accelerating clinical and translational research metabolomics/proteomics and genomics at iub...
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ACCELERATING CLINICAL AND TRANSLATIONAL RESEARCH
www.indianactsi.org
Metabolomics/Proteomics and Genomics at IUB
Indiana CTSI – Purdue Retreat
Monday, April 21, 2014
Jonathan Trinidad – Director of Biological Mass Spectrometry
ACCELERATING CLINICAL AND TRANSLATIONAL RESEARCH
www.indianactsi.org
Two Synapt G2 instruments acquired as part of becoming a Waters Centers of Innovation
Newest generation IMS Q-ToF
Ion mobility allows for structural characterization
Tandem MS using CID or ETD
Capable of MSE data acquisition
Ion Mobility Mass Spectrometry gives IU Bloomington Unique Analytical
Capabilities
ACCELERATING CLINICAL AND TRANSLATIONAL RESEARCH
www.indianactsi.org
Additional instrumentation in use at IU Bloomington.
LTQ Orbitrap XL: Linear ion trap coupled to an Orbitrap analyzer
LTQ Velos Pro: Newest generation linear ion trap
Qtrap 4000: Triple quadrupole mass spectrometer
ACCELERATING CLINICAL AND TRANSLATIONAL RESEARCH
www.indianactsi.org
Biological samples remain too complex for complete proteomic
characterizationWe specialize in the upfront biochemical fractionation of samples prior to MS analysis.
In the case of protein level characterization, fractionation increases the overall coverage.
For global analyses of post-translational modifications, targeted enrichment is critical.
ACCELERATING CLINICAL AND TRANSLATIONAL RESEARCH
www.indianactsi.org
To analyze PTM signaling pathways, we target and enrich proteins/peptides with specific modifications to profile these species at large scale.
PhosphorylationUbiquitinationGlcNAcylation (N-acetylglucosamine)N- and O- linked extracellular glycosylationLysine acetylation
We use multidimensional chromatography to maximize our ability to characterize complex samples
ACCELERATING CLINICAL AND TRANSLATIONAL RESEARCH
www.indianactsi.org
Genomics and Bioinformatics at IU
Bloomington
ACCELERATING CLINICAL AND TRANSLATIONAL RESEARCH
www.indianactsi.org
Biomek FXp robot
We specialize in automated next-generation library construction.
All steps in library construction can be performed in 96-well format, which minimizes costs.•Nucleic acid QC analysis•Fragmentation•Library construction
E220 ultra-sonicator
ACCELERATING CLINICAL AND TRANSLATIONAL RESEARCH
www.indianactsi.org
Illumina MiSeq
In-house next generation sequencing
Two Illumina MiSeqs.•8Gb in 40 hours. •Complete analysis of small sequencing projects.•Rapid quality control analysis of large projects prior to outsourced HiSeq analysis.
ACCELERATING CLINICAL AND TRANSLATIONAL RESEARCH
www.indianactsi.org
Towards the Development of an Integrated Systems Biology
Technology Platform
Our overall goal is to provide a networked state-wide Systems Biology in Medicine Program that integrates state-of-the-art technological, clinical, and translational research in a single platform.
ACCELERATING CLINICAL AND TRANSLATIONAL RESEARCH
www.indianactsi.org
Towards the Development of an Integrated Systems Biology
Technology PlatformWe will conduct in depth, complex molecular measurements (transcriptomics, proteomics, and metabolomics) across the arc of disease progression, treatment and remission.
Information from this measurement platform will inform treatment strategies, and enable development of models to probe the mechanism of disease onset and reversal.