1. 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

2. 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 MS E data acquisition Ion Mobility Mass Spectrometry gives IU Bloomington Unique Analytical Capabilities

3. 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

4. ACCELERATING CLINICAL AND TRANSLATIONAL RESEARCH www.indianactsi.org Biological samples remain too complex for complete proteomic characterization We 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.

5. 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. Phosphorylation Ubiquitination GlcNAcylation (N-acetylglucosamine) N- and O- linked extracellular glycosylation Lysine acetylation We use multidimensional chromatography to maximize our ability to characterize complex samples

6. ACCELERATING CLINICAL AND TRANSLATIONAL RESEARCH www.indianactsi.org Genomics and Bioinformatics at IU Bloomington

7. 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

8. 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.

9. 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.

10. ACCELERATING CLINICAL AND TRANSLATIONAL RESEARCH www.indianactsi.org Towards the Development of an Integrated Systems Biology Technology Platform We 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.