Facility Mission
The mission of the Proteomics and Metabolomics Facility is to serve as an enabling resource for research and development programs at Colorado State University.
We strive to build instrumental capabilities that exceed the normal resources of individual research programs, and make those technologies available as a shared resource. We also aim to provide an environment rich in expertise and educational resources, and to foster collaboration across the CSU community and beyond.
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NPR news story featuring the Proteomics and Metabolomics Facility: "Molecular Profiles Point the Way to a Better Pint of Beer"
PMF research highlighted in the April 2013 issue of LC-GC North America "Nontargeted Metabolite Profiling by UHPLC-MS: A Case Study in Beer Reveals Effect of Temperature on Nonvolatile Small Molecules During Storage"
Facility Publications Proteomics - Metabolomics - Genomics
(PMF personnel in bold)
Schauer, KL, Broccardo CJ, Webb KM, Covey PA, Prenni JE 2013 “Mass Spectrometry Contamination from Tinuvin 770, a Common Additive in Laboratory Plastics” Journal of Biomolecular Techniques (Accepted, In press)
Kalashnikova AA, Duane WD, McBryant SJ, Herman JA, Deluca J, Luger K, Prenni JE, Hansen JC 2013 "Linker Histone H1.0 Interacts with an Extensive Network of Proteins Involved in mRNA Metabolism" Nucleic Acids Research (Accepted, in press)
Brandt LE, Ehrhart EJ, Scherman H, Olver CS, Bohn AA, Prenni JE 2013 “Characterization of the canine urinary proteome” Veterinary Clinical Pathology (Accepted, in press)
Freund DM, Prenni JE, Curthoys NP 2012 “Response of the Mitochondrial Proteome of Rat Renal Proximal Convoluted Tubules to Chronic Metabolic Acidosis” AJP - Renal Physiology 2012 Jan;304(2);F145-55.
Bisson GP, Mehaffy C, Broeckling C, Prenni J, Rifat D, Lun DS, Burgos M, Weissman D, Karakousis PC, Dobos K., 2012 “Upregulation of the phthiocerol dimycocerosate biosynthetic pathway by rifampicin-resistant, rpoB-mutant Mycobacterium tuberculosis.” J Bacteriol. 2012 Sep 21
Prenni JE, Vidal, M., Olver C.S. Preliminary Characterization of the murine memrane reticulocyte proteome. Blood Cells, Molecules, and Diseases, 2012, In Press. (PMID:22633119
Cho, YS, Dobos KM, Prenni JE, Yang H, Hess A, Rosenkrands I, Andersen P, Ryoo SW, Bai GH, Brennan MJ, Izzo A, Bielefeldt-Ohmann H, Belisle JT*, “Deciphering the proteome of the in vivo diagnostic reagent “purified protein derivative” from Mycobacterium tuberculosis” Proteomics 2012, 12, 979–991.
Fujimoto S; Seebart C; Guastafierro T; Prenni J; Caiafa P; Zlatanova J “Proteome analysis of protein partners to nucleosomes containing canonical H2A or the variant histones H2A.Z or H2A.X" Biological Chemistry, 2011 Nov 23. (Epub ahead of print).
Machain-Williams C., Mammen MP, Zeidner NS, Beaty BJ, Prenni JE, Nisalak A, Blair CD “Association of Human Immune Response to Aedes aegypti Salivary Proteins with Dengue Disease Severity”,Parasite Immunol 2011 Oct 13
Prenni JE; Scherman H; Olver C, (2011) “Methods in Animal Proteomics” P.D. Eckersall & P.D. Whitfield (Eds), Types of Sample and Experimental Planning (pp 11-39). John Wiley & Sons Lt
Kruh, N.; Troudt, J.; Izzo, A.; Prenni, JE; Dobos, KM. "Portrait of a Pathogen: The Mycobacterium tuberculosis Proteome In Vivo" 2010, PLoS One. Nov 11;5(11): e13938.
Seebart, C.; Prenni, J.; Tomschik, M.; Zlatanova, J. “New Nuclear Partners for Nucleosome Assembly Protein 1: Unexpected Associations” 2010, Biochem. Cell Biol. 88(6): 927-936.
Goldstrohm D.A.; Broeckling C.D.; Prenni J.E.; Curthoys N.P “Importance of Manual Validation for the Identification of Phosphopeptides using a Linear Ion Trap Mass Spectrometer” 2010, J Biomol Tech., 22(1): 10–20.
Szerlong HJ; Prenni JE; Nyborg JK; Hansen JC. “Activator-dependent p300 acetylation of chromatin in vitro: enhancement of transcription by disruption of repressive nucleosome-nucleosome interations". 2010 J Biol Chem. Aug 18.
Mehaffy, C.; Hess, A.;Prenni, JE.;Mathema, B.;Kreiswirth, B.;Dobos, K.M. "Descriptive proteomic analysis shows protein variability between closely related clinical isolates of Mycobacterium tuberculosis2010 Proteomics, Mar 9;10(10):1966-1984.
Wamsley, S.; Broeckling, C.; Hess, A.; Prenni, J.; Curthoys, N. "Proteomic Analysis of Brush Border Membrane Vesicles Isolated from Purified Proximal Convoluted Tubules" 2010 Am J Physiol Renal Physiol, 298(6):F1323-31.
Mueller, N.H.; Walters, M.S.; Marcus, R.; Graf, L.L.; Prenni, J.E.; Gilden, D.; Silverstein, S.J.; Cohrs, R.J. “Identification of Phosphorylated Residues on Varicella-Zoster Virus Immediate Early Protein ORF63” 2010, J Gen Virol, May;91(Pt 5):1133-7.
Olver, C.S; Webb, T.L; Long, L.J.; Scherman, H.; Prenni, J.E. “Comparison of methods for albumin and immunoglobulin depletion from equine serum.” Vet Clin Pathol. 2010 Aug 18.
Dooley, G.P.; Reardon, K.F.; Prenni, J.E.; Legare, M.E.; Foradori, C.D.; Tessari, J.E.; and Hanneman, W.H. “Proteomic Analysis of Diaminochlorotriazine (DACT) Adducts in Wister Rat Pituitary Glands and LbT2 Rat Pituitary Cells” Chemical Research in Toxicology 2008.
Prenni, J.E.; Avery, A.C.; Olver, C.S. "Proteomics: A review and an example using the reticulocyte membrane proteome." Veterinary Clinical Pathology, 2007, 36(1) 13-24.
Lyons, T.R.; Thorburn, J.; Ryan, P.W.; Thorburn, A.; Anderson, S.M.; Kassenbrock, C.K. "Regulation of the Pro-apoptotic Scaffolding Protein POSH by Akt " Journal of Biological Chemistry, 2007, 282(30), 21987-21997 .
Dooley, G.P.; Prenni, J.E.; Cranmer, B.K.; Prentiss P.L.; Andersen, M.E.; Tessari, J.D. "Identification of a Novel Hemoglobin Adduct in Sprague Dawley Rats Exposed to Atrazine" Chemical Research In Toxicology, 2006 , 19(5), 692-700.
Eckstein, T.M.; Chandrasekaran, S.; Mahapatra, S.; McNeil, M.R.; Chatterjee, D.; Rithner, C.D.; Ryan, P.W.; Belisle, J.T.; Inamine, J.M. "A Major Cell Wall Lipopeptide of Mycobacterium avium subspecies paratuberculosis" J. Biol. Chem. , 2006 , 281(8), 5209-5215.
Shen, M, Broeckling CD, Chu EY, Ziegler G, Baxter IR, Prenni JE, Hoekenga OA, 2013 “Leveraging non-targeted metabolite profiling via statistical genomics” PLOSONE (Accepted, in press)
Broeckling CD, Heuberger AL, Prenni JE 2013 “Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS)” J Vis Exp. (Accepted, In press)
Ryan EP, Heuberger AL, Broeckling CD, Borresen E, Oillia C, Prenni JE 2013 “Advances in Nutritional Metabolomics” Current Metabolomics, 1, 109-120.
Hong, MG, Karlsson R, Magnusson PKE, Lewis MR, Isaacs W, Zheng LS, Xu J, Gronberg H, Ingelsson E, Pawitan Y, Broeckling CD, Prenni JE, Wiklund F, Prince JA 2012 “A Genome-Wide Assesment of Variability in Human Serum Metabolism” Human Mutation, Dec 24 (Epub ahead of print).
Bisson GP, Mehaffy C, Broeckling C, Prenni J, Rifat D, Lun DS, Burgos M, Weissman D, Karakousis PC, Dobos K., 2012 “Upregulation of the phthiocerol dimycocerosate biosynthetic pathway by rifampicin-resistant, rpoB-mutant Mycobacterium tuberculosis.” J Bacteriol. 2012 Sep 21
Heuberger AL, Broeckling C, Lewis M, Salazar L, Bouckaert P, Prenni, JE., 2012, Metabolomic profiling of beer reveals effect of temperature on non-volatile small molecules during short-term storage. Food Chemistry, In Press.
Broeckling, C.D. Heuberger, A.L., Prince, J.A., Ingelsson, E., Prenni, J.E., Assigning precursor-product ion relationships in indiscriminant MS/MS data from non-targeted metabolite profiling studies. Metabolomics, 2012, In Press.
Thompson MD, Mensack MM, Jiang W, Zhu Z, Lewis MR, McGinley JN, Brick MA, Thompson HJ. "Cell signaling pathways associated with a reduction in mammary cancer burden by dietary common bean (Phaseolus vulgaris L.)." Carcinogenesis. 2012 Jan;33(1):226-32. Epub 2011 Nov 9
Al-Mubarak R, Vander Heiden J, Broeckling CD, Balagon M, Brennan PJ, Vissa VD. "Serum metabolomics reveals higher levels of polyunsaturated Fatty acids in lepromatous leprosy: potential markers for susceptibility and pathogenesis." 2011 PLoS Negl Trop Dis. Sep;5(9):e1303.
Ryan E.P.; Heuberger A.L.; Weir T.L.; Barnett B.; Broeckling C.D.; Prenni J.E. “Rice Bran Fermented with Saccharomyces boulardii Generates Novel Metabolite Profiles with Bioactivity.” 2011. J Agric Food Chem. 59(5): 1862–1870.
Heuberger AL; Lewis MR; Chen M-H; Brick MA; Leach JE; Ryan EP; “Metabolomic and Functional Genomic Analyses Reveal Varietal Differences in Bioactive Compounds of Cooked Rice.” PLoS ONE, 2010. 5(9): e12915.
Broz AK, Broeckling CD, De-la-Peña C, Lewis MR, Greene E, Callaway RM, Sumner LW, Vivanco JM. "Plant neighbor identity influences plant biochemistry and physiology related to defense." BMC Plant Biol. 2010 Jun 17;10:115.
Mensack MM, Fitzgerald VK, Ryan EP, Lewis MR, Thompson HJ, Brick MA. "Evaluation of diversity among common beans (Phaseolus vulgaris L.) from two centers of domestication using 'omics' technologies." BMC Genomics. 2010 Dec 2;11:686
Mensack MM, Fitzgerald VK, Lewis MR, Thompson HJ. "Characterization of low molecular weight chemical fractions of dry bean (Phaseolus vulgaris) for bioactivity using Caenorhabditis elegans longevity and metabolite fingerprinting." J Agric Food Chem. 2010 Jun 9;58(11):6697-705.
Wallenstein, M.D.; Hess, A.M.; Lewis, M.R.; Steltzer, H.;Ayres, E. "Decomposition of aspen leaf litter results in unique metabolomes when decomposed under different tree species." Soil Biology & Biochemistry, Jan 2010, 1-7.
Bhamidi, S.; Scherman, M.S.; Rithner, C.D.; Prenni, J.E.; Chatterjee, D.; Khoo, K.; and McNeil, M.R. “The Identification and Location of Succinyl Residues and the Characterization of the Interior Arabinan Region Allows for a Model of the Complete Primary Structure of Mycobacterium Tuberculosis Mycolyl Arabinogalactan” Journal of Biological Chemistry, Feb 2008.
Prenni AJ, Tobo1 Y, Garcia E, DeMott PJ, McCluskey CS, Kreidenweis SM, Prenni JE, Huffman JA, Pöhlker C, Pöschl U 2012 “The impact of rain on ice nuclei populations at a forested site in Colorado” Geophysical Research Letters (In press).
Jensen RW, Rivest J, Li W, Vissa V. "DNA fingerprinting of Mycobacterium leprae strains using variable number tandem repeat (VNTR) - fragment length analysis (FLA)." J Vis Exp. 2011 Jul 15;(53)
O'Donoghue LE, Rivest JP, Duval DL. "Polymerase chain reaction-based species verification and microsatellite analysis for canine cell line validation."