New Approches of Sample Preparation and Fractionation
Hongshan Li, Ph.D., Senior Principal Scientist, Proteomics, Pall
This talk will discuss the advantage and dis-advantage of new resins (HEA,PPA and MEP) combination of IEX, IMAC and SDR.

11:30 Novel Inactivation Technology that Preserves the in vivo Proteome
Mats Borén, Ph.D., Head of Research, Denator Biotechnology AB
The talk focuses on the massive ex vivo degradation of the proteome that usually is provoked in most pre-analytical proteomics workflows. Rapid inactivation and stabilization of the proteome is shown to be crucial for analysis of an in-vivo-like proteome instead of the degradome. A novel methodology utilizing rapid and irreversible heat fixation of the proteome is presented as a solution to the ex-vivo degradation problem. The benefit of this new technology is exemplified within several standard proteomic workflows.

12:00 pm Lunch and Learn Workshops (Sponsorship Available) or Lunch on Your Own



1:25 Chairperson’s Remarks

1:30 In Situ Synthesis of Protein Arrays
Mingyue He, Ph.D, Technology Research, The Babraham Institute
In situ protein synthesis technologies exploit cell-free expression systems to produce protein arrays on glass slides directly from co-distributed or pre-arrayed DNA. These methods avoid the laborious and costly processes of DNA cloning, expression and purification of individual proteins and eliminate the need for storage of functional proteins on the surface over time. We have developed novel cell-free protein array methods, which not only allow conversion of arrayed DNA into protein arrays in hours but also ‘print’ multiple copies of a protein array through repeated use of a single DNA array. Their application for screening proteins will be discussed.

2:00 Integrative Biomarker Discovery Strategies
Martin Latterich, Ph.D., Associate Professor, Pharmacy, University of Montreal
The burgeoning field of personalized medicine will require the identification and validation of new biomarkers that have prognostic or diagnostic value. Some of the challenges facing us today are well-defined patient cohorts, and highly reproducible analytical methods, as well as cost effective methods of validating often large sets of biomarker candidates. We have developed an integrated strategy for both the discovery, as well as the validation of biomarkers from different types of patient samples that includes aspects of sampling, storage, isobaric tagging, and subsequent MIDAS-MRM validation.

2:30 Escorting Protein Biomarkers Down the Discovery Pipeline Using Mass Spectrometry Immunoassay: A Case Study of Work in Progress with Type 2 Diabetes Biomarkers
Chad Borges, M.D., Assistant Research Scientist, The Biodesign Institute, Arizona State University
A protein biomarker of disease is not just "a protein"—it is something about a protein—generally either a change in concentration, amino acid sequence, and/or qualitative/quantitative changes in posttranslational modification. Since human knowledge of protein biochemistry is far from complete, our laboratory operates on the hypothesis that every protein is a potential biomarker platform and that all three of the above biomarker qualifiers must be considered for all proteins. Toward this end, the application of mass spectrometric immunoassay (MSIA) towards plasma samples from over 100 individuals has recently facilitated our detection and preliminary validation of several characterized biomarkers towards Type 2 Diabetes (T2D) diagnosis and monitoring—including a situation in which two biomarkers are carried by a single protein and monitored by a single mass spectrometry based assay. A clinical study designed to generate plasma samples for T2D biomarker validation has been arranged and further MSIA-based high throughput validation of these biomarkers will continue as soon as these samples are collected. The nature of these protein biomarkers (and others like them) strongly suggests the need for mass spectrometry as a diagnostic tool in the clinical setting.

3:00 Networking Refreshment Break, Poster and Exhibit Viewing           Sponsored by


Protein Analysis

3:45 Microfluidic Cassette for Rapid Isolation of Granulocytes from Whole Blood for Genomic and Proteomic Applications
Dr Ken Kotz, R&D Operations, Surgery, Massachusetts General Hospital

4:15 Cerebrospinal Fluid and Proteomic Analyses
Pawel Ciborowski, Ph.D., Assistant Professor, Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center

Proteomic analysis of cerebrospinal fluid (CSF):

  • CSF sample handling and preparation for various proteomic analyses
  • Issues related to CSF sample pooling when limited material is available
    CSF sample normalization
  • Validation of proteomic results in CSF analyses
  • Data interpretation in CSF proteomic analyses

4:45 Development of Protein Chemistry Methods for the Detection of Protein Post-Translational Modifications (PTM’s)
Zhaohui Sunny Zhou, Ph.D., Faculty Fellow, The Barnett Institute of Chemical and Biological Analysis; Associate Professor, Department of Chemistry and Chemical Biology, Northeastern University
Over one hundred different protein post-translational modifications (PTM’s) have been reported, playing critical roles in myriad biological processes in humans. Due to the relative low abundance of these modified proteins, detection of these PTM’s remains a major challenge in proteomic research.

Our laboratory has successfully developed several biochemical and chemical methods to selectively derivatize the modified proteins with various chemical tags, allowing specific fluorescent staining for quantification and global profiling, for example. Moreover, by introducing affinity tags, specific modified proteins can be markedly affinity enriched, drastically simplifying sample complexity and subsequent proteomic analysis. Examples demonstrating our approach include protein deamidation, methylation and homocysteinylation, which play key roles in aging, cancer and cardiovascular diseases.

5:15 Reception in the Exhibit Hall

6:30 End of Day

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