Current and emerging services in proteomics and metabolomics through the Center for Mass Spectrometry and Proteomics

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1 Current and emerging services in proteomics and metabolomics through the Center for Mass Spectrometry and Proteomics Pratik Jagtap, PhD Managing Director, CMSP z.umn.edu/cmsppresents

2 Who are we? Center for Mass Spectrometry and Proteomics Operated through the Department of Biochemistry, Molecular Biology and Biophysics. Serving Mass Spectrometry (MS) related biological research needs across UofM campus and external institutions/private companies. Fee-for-service Internal Service Organization (ISO). Supported by all Colleges at UofM who use CMSP and OVPR services (plus variety of granting sources). Extensive collaboration with Minnesota Supercomputing Institute / OIT / UM Informatics Institute. Primary mission to support research efforts at the University of Minnesota, but also train others in the use of advanced technologies and research approaches. Workshops in proteomics / MS 3-times per year (train and manage expectations)

3 What Do we do? 2015 Regents of the University of Minnesota. All rights reserved Regents of the University of Minnesota, All rights reserved.

4 All types of molecules from big to small Intact proteins Metabolites CMSP provides expertise, equipment, training, and support for analyzing all types of biological molecules - with a focus on proteomic and metabolomic applications.

5 Example Projects

6 Proteomics Workflow Nat Methods Nov; 11(11):

7 Quantitative proteomics: many methods available Labeled versus Label-free

8 Targeted Proteomics In addition to large-scale discovery studies, proteins, metabolites or other molecules of interest can be validated by targeted mass spectrometry methods. Often proteomics discovery is followed by validation of candidates Traditionally done by Western blot or ELISA Targeted MS becoming more accepted

9 Discovery Metabolomics Discovery metabolomics * **Not trivial (incomplete databases, adducts, etc) ** *LC-MS (different formats), GC-MS Nature Reviews Molecular Cell Biology 13,

10 Targeted Metabolomics Targeted metabolomics *Synthetic standard * Nature Reviews Molecular Cell Biology 13, High throughput Hundreds of samples can be quantified for a panel of metabolites (clinical cohorts etc.)

11 PUBLISHED MANUSCRIPTS Metaproteomic analysis using the Galaxy framework. Proteomics. (2015) doi: /pmic Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries. Rudney et al., BMC Microbiome DOI: /s z ONGOING STUDIES Metaproteomics The large-scale characterization of the entire protein complement of environmental microbiota at a given point in time Metaproteomic analysis of human cervical-vaginal fluid in residual Pap tests: Insights into the cervical microbiome. Somaieh Afiuni-Zadeh, Marnie Peterson and Amy Skubitz. Lung Tissue Metaproteomics - COPD-Associated Lung Cancer. Brian Sandri, Alexa Pragman and Chris Wendt. Metaproteomics of Broncheo-alveolar lavage fluid from acute respiratory distress syndrome and hematopoietic stem cell transplant recipients. Kevin Viken and Maneesh Bhargava

12 PUBLISHED MANUSCRIPTS Proteogenomics Genomic and transcriptomic information is used to help identify novel peptides (not present in reference protein sequence databases) from mass spectrometry based proteomic data. This new information can be used to provide protein-level evidence of gene expression and to help refine gene models. Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework. J Proteome Res. (2014) : doi: /pr500812t. Multi-omic data analysis using Galaxy. Nat Biotechnol. (2015) 33(2): doi: /nbt.3134 Characterizing Cardiac Molecular Mechanisms of Mammalian Hibernation via Quantitative Proteogenomics. J Proteome Res. (2015) 14(11): doi: /acs.jproteome.5b Proteogenomic Analysis of a Hibernating Mammal Indicates Contribution of Skeletal Muscle Physiology to the Hibernation Phenotype. J. Proteome Res., (2016) DOI: /acs.jproteome.5b01138 z.umn.edu/galaxypreferences

13 Our Clients Over 52 departments. Customers from over 17 states Regents of the University of Minnesota. All rights reserved Regents of the University of Minnesota, All rights reserved.

14 Center for Mass Spectrometry and Proteomics With years of experience serving the entire biological science area of the University, the CMSP staff has a wide range of expertise in analytical methods used to characterize a broad range of molecule types Regents of the University of Minnesota. All rights reserved Regents of the University of Minnesota, All rights reserved.

15 WHERE ARE WE LOCATED? The CMSP - a subunit of the Department of Biochemistry, Molecular Biology and Biophysics (BMBB) - is based on both campuses. Phone: (Minneapolis) (St. Paul) tgriffin@umn.edu (Tim Griffin) pjagtap@umn.edu (Pratik Jagtap) Website: cbs.umn.edu/cmsp/home Twitter: twitter.com/cmsproteomics

16 cbs.umn.edu/cmsp/home z.umn.edu/cmsppresents 2015 Regents of the University of Minnesota. All rights reserved Regents of the University of Minnesota, All rights reserved.