Purdue University
APT: The Analytical Proteomics Team
Team Leader: Fred Regnier, Ph.D.
Overall Project Goal:
The overall goal of this CPTAC program is to evaluate analytical platforms for validation of breast and prostate cancer biomarker candidates in plasma or serum based on affinity selector targeting of proteins. Proteins and/or peptides thus selected are identified and quantified by either 1) multidimensional mass spectrometry based methods involving electrospray ionization (ESI) or matrix assisted laser desorption ionization (MALDI), 2) ion mobility separator based fractionation before multidimensional mass spectrometry, or 3) immunological arrays on a microfabricated BioCD. Antibody arrays on a BioCD are read either by spinning disc interferometry or laser induced fluorescence to allow quantification of one to a hundred antigens in one hundred or more plasma samples simultaneously within an hour.
Laboratory Studies:
In addition to performing inter-laboratory studies within the CPTC, a central thrust of this program is to evaluate the utility of unbiased versus targeted methods in recognizing and identifying potential biomarkers using a series of separation technologies ranging from chromatographic and electrophoretic systems to ion mobility separators and immunological arrays. A complication in validation is that biomarkers are often minor isoforms of a protein. Subsequent to an initial high selectivity fractionation of plasma, the degree to which mass spectrometry and immunological assay platforms differentiate between cancer associated structure variants of 10-20 proteins is being evaluated in terms of specificity, accuracy, cost per patient, and throughput.
Protein targeting strategies being examined range from immunoaffinity and lectin selection methods to chemical derivatization of unique functionalities such as those associated with post-translational modifications. The full range of label free, stable isotope coding and chemical derivatization methods being used in modern proteomics are being evaluated for this clinical proteomics application. Because biomarker candidates often carry multiple cancer associated structural features, serial analytical strategies can be used to target these features individually as a means to increase selectivity. The relatively utility of chromatographic, ion mobility separator, mass spectral, and immunological assay methods alone and in combination are being evaluated to determine their efficacy in biomarker identification and quantification in plasma.
Team Expertise:
Team Leader:
Fred E. Regnier, Ph.D.
J.H. Law Distinguished Professor, Analytical Chemistry
Scientific Director for Analytical Proteomics and Metabolomics, Bindley Bioscience Center
Purdue University
After completing a Ph.D. at Oklahoma State University (1965) and Post Doctoral work at the University of Chicago (1966) and Harvard (1968), Professor Regnier became an Assistant Professor of Biochemistry (1968) at Purdue University. During twenty years in Biochemistry at Purdue he was an Associate Professor (1971-76), Professor (1976-90) and Associate Director of the Agricultural Experiment Station (1976-78). He became a Professor of Chemistry in the Chemistry Department at Purdue in 1990 and was promoted to Distinguished Professor in 2004. He is the author of over 300 publications, 40 patents, and several books on various aspects of chemistry, biochemistry, and particularly separation science and immunological assays as they relate to proteins.
Professor Regnier has for several decades been involved in the transfer of technology to society through patents from his laboratory, company creation, and continuing education. Along with Professor Barry Karger (Northeastern University), he co-founded Bioseparations in 1984 to provide advanced courses in analytical chemistry to scientists in the pharmaceutical industry. During the course of the next four years Bioseparations presented courses to more than a thousand scientists in U.S and European pharmaceutical companies. He then co-founded PerSeptive Biosystems (PBIO) with Noubar Afeyan in 1988 based on licensed Purdue technology, and actively participated in the growth of that company to 500 people in the U. S., Europe, and Asia. The sale of large-scale pharmaceutical manufacturing systems and scientific instruments by PBIO to more than 300 pharmaceutical and biotechnology companies grew to $100 million in 1997, when the company was sold to Applied Biosystems (ABI). In 2000, he co-founded Beyond Genomics (BG) with Jan van der Greef (University of Leiden), David Clemmer (Indiana University), and Scott McLuckey (Purdue University). BG provides advanced drug discovery tools to the pharmaceutical and biotechnology industry. The company has grown to 60 people with facilities in Europe and North America and has ongoing drug discovery relationships with major pharmaceutical companies. Most recently, he co-founded Quadraspec with David Nolte, Chard Barden, and Eric Davis. The focus of Quadraspec is on very high throughput immunological assay technology for health assessment.
Proteomic Technology Specialists
Fred Regnier, Mu Wang, David Clemmer, Jiri Adamec, Steven Valentine and Scott McLuckey
Clinical Cancer Researchers
Christopher Sweeney, Bryon Schneider and Julie Engel
Bioinformaticians
Xiang Zhang, Predrag Radivojacm Jake Chen, and Randy Arnold
Biostatisticians
Chang Yu Shen and Haixu Tang
Biologists
Harikrishna Nakshatri
Participating Institutions:
Purdue University
Indiana University Purdue University at Indianapolis
Indiana University School of Medicine
Indiana University
Predictive Physiology and Medicine Inc.
Hoosier Oncology Group
Other Essential Personnel:
Richard Borch, Charles Buck, Julie Nagel, Stephen Williams, Jacob Vinson, Aaron Jewell, Bryon Garrad, Jayme Harvey, Shelly Huck, Thomas Kendrick, Kristina Kirkpatrick
About Purdue:
Purdue University was born from President Abraham Lincoln’s Morrill Land Grant Act of 1862, which stated that the government would turn over public lands to any state that would agree to use the land sale proceeds to maintain a college teaching agriculture and the “mechanic arts”. In 1869, with a gift from John Purdue, Purdue University was established. Purdue University is a leading research institution with historical strengths in science, engineering, and agriculture. The university offers more than 400 undergraduate majors in the schools/colleges of Agriculture, Consumer and Family Sciences, Education, Engineering, Health Sciences, Liberal Arts, Management, Nursing, Pharmacy, Science, Technology and Veterinary Medicine. Purdue is one of the leading institutions in the U.S. in analytical chemistry, mass spectrometry, and separation science.
