Metabolomics and Proteomics Core Facilities are composed of several major operations that involve a

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RESEARCH CONTRIBUTION HIGHLIGHT
LIST OF SERVICES
OVERVIEW

• High throughput protein/metabolite profiling with
  LC-MSn or GCxGC-MS
• Various off-line HPLC separations and molecule
  isolation
• Identification and characterization of molecules
• Automated/manual sample preparation and Solid
  Phase Extraction (SPE)
• Automated/manual computer search and data
  analyses
• Methods development and consultation
• Bioinformatic consultation
• Complete training in metabolomics/proteomics
  technologies

Metabolomics and Proteomics Core Facilities are
composed of several major operations that involve
a variety of expertise for metabolomic and
proteomic analysis. Each laboratory provides
complementary expertise that globally serves to
enhance the research capabilities of the Life
Science research community on campus and in the
region. The Bindley Bioscience Center provides
research administrative oversight to coordinate
the functional linkages between these various
operations and to ensure the continued
improvement of the technical capabilities.

• Cellular response to stimuli is reflected by
  changes in concentration of metabolites and/or
  protein expression, post-translation
  modifications or post-translational processing of
  proteins. The identification of these changes is
  essential for understanding biological processes.
  In proteomics, large number of proteins from one
  or more samples is analyzed simultaneously and at
  least one or more quantitative and qualitative
  analyses are made on the sample components.
  Sample complexity generally varies from a few
  thousand to tens of thousands of proteins. It is
  recognized that complex samples require extensive
  separation before any quantitative and
  qualitative analyses can be used. The metabolome,
  on the other hand, is unique from the proteome in
  that it is not directly encoded by the genome.
  This makes the task for characterizing the
  metabolome more difficult because there is not a
  unique correspondence between the number of genes
  and metabolites present. Metabolomics and
  Proteomics Core Facilities use state-of-the-art
  technologies, develop new methods, and provide
  resources for both qualitative and quantitative
  analysis. Examples of ongoing projects include
• Determination of Energy Related Metabolites by
  GC/MS and LC/MS (with Dr. Ho from Laboratory of
  Renewable Resources Engineering at Purdue
  University). To improve precision in absolute
  quantification, we have introduced a new
  post-biosynthetic stable isotope encoding concept
  called Group Specific Internal Standard
  Technology (GSIST). In GSIST, Metabolite
  standards and experimental samples are
  derivatized with two different labeling agents
  that are chemically identical but isotopically
  distinct (12C vs 13C). After mixing these
  derivatized metabolites, each molecule from
  control or standard sample serves as an internal
  standard for determining the concentration of the
  chemically identical component in experimental
  sample. This Method was used in studies focused
  on improvement of the conversion of
  lignocellulosic biomass to ethanol by recombinant
  saccharomyces yeast.
• Use of proteomics and metabolomics techniques for
  Biomarker Identification in Vertebrate and
  Invertebrate Species Exposed to Various
  Environmental Stressors
• (with Dr. Sepulveda from Forestry and Natural
  Resources at Purdue University). A 2DGE and
  GCxGC/MS analyses are utilized to evaluate
  proteomic and metabolomic changes unique to
  specific environmental stressors. Significant
  variations were observed in great blue heron
  (Ardea herodias) eggs exposed to varying
  polychlorinated biphenyl (PCB) concentrations,
  different populations of a freshwater amphipod,
  Diporeia, residing in Lake Michigan as well as
  Diporeia exposed to atrazine and its metabolite
  desethylatrazine (DEA).
•  Oxidative Stress in Drosophila (with Dr.
  Pittendrigh from Department of Entomology at
  Purdue University). Novel proteomics and
  metabolomics approaches were developed for the
  quantification and identification of
  differentially expressed proteins and metabolites
  involved in energy metabolism of Drosophila
  exposed to oxidative stressors such as peroxide
  and methamphetamine.
•  Lipidomic Profiling of Cells Infected by Dengue
  Virus (with Dr. Kuhn from Biological Sciences at
  Purdue University). Improved HPLC-MS approach
  was used for the identification of phospholipid
  biomarkers of Dengue virus infection. Of those,
  23 phospholipids were up or down regulated in 80
  of the experimental samples. Future work will
  expand to cholesterol and sphingolipid
  evaluations.
•  Determination of Ganoderic Acids in Mushrooms as
  Potential Therapeutic Agents for Cancer (with Dr.
  Sliva from Indiana University). GSIST approach
  was used to identify active componds in Ganoderma
  mushroom extract These compounds are under
  investigation as potential cancer therapeutic
  agents. A protocol was also developed to evaluate
  ganoderic acids in rat plasma collected over 24
  hours after ingestion and their adsorption
  profile was determined while simultaneously
  monitoring for related metabolites.

RESOURCES
QUALITY CONTROL AND ASSURANCES

• Proteomics and Metabolomics Facilities share
  roughly 3,000 ft2 space of the BIND, HORT, and
  HANS buildings at Purdue University. Major
  equipment includes
• Waters Micromass Q-TOF micro coupled to HPLC
  (equipped with regular and nano electrospray
  ionization source capable of MS/MS analyses).
  The instrument is a high resolution
  time-of-flight (TOF) mass spectrometer that
  enables automated exact mass measurements. The
  instrument also features a quadrupole mass filter
  and collision cell for MS/MS analyses.
• LECO Pegasus 4D GCxGC-TOF (capable of MS
  analyses) enables to detect hundreds-to-thousands
  more compounds than previously seen using
  conventional GC techniques. Powerful, easy-to-use
  Windows-based ChromaTOF software simplifies
  component identification providing a significant
  increase in efficiency and productivity.
• Agilent MSD/TOF coupled to HPLC (equipped with
  regular and nano electrospray ionization source
  capable of MS analyses). The MSD TOF offers
  outstanding mass resolution and accuracy.
• Waters Micromass LCT Premier (TOF) coupled to
  HPLC (equipped with regular and nano electrospray
  ionization source capable of MS analyses). The
  instrument is equipped with W-Optics, novel
  method for enhancing resolution without
  increasing footprint.
• Agilent nanoLC-ion trap XCT plus can perform
  multiple MS/MS scan with rapid scanning speed and
  very high sensitivity. The XCT plus is coupled
  to the Chip Cube system for low sample volume
  analyses.
• AB QSTAR Pulsar (Q/TOF) coupled to nanoUPLC
  (Waters) combines ESI ionization with the hybrid
  quadrupole TOF analyzer for multi charge, high
  resolution analysis.
• AB 4800 MALDI TOF/TOF provides high sensitivity
  and mass accuracy. In addition, since there is
  usually only a singly charged ion formed, it is a
  good choice for the analysis of heterogeneous
  samples. Furthermore, the static nature of the
  sample allows for multiple evaluations on a
  single sample. 

The inclusion of mass spectral data from
higher-throughput methods creates a bottleneck
with laborious data management and analysis
phases that are increasingly error prone due to
the complexity of the information. To overcome
this issue innovative and efficient
bioinformatics infrastructure has been created at
the Bindley for data management and data mining.
The Purdue Discovery Pipeline (PDP) automatically
performs online experimental data quality
control. Data that meet quality standards are
transferred into a common data format and
archived in the central database. The user can
build a data mining workflow from a pool of
available informatics tools.
CONTACT INFORMATION
Jiri Adamec, Ph.D. Purdue University Bindley
Bioscience Center, BIND 112 1203 W. State
Street West Lafayette, IN 47907 Email
jadamec_at_purdue.edu Phone      [phone] Fax
       765-496-1518