Source: UNIV OF MINNESOTA submitted to NRP
MASS SPECTROMETRY CORE FACILITY OPERATION
Sponsoring Institution
State Agricultural Experiment Station
Project Status
COMPLETE
Funding Source
STATE
Reporting Frequency
Annual
Accession No.
0061757
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
(N/A)
Project Start Date
Jul 1, 2012
Project End Date
Jun 30, 2017
Grant Year
(N/A)
Program Code
[(N/A)]- (N/A)
Recipient Organization
UNIV OF MINNESOTA
(N/A)
ST PAUL,MN 55108
Performing Department
Biochemistry
Non Technical Summary
In modern biology and agriculture, there is a need to identify biologically active molecules. These would include small organic compounds and their metabolites as well as proteins and their post-translational modifications. Mass spectrometry is the most powerful analytical technique for the identifying and quantifying organic molecules. The Center for Mass Spectrometry and Proteomics (CMSP) has functioned as a core facility for researchers at the University of Minnesota. Numerous research projects are dependant upon the sophisticated analytical instrumentation necessary for modern biological research. A total of over200 faculty from 50 University departments as well as researchers from other Universities and government agencies have made use of the CMSP facilities. The importance can be seen in the over 100 research publications that made use of this equipment.
Animal Health Component
(N/A)
Research Effort Categories
Basic
100%
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
1020199200010%
1333999200010%
2060699200010%
2062499200010%
2113110200010%
3043999200010%
3113999200010%
5023999200010%
7015010200010%
7125010200010%
Knowledge Area
206 - Basic Plant Biology; 133 - Pollution Prevention and Mitigation; 102 - Soil, Plant, Water, Nutrient Relationships; 311 - Animal Diseases; 211 - Insects, Mites, and Other Arthropods Affecting Plants; 712 - Protect Food from Contamination by Pathogenic Microorganisms, Parasites, and Naturally Occurring Toxins; 304 - Animal Genome; 502 - New and Improved Food Products; 701 - Nutrient Composition of Food;

Subject Of Investigation
3999 - Animal research, general; 0199 - Soil and land, general; 3110 - Insects; 0699 - Trees, forests, and forest products, general; 5010 - Food; 2499 - Plant research, general;

Field Of Science
2000 - Chemistry;
Goals / Objectives
The overall objective is for the Center of Mass Spectrometry and Proteomics to function as the core biological mass spectrometry for researchers throughout the University of Minnesota. Presently, 13 mass spectrometers are used to conduct this research. They consist of: a Thermo-Fischer QExactive MS,a Thermo-Fischer LTQ Velos orbitrap MS,an AB-Sciex QTrap 5500 MS,an AB-Sciex QTrap 4000 MS,Bruker Biflex MALDI-TOF MS, one Thermo-Fischer LCQ ion trap MS, a Thermo-Fischer LTQ linear ion trap MS, a LECO Pegasus 4D GCxGC tof MS, a Waters LTC Premier XE MS, an Agilent 6130 quadrupole MS, an AB-Sciex 5600+, a Thermo-Fischer Orbitrap Fusion and a Varian Saturn 3 ion trap GC/MS. Eight of the mass spectrometers have a HPLC interfaced to them. The analytical instrumentation allows users to identify, quantify or characterize chemical compounds from small volatile molecules to whole proteins. Methodology will be developed to expand the scope and usefulness of the instrumentation to fit research needs. New instrumentation was added during the last year and will be continued to be added. Specific objectives include: 1) To analyze by EI, CI, ESI, APCI, DESI or Maldi ionization mass spectrometry for samples submitted by researchers. 2) To assist in the interpretation of the acquired spectra for structural elucidation, confirmation, quantification, stable isotope incorporation, protein identification or post-translational modification. 3) To assist in experimental design so that samples suitable for analysis are submitted. 4) To instruct students, post doctoral researchers and faculty in the potential of this service and that of other analytical techniques that might be useful in their research. 5) To acquire new state-of-the-art analytical instrumentation.
Project Methods
After consultation with the users, the method of analysis is determined and the samples are submitted to the mass spectrometry facility (CMSP). End users are encouraged to be present when samples are run or for interpretation of the data. Major users can be shown how to analyze their samples after instruction on the use and operation of the instrumentation or the analysis software. Results are reported to the individuals and accompanied with pertinent printouts, spectra, chromatograms or computer files. Assistance is given for further experimental design or interpretation of the mass spectral data. Data files are archived for later retrieval. Training is provided to students on the operation of the instrumentation and several workshops on proteomics are given throughout the year.

Progress 07/01/12 to 06/30/17

Outputs
Target Audience:The Center for Mass Spectrometry and Proteomics (CMSP) functions as a core facility for researchers throughout the University of Minnesota. Numerous research projects in the area of proteomics and metabolomics are dependent on the analytical information obtained with use of the available instrumentation. This information is provided to the researchers and the results are published in many scientific journals (See: z.umn.edu/cmsppublications). A total of 259 Principal Investigators and 670 individual researchers (PIs, graduate students, post-doctoral researchers, etc.) from more than 45 different University areas as well as investigators from 137 other Universities or government agencies and private industry made use of the facility during the current reporting period. Plant sciences, Microbiology, Biofuels, Natural product identification, Microbial degradation of fracking waters, Obesity studies, Flavor and Food science, Nutrition, Cancer research, Animal health, Diabetic studies, metaproteomics, proteogenomics and differential protein expression were just some of the areas impacted by making use of this instrumentation. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Workshops. The CMSP providedworkshops for members of the University community as well as external trainees. Theseare intensive 3 full-day events that introduce users to biological mass spectrometry and all essential aspects, including design, sample preparation, instrumentation and data analysis. The workshopsare provided twice a year (March and August), free to UMN graduate students, postdocs and faculty, with a fee charged to participants from outside institutions and companies. The workshops are almost always fully subscribed at an enrollment of 18, many times with a waiting list due to excess demand. BIOCHEMISTRY 4325 - Laboratory in Mass Spectrometry. In 2009 the CMSP introduced a formal, for-credit course for undergraduate and graduate students, BioC4325. This is a one-credit class that meets for 4 days in January, the week before start of classes. The coursefollows the same format as the workshop, with an additional day where students critique relevant research papers and present findings in groups. The course enrolls up to 18 students and provides documented training in mass spectrometry. Dr. Griffin serves as the lead instructor, while CMSP staff share the teaching tasks across the different days of the course. Informal one-on-one training. On almost a daily basis, CMSP staff offer training to researchers in sample preparation methods, instrumental analysis of samples and also software for data analysis. Such researchers use this training in their own projects, and take it with them for future research activities positions. How have the results been disseminated to communities of interest?Students from the University and other local colleges were given tours of the facilities. The laboratory is a routine stop for tours of faculty candidates being recruited to the University of Minnesota. The undergraduate teaching labs also made use of the facility. CMSP Staff also presented numerous scientific posters and oral presentations at the University and at scientific conferences. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? During the reporting period a total of 259 Principal Investigatorsand 670 individual researchers (PIs, graduate students and post-doctoral researchers, etc.)from over 45 diverse departments throughout the University of Minnesota made use of the facilities at the Center for Mass Spectrometry and Proteomics. In addition, researchers from 137 external academic, government and private industry institutions contracted their mass spectrometry research projects through the CMSP. Many scientific research publications (179 from the years 2013-2017) resulted from these efforts (see z.umn.edu/cmsppublications). In addition to supplying high-level scientific data, the CMSP also trained many users through both a series of workshops and undergraduate classroom instruction (See https://cbs.umn.edu/cmsp/workshopoct2016#overlay-context=cmsp/workshops). Individual instructional training on instrument use anddata analysis was given to graduate students, postdoctoral fellows, staff and faculty utilizing the instruments and services ofCMSP. Numerous tours were given to students from the University and from other colleges. Lectures were presented on the techniques and instrumentation available in the facility. National scientific meetings such as the Association of Biomolecular Resource Facilities (ABRF) and the American Society of Mass Spectrometry (ASMS) were attended by CMSP staff and results were presented at these conferences.

Publications

  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Kigar SL, Chang L, Guerrero CR, Sehring JR, Cuarenta A, Parker LL, Bakshi VP, Auger AP. (2017) N6-methyladenine is an epigenetic marker of mammalian early life stress. Sci Rep. 22;7(1):18078. doi: 10.1038/s41598-017-18414-7. Okon A, Han J, Dawadi S, Demosthenous C, Aldrich CC, Gupta M, Wagner CR. (2017) Anchimerically Activated ProTides as Inhibitors of Cap-Dependent Translation and Inducers of Chemosensitization in Mantle Cell Lymphoma. J Med Chem.60(19):8131-8144. Doi: 10.1021/acs.jmedchem.7b00916. Bowler RP, Wendt CH, Fessler FB, Foster MW, Kelly RS, Lasky-Su J, Rogers AJ, Stringer KA, and Winston BW; on behalf of the American Thoracic Society Workgroup on Metabolomics and Proteomics. (2017) New Strategies and Challenges in Lung Proteomics and Metabolomics An Official American Thoracic Society Workshop Report Ann Am Thorac Soc Vol 14, No 12, pp 17211743. Murie C, Sandri B, Griffin TJ, Wendt C, Larsson O. (2017) Normalization of Mass Spectrometry Data (NOMAD). bioRxiv doi: http://dx.doi.org/10.1101/105783. Adv Biol Regul.. pii: S2212-4926(17)30174-4. doi: 10.1016/j.jbior.2017.11.005.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Christenson JK, Richman JE, Jensen MR, Neufeld JY, Wilmot CM, Wackett LP. (2017) ?-Lactone Synthetase Found in the Olefin Biosynthesis Pathway. Biochem. pr 11;199(9).6b01199.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Patrinostro X, O'Rourke AR, Chamberlain CM, Moriarity BS, Perrin BJ, Ervasti JM. (2017) Relative importance of ?cyto- and ?cyto-actin in primary mouse embryonic fibroblasts. Mol Biol Cell.. pii: mbc.E16-07-0503. doi: 10.1091/mbc.E16-07-0503.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Aukema KG, Escalante DE, Maltby MM, Bera AK, Aksan A, Wackett LP. (2017) In Silico Identification of Bioremediation Potential: Carbamazepine and Other Recalcitrant Personal Care Products. Environ Sci Technol. 17;51(2):880-888. doi: 10.1021/acs.est.6b04345.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Baldridge GD, Higgins LA, Witthuhn BA, Markowski TW, Baldridge AS, Armien AG, Fallon AM. (2017) Proteomic analysis of a mosquito host cell response to persistent Wolbachia infection. Res Microbiol. S0923-2508(17)30087-6. doi: 10.1016 PMID: 28435138 Guerrero CR, Jagtap PD, Johnson JE, Griffin TJ. (2017) Using Galaxy for Proteomics Chapter 13 Pages 289 - 320 Series: New Developments in Mass Spectrometry (Book 5)Proteome Informatics Editor: Conrad Bessant Publisher: Royal Society of Chemistry; Gld edition Hodgson S, Griffin TJ, Reilly C, Harvey S, Witthuhn BA, Sandri BJ, Kunisaki KM, Wendt CH. (2017) Plasma sphingolipids in HIV-associated chronic obstructive pulmonary disease BMJ Open Respiratory Research 4 (1) e000180; DOI: 10.1136/ PMID:28409005 Christenson JK, Jensen MR, Goblirsch BR, Mohamed F, Zhang W, Wilmot CM, Wackett LP. (2017) Active Multi-Enzyme Assemblies for Long-Chain Olefinic Hydrocarbon Biosynthesis. J Bacteriol. 21. pii: JB.00890-16. doi: 10.1128/JB.00890-16. Presley GN, Schilling JS. (2017) Distinct growth and secretome strategies by two taxonomically- divergent brown rot fungi. Appl Environ Microbiol.. pii: AEM.02987-16. Doi: 10.1128
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Guhathakurta P, Prochniewicz E, Roopnarine O, Rohde JA, Thomas DD. (2017) A Cardio- myopathy Mutation in the Myosin Essential Light Chain Alters Actomyosin Structure. Biophysical Journal, Vol. 113, Issue 1, p91100 Eiden CG, Aldrich CC. (2017) Synthesis of a 3-Amino-2,3-dihydropyrid-4-one and Related Heterocyclic Analogs as Mechanism-Based Inhibitors of BioA, a Pyridoxal-Phosphate (PLP) Dependent Enzyme. J Org Chem. doi: 10.1021/acs.joc.7b00847. Xia H, Gilbertsen A, Herrera J, Racila E, Smith K, Peterson M, Griffin T, Benyumov A, Yang L, Bitterman PB, Henke CA. (2017) Calcium-binding protein S100A4 confers mesenchymal progenitor cell fibrogenicity in idiopathic pulmonary fibrosis. J Clin Invest. 30;127(7):2586-2597. Eiden CG, Maize KM, Finzel BC, Lipscomb JD, Aldrich CC. (2017) Rational Optimization of Mechanism- Based Inhibitors through Determination of the Microscopic Rate Constants of Inactivation. J Am Chem Soc. 31: 139(21):7132-7135. Khairutdinov BI, Ermakova EA, Yusypovych YM, Bessolicina EK, Tarasova NB, Toporkova YY, Kovaleva V, Zuev YF, Nesmelova IV. (2017) NMR structure, conformational dynamics, and biological activity of PsDef1 defensin from Pinus sylvestris. Biochim Biophys Acta. 1865 (8):1085-1094.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Chen D, Tavana O, Chu B, Erber L, Chen Y, Baer R, Gu W. (2017) NRF2 Is a Major Target of ARF in p53-Independent Tumor Suppression.Mol Cell.5;68(1):224-232.doi:10.1016 Tu X, Latham JA, Klema VJ, Evans RL 3rd, Li C, Klinman JP, Wilmot CM. (2017) Crystal structures reveal metal-binding plasticity at the metallo-?-lactamase active site of PqqB from Pseudomonas putida. J Biol Inorg Chem. doi: 10.1007/s00775-017-1486-8. Dawadi S, Kordus SL, Baughn AD, Aldrich CC. (2017) Synthesis and Analysis of Bacterial Folate Metabolism Intermediates and Antifolates. Org Lett. 10.1021/acs.orglett.7b02487. Christenson JK, Robinson SL, Engel TA, Richman JE, Kim AN, Wackett LP. (2017) OleB from bacterial hydrocarbon biosynthesis is a ?-lactone decarboxylase sharing key features with haloalkane dehalogenases. Biochemistry. doi: 10.1021/acs.biochem.7b00667. Bhargava M, Viken K, Wang Q, Jagtap P, Bitterman P, Ingbar D, Wendt C. (2017) Bronchoalveolar Lavage Fluid Protein Expression in Acute Respiratory Distress Syndrome Provides Insights into Pathways Activated in Subjects with Different Outcomes. Sci Rep.;7(1):7464. doi:10.1038/s41598-017-07791-8.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Bower R, Tritschler D, Mills KV, Heuser T, Nicastro D, Porter ME. (2017) DRC2/CCDC65 is a central hub for assembly of the N-DRC and other regulators of ciliary and flagellar motility. Mol Biol Cell. 22. pii: mbc.E17-08-0510. doi: 10.1091/mbc.E17-08-0510. Chambers MC, Jagtap PD, Johnson JE, McGowan T, Kumar P, Onsongo G, Guerrero CR, Barsnes H, Vaudel M, Martens L, Gr�ning B, Cooke IR, Heydarian M, Reddy KL and Grifffin TJ. (2017) An Accessible Proteogenomics Informatics Resource for Cancer. Cancer Res 77:e43-e46. DOI: 10.1158/0008-5472. CAN-17-0331 Peterson KN, Tan DT, Bezares-Cruz JC, Novak PJ. (2017) Estrone biodegradation in laboratory- scale systems designed for total nitrogen removal from wastewater. Environ Sci: Water Res Technol. https://doi.org/10.1039/C7EW00164A Cox MK, Peterson KN, Tan D, Novak PJ, Schoenfuss HL, Ward JL. (2017) Temperature modulates estrone degradation and biological effects of exposure in fathead minnows. Sci Total Environ. pii: S0048-9697(17)32771-7. doi: 10.1016/j.scitotenv.2017.10.069. Jensen MR, Goblirsch BR, Christenson JK, Esler MA, Mohamed FA, Wackett LP, Wilmot CM. (2017) OleA Glu117 is key to condensation of two fatty-acyl coenzyme A substrates in long-chain olefin biosynthesis.Biochem J.. pii: BCJ20170642. doi: 10.1042/BCJ20170642.


Progress 10/01/15 to 09/30/16

Outputs
Target Audience:The Center for Mass Spectrometry and Proteomics (CMSP) functions as a core facility for researchers throughout the University of Minnesota. Numerous research projects in the area of proteomics and metabolomics are dependent on the analytical information obtained with use of the available instrumentation. This information is provided to the researchersand the results are published in many scientific journals (See: z.umn.edu/cmsppublications). A total of 102 Principal Investigators from more than 45 different University areas as well as investigators from 40 other Universities or government agencies and private industrymade use of the facility during the current reporting period. Plant sciences, Microbiology, Biofuels, Natural product identification, Microbial degradation of fracking waters, Obesity studies, Flavor and Food science, Nutrition, Cancer research, Animal health, Diabetic studies, metaproteomics, proteogenomics and differential protein expression were just some of the areas impacted by making use of this instrumentation. Changes/Problems:During the reporting period a new Bruker Autoflex MALDI-TOF-TOF instrument was installed, replacing the old Bruker Biflex MALDI-TOF. The new instrument is capable of doing MS/MS, which is a beneficial addition, as the old instrument did not have this capability. The SCIEX 5600+ instrument has been installed and optimized to provide data of acceptable quality. It is expected that this instrument will be put intogeneral use for discovery proteomics experiments. The Thermo LTQ VELOS instrument has been experiencing more frequent operational problems in the last year, necessitating several visits by service engineers from the instrument vendor, and considerable CMSP staff time in troubleshooting. This may be a sign of the aging of the instrument (it is presently eight years old), and replacement of the instrument will likely be a point of discussion in the next year or so. What opportunities for training and professional development has the project provided?The CMSP staff provided training for undergraduate, graduate and post doctoral students with hands-on instructions on sample preparation, instrument usage and data interpretation. A series of three workshops were presented on proteomics with attendees coming from both the University and outside academic institutions and industry (http://z.umn.edu/cmspworkshopaug2014). How have the results been disseminated to communities of interest?Visiting students from the University and other local colleges were given tours of the facilities. The undergraduate teaching labs also made use of the facility. CMSP Staff also presented scientific posters and oral presentations at the University and at scientific conferences (http://cbs.umn.edu/cmsp/proteomics-presentations). What do you plan to do during the next reporting period to accomplish the goals?The CMSP will continue to provide high quality data to researchers. The four newer instruments (Thermo Q-Exactive, Thermo Fusion, SCIEX 5600+ and the Bruker Autoflex MALDI-TOF) will provide increased sensitivity and higher resolution data to the current customer base and should attract new customers to use the facilities.

Impacts
What was accomplished under these goals? During the reporting period a total of 102 Principal Investigators from many diverse departments throughout the University of Minnesota made use of the facilities at the Center for Mass Spectrometry and Proteomics. In addition, researchers from 40 external academic, government and private industry institutions contracted their mass spectrometry research projects through the CMSP. Many scientific research publications resulted from these efforts (see z.umn.edu/cmsppublications). In addition to supplying high-level scientific data, the CMSP also trained many users through both a series of workshops and undergraduate classroom instruction (See z.umn.edu/cmspworkshopaug2014). Instructional training on instrument use and data analysis was given to graduate students,postdoctoral fellows,staff and faculty utilizing the instruments and services of CMSP. Numerous tours were given to students from the University and from other colleges. Lectures were presentedon the techniques and instrumentation available in the facility. National scientific meetings such as the Association of Biomolecular Resource Facilities (ABRF) and the American Society of Mass Spectrometry (ASMS) were attended by CMSP staff and results were presented at these conferences.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Zhao X, Kotilinek LA, Smith B, Hlynialuk C, Zahs K, Ramsden M, Cleary J, Ashe KH. (2016) Caspase-2 cleavage of tau reversibly impairs memory. Nat Med. Oct 10. doi: 10.1038/nm.4199. Evans RL, Latham JA, Klinman JP, Wilmot CM, Xia Y. (2016) 1H, 13C, and 15N resonance assignments and secondary structure information for Methylobacterium extorquens PqqD and the complex of PqqD with PqqA. Biomol NMR Assign doi:10.1007/s12104-016-9705-81 Godin LM, Sandri BJ, Wagner DE, Meyer CM, Price AP, Akinnola I, Weiss DJ, Panoskaltsis-Mortari A (2016 ).Decreased Laminin Expression by Human Lung Epithelial Cells and Fibroblasts Cultured in Acellular Lung Scaffolds from Aged Mice. PLoS One.11(3):e0150966. Devamani T, Rauwerdink AM, Lunzer M, Jones BJ, Mooney JL, Tan MA, Zhang ZJ, Xu JH, Dean AM, Kazlauskas RJ (2016).Catalytic Promiscuity of Ancestral Esterases and Hydroxynitrile Lyases. J Am Chem Soc. 2016 Jan 27;138(3):1046-56. doi: 10.1021/jacs.5b12209. Gulcev M, Reilly C, Griffin TJ, Broeckling CD, Sandri BJ, Witthuhn BA, Hodgson SW, Woodruff PG, Wendt CH. (2016) Tryptophan catabolism in acute exacerbations of chronic obstructive pulmonary disease. Int J Chron Obstruct Pulmon Dis.;11:2435-2446. Lewis AK, Dunleavy KM, Senkow TL, Her C, Horn BT, Jersett MA, Mahling R, McCarthy MR, Perell GT, Valley CC, Karim CB, Gao J, Pomerantz WC, Thomas DD, Cembran A, Hinderliter A, Sachs JN. (2016) Oxidation increases the strength of the methionine-aromatic interaction. Nat Chem Biol. doi: 10.1038/nchembio.2159. [Epub ahead of print] Rebbeck RT, Nitu FR, Rohde D, Most P, Bers DM, Thomas DD, Cornea RL. (2016) S100A1 Protein Does Not Compete with Calmodulin for Ryanodine Receptor Binding but Structurally Alters the Ryanodine Receptor"Calmodulin Complex. J Biol Chem;291(30):15896-907. Tivendale ND, Jewett EM, Hegeman AD, Cohen JD. (2016) Extraction, purification, methylation and GC-MS analysis of short-chain carboxylic acids for metabolic flux analysis. J Chromatogr B Analyt Technol Biomed Life Sci. 1028:165-74. doi: 10.1016/j.jchromb.2016.05.042.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Colson BA, Thompson AR, Espinoza-Fonseca LM, Thomas DD. (2016) Site-directed spectroscopy of cardiac myosin-binding protein C reveals effects of phosphorylation on protein structural dynamics PNAS U S A. 2016 Mar 22;113(12):3233-8. doi: 10.1073/pnas.1521281113. Abulaban KM, Song H, Zhang X, Kimmel PL, Kusek JW, Nelson RG, Feldman HI, Vasan RS, Ying J, Mauer M, Nelsestuen GL, Bennett M,Brunner HI, Rovin BH. (2016) Predicting decline of kidney function in lupus nephritis using urine biomarkers. Lupus. 25(9):1012-8. doi: 10.1177/0961203316631629. Reck J, Schauer AM, VanderWaal Mills K, Bower R, Tritschler D, Perrone CA, Porter ME. (2016) The role of the dynein light intermediate chain in retrograde IFT and flagellar function in Chlamydomonas. Mol Biol Cell. 2016 Jun 1. pii: mbc.E16-03-0191. Goldford JE, Libourel IG. (2016) Unsupervised Identification of Isotope-Labeled Peptides. Anal Chem. 2016 Jun 7;88(11):6092-9. doi: 10.1021/acs.analchem.6b01703. Ballinger MA, Hess C, Napolitano MW, Bjork JA, Andrews MT. (2016) Seasonal Changes in Brown Adipose Tissue Mitochondria in a Mammalian Hibernator: from Gene Expression to Function. Am J Physiol Regul Integr Comp Physiol. doi: 10.1152/ajpregu.00463.2015. Wendt CH, Nelsestuen G, Harvey S, Gulcev M, Stone M, Reilly C. (2016) Peptides in Bronchoalveolar Lavage in Chronic Obstructive Pulmonary Disease. PLoS One. 26;11(5):e0155724. doi: 10.1371/journal.pone.0155724. Bhargava M, Viken KJ, Dey S, Steinbach MS, Wu B, Jagtap PD, Higgins L, Panoskaltsis-Mortari A, Weisdorf DJ, Kumar V, Arora M, Bitterman PB, Ingbar DH, Wendt CH. (2016) Proteome Profiling in Lung Injury Following Hematopoietic Stem Cell Transplantation.Biol Blood Marrow Transplant. (8):1383-90. doi: 10.1016/j.bbmt.2016.04.021. Butterick TA, Hocum Stone L, Duffy C, Holley C, Cabrera JA, Crampton M, Ward HB, Kelly RF, McFalls EO. (2016) Pioglitazone increases PGC1-? signaling within chronically ischemic myocardium.Basic Res Cardiol.111(3):37. doi: 10.1007/s00395-016-0555-4. Van Riper SK, Higgins L, Carlis JV, Griffin TJ. (2016) RIPPER: a framework for MS1 only metabolomics and proteomics label-free relative quantification. Bioinformatics. btw091. Thu YM, Van Riper SK, Higgins L, Zhang T, Becker JR, Markowski TW, Nguyen HD, Griffin TJ, Bielinsky AK. (2016) Slx5/Slx8 Promotes Replication Stress Tolerance by Facilitating Mitotic Progression. Cell Rep. pii: S2211-1247(16)30430-2. doi: 10.1016/j.celrep.2016.04.017. Zhou T, Chung Y, Chen J, and Chen Y (2016) Site-Specific Identification of Lysine Acetylation Stoichiometries in Mammalian Cells. J. Proteome Res. 2016, 15, 1103?1113 DOI: 10.1021/acs. Afiuni-Zadeh S, Rogers JC, Snovida SI, Bomgarden RD, Griffin TJ. (2016) . AminoxyTMT: A novel multi-functional reagent for characterization of protein carbonylation. Biotechniques. 1;60(4):186-96. doi: 10.2144/000114402. Ranade AR, Higgins L, Markowski TW, Glaser N, Kashin D, Bai R, Hong KH, Hamel E, H�fle G, Georg GI. (2016) Characterizing the Epothilone Binding Site on ?-Tubulin by Photoaffinity Labeling: Identification of ?-Tubulin Peptides TARGSQQY and TSRGSQQY as Targets of an Epothilone Photoprobe for Polymerized Tubulin. J Med Chem: 59(7):3499-514.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Yeh HS, Chang JW, Yong J. (2016) Ribo-Proteomics Approach to Profile RNA-Protein and Protein-Protein Interaction Networks. Methods Mol Biol. 2016;1421:165-74. doi: 10.1007/978-1-4939-3591-8_14. Kazemizadeh Gol MA, Lund TC, Levine SC, Adams ME. (2016) Quantitative Proteomics of Vestibular Schwannoma Cerebrospinal Fluid: A Pilot Study. Otolaryngol Head Neck Surg 154(5): 902-6. doi: 10.1177/0194599816630544. Anderson KJ, Vermillion KL, Jagtap P, Johnson JE, Griffin TJ, Andrews MT. (2016) Proteogenomic analysis of a hibernating mammal indicates contribution of skeletal muscle physiology to the hibernation phenotype. J Proteome Res. Chen Y. (2016) Quantitative Analysis of the Sirt5-Regulated Lysine Succinylation Proteome in Mammalian Cells. Methods Mol Biol: 1410:23-37. doi: 10.1007/978-1-4939-3524-6_2. Fan KT, Rendahl AK, Chen WP, Freund DM, Gray WM, Cohen JD, Hegeman AD (2016) Proteome Scale-Protein Turnover Analysis Using High Resolution Mass Spectrometric Data from Stable-Isotope Labeled Plants. J Proteome Res. 2016 Jan 29. [Epub ahead of print] Lane MD, Seelig B. (2016) Highly efficient recombinant production and purification of streptococcal cysteine protease streptopain with increased enzymatic activity. Protein Expr Purif.: S1046-5928(16)30002-X. doi: 10.1016 Baldridge GD, Markowski TW, Witthuhn BA, Higgins LA, Baldridge AS, Fallon AM. (2016) The Wolbachia WO bacteriophage proteome in the Aedes albopictus C/wStr1 cell line: evidence for lytic activity? In Vitro Cell.Dev.Biol.Animal 52:7788 McCarthy MR, Thompson AR, Nitu F, Moen RJ, Olenek MJ, Klein JC, Thomas DD. (2015) Impact of methionine oxidation on calmodulin structural dynamics. Biochem Biophys Res Commun. 2015 Jan 9;456(2):567-72. doi: 10.1016/j.bbrc.2014.11.091. Oliva Ch�vez AS, Fairman JW, Felsheim RF, Nelson CM, Herron MJ, Higgins L, Burkhardt NY, Oliver JD, Markowski TW, Kurtti TJ, Edwards TE, Munderloh UG. An O-Methyltransferase Is Required for Infection of Tick Cells by Anaplasma phagocytophilum. PLoS Pathog. 2015 Nov 6;11(11):e1005248. doi: 10.1371/journal.ppat.1005248. eCollection 2015. Wang YC, Distefano MD. (2015) Synthetic isoprenoid analogues for the study of prenylated proteins: Fluorescent imaging and proteomic applications. Bioorg Chem. :64:59-65.


Progress 10/01/14 to 09/30/15

Outputs
Target Audience:In modern biology and agriculture, there is a need to identify biologically active molecules. These would include small organic compounds and their metabolites as well as proteins and their post-translational modifications. Mass spectrometry is the most powerful analytical technique for the identifying and quantifying organic molecules. The Center for Mass Spectrometry and Proteomics (CMSP) has functioned as a core facility for researchers at the University of Minnesota. Numerous research projects are dependant upon the sophisticated analytical instrumentation necessary for modern biological research. A total of over 300 faculty from 50 University departments as well as researchers from other Universities and government agencies have made use of the CMSP facilities. The importance can be seen in the over manyresearch publications that made use of this equipment. Changes/Problems:During the year, the Sciex QStar XL and Bruker Biflex wereshut down due to inability to get them working again. The Saturn ion trap was damaged whenKazlauskas Lab upstairs wasflooded and water came through ceiling onto the instrument. As mentioned in previous reports,LCQ ion trap instrument has beenturned offand the Sciex MALDI-TOF/TOF 4800 has been transferredto chemistry. Q-Exactive (Thermo Finnigan) has been installed and in use for discovery metabolomics research (Tim Griffin, PI).Thermo Finnigan Fusion instrument (PI Yue Chen)is in use for discovery proteomics experiments. TheSciex 5600+ instrumenthasbeen installed within the facility as part of faculty hire program. It is still getting optimized to provide data of acceptable quality. This has required several visits by service engineers from the mass spectrometer vendor and troubleshooting by CMSP Staff. The operational costs for isntruments and reagents has increased as well. We are taking appropriate measures to address these issues. What opportunities for training and professional development has the project provided?The CMSP staff provided training for undergraduate, graduate and post doctoral students with hands-on instructions on sample preparation, instrument usage and data interpretation. A series of three workshops were presented on proteomics with attendees coming from both the University and outside agencies (http://z.umn.edu/cmspworkshopaug2015). A one-day workshop was also provided to an undergraduate minority group on mass spectrometry. Visiting students from local colleges were also given tours of the facilities. The undergraduate teaching labs also made use of the facility. CMSP Staff also present scientific posters, oral presentations at the University and at scientific conferences (z.umn.edu/cmspresentations). How have the results been disseminated to communities of interest?Scientific knowledge was transferred through journal articles (See z.umn.edu/cmsppublications), presentations at scientific meetings (z.umn.edu/cmspresentations), and individual communication with scientists throughout the country and across the world. What do you plan to do during the next reporting period to accomplish the goals?The center will continue to provide high quality data to researchers. New cutting-edge instrumentation has been added to the facility. A new Q-Exactive (Thermo Finnigan) has been installed and in use for discovery metabolomics research (Tim Griffin, PI). Two new instruments (AB Sciex 5600+ and Thermo Finnigan Fusion) have been installed and are in usewithin the facility as part of faculty hire program. Recently, a new Bruket Autoflex TOF/TOF system was installed at the facility.We anticipate use of these instruments to expand our services.

Impacts
What was accomplished under these goals? The Center for Mass Spectrometry and Proteomics (CMSP) functions as a core facility for researchers throughout the University of Minnesota. Numerous research projects in the area of proteomics and metabolomics are dependent on the analytical information obtained with use of the available instrumentation. This information is given to the users and the results published in many scientific journals (See: z.umn.edu/cmsppublications). A total of over 110 principal investigators from over 45 different University areas as well as investigators from 25 other Universities or government agencies made use of the facility. Plant sciences, Microbiology, Biofuels, Natural product identification, Microbial degradation of fracking waters, Obesity studies, Flavor and Food science, Nutrition, Cancer research, Animal health, Diabetic studies, metaproteomics, proteogenomics and differential protein expression were just some of the areas impacted by making use of this instrumentation. In addition to supplying high-level scientific data, the CMSP also trained many users through both a series of Report Date 01/07/2016 Page 1 of 5 Accession No. 61757 Project No. MIN-70-040 workshops and undergraduate classroom instruction (See z.umn.edu/cmspworkshopaug2014 and z.umn.edu/cmspeducation). Numerous tours were given to students from other colleges and lectures given on the techniques and instrumentation. National scientific meetings such as Association of Biomolecular and Research Facilities (ABRF), US HUPO, American Society of Mass Spectrometry (ASMS), Galaxy Community Conference (GCC) were attended and results presented at them. Instructional training was given to graduate students and post doctoral fellows.

Publications

  • Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: June 2015 "The Workshop, oral presentation and poster presentations" by Center for Mass Spectrometry and Proteomics Staff at the "63rd Annual Conference of American Society of Mass Spectrometry and Allied Topics" at St.Louis, MO. March 2015 "The Galaxy Framework as a Bioinformatics solution for proteomics and multi-omics studies" by Pratik Jagtap at the "Association of BioMolecular Resource Facilities 2015 Conference" at St.Louis, MO. December 2014 "Protein Mass Spectrometry" by LeeAnn Higgins for BIOC 4125 Laboratory in Molecular Biology October 2014 " Recyclomics Old Datasets, New Databases..." by Pratik Jagtap at Biological Mass Spectrometry Meeting Group (Griffin Lab). September 2014 "Introduction to CMSP" by Pratik Jagtap at the Biodale Science Salon organized by Minnesota Academy of Sciences and Biotechnology Institute at St. Paul, MN.
  • Type: Journal Articles Status: Accepted Year Published: 2015 Citation: Karim CB, Espinoza-Fonseca LM, James ZM, Hanse EA, Gaynes JS, Thomas DD, Kelekar A. (2015) Structural Mechanism for Regulation of Bcl2 protein Noxa by phosphorylation. Sci Rep 5:14557. Miller MC, Ippel H, Suylen D, Klyosov AA, Traber PG, Hackeng T, Mayo KH. (2015) Binding of polysaccharides to human galectin-3 at a noncanonical site in its carbohydrate recognition domain. Glycobiology 26(1):88-99. Rudney JD, Jagtap PD, Reilly CS, Chen R, Markowski TW, Higgins LA, Johnson JE, Griffin TJ. (2015) Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries.3(1). DOI:10.1186/s40168-015-0136 Barnidge DR, Krick TP, Griffin TJ, Murray DL (2015) Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry to detect monoclonal immunoglobulin light chains in serum and urine. Rapid Commun Mass Spectrom;29(21):2057-60. doi: 10.1002/rcm.731 Vermillion KL, Jagtap P, Johnson JE, Griffin TJ, Andrews MT. (2015) Characterizing cardiac molecular mechanisms of mammalian hibernation via quantitative proteogenomics J. Proteome Res, DOI: 10.1021/acs.jproteome.5b00575 Baldridge GD, Markowski TW, Witthuhn BA, Higgins LA, Baldridge AS, Fallon AM. (2015) The Wolbachia WO bacteriophage proteome in the Aedes albopictus C/wStr1 cell line: evidence for lytic activity? In Vitro Cellular & Developmental Biology - Animal pp 1-12 Khan SA, Wollaston-Hayden EE, Markowski TW, Higgins L, Mashek DG. (2015) Quantitative analysis of the murine lipid droplet-associated proteome during diet-induced hepatic steatosis. J Lipid Res. 2015 Sep 28. pii: jlr.M056812. [Epub ahead of print] Skinner NE, Wroblewski MS, Kirihara JA, Nelsestuen GL, Seaquist ER. (2015) Sitagliptin Results in a Decrease of Truncated Apolipoprotein C1. Diabetes Ther. Jagtap PD, Blakely, Murray, Stewart S, Kooren J, Johnson JE, Rhodus NL, Rudney J, Griffin TJ. (2015) Metaproteomic analysis using the Galaxy framework. Proteomics. Jun 9: 10.1002 Thumbigere-Math V, Michalowicz BS, de Jong EP, Griffin TJ, Basi DL, Hughes PJ, Tsai ML, Swenson KK, Rockwell L, Gopalakrishnan R, (2015) Salivary proteomics in bisphosphonate-related osteonecrosis of the jaw Oral Diseases 21(1):46-56. Dahlin JL, Nissink JW, Strasser JM, Francis S, Higgins L, Zhou H, Zhang Z, Walters MA. (2015) PAINS in the assay: chemical mechanisms of assay interference and promiscuous enzymatic inhibition observed during a sulfhydryl-scavenging HTS. J Med Chem. 12;58(5):2091-113. Boekel J, Chilton JM, Cooke IR, Horvatovich PL, Jagtap PD, K�ll L, Lehti� J, Lukasse P, Moerland PD, Griffin TJ. (2015) Multi-omic data analysis using Galaxy. Nat Biotechnol. 33(2):137-139. Zhang X, DeHaan LR, Higgins LA, Markowski TW, Wyse DL, Anderson JA. (2014) New insights into high-molecular-weight glutenin subunits and sub-genomes of the perennial crop Thinopyrum intermedium (Triticeae). Journal of Cereal Science. 59(2):203-210. Jagtap PD , Johnson JE, Onsongo G, Sadler FW, Murray K, Wang Y, Sheynkman GM, Bandhakavi S, Smith LM, and Griffin TJ (2014) Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework.J. Proteome Res., J 10.1021/pr500812t Bhargava M, Becker TL, Viken KJ, Jagtap PD, Dey S, Steinbach MS, Wu B, Kumar V, Bitterman PB, Ingbar DH, Wendt CH. (2014) Proteomic Profiles in Acute Respiratory Distress Syndrome Differentiates Survivors from Non-Survivors. PLoS One.9(10):e109713.


Progress 10/01/13 to 09/30/14

Outputs
Target Audience: The CMSP staff provided training for undergraduate, graduate and post doctoral students with hands-on instructions on sample preparation, instrument usage and data interpretation. A series of three workshops were presented on proteomics with attendees coming from both the University and outside agencies (http://z.umn.edu/cmspworkshopaug2014). A one-day workshop was also provided to an undergraduate minority group on mass spectrometry. Visiting students from local colleges were also given tours of the facilities. The undergraduate teaching labs also made use of the facility. CMSP Staff also present scientific posters, oral presentations at the University and at scientific conferences (z.umn.edu/cmspresentations). Changes/Problems: A new Q-Exactive (Thermo Finnigan) has been installed and in use for metabolomics research (Tim Griffin, PI). Two new instruments (AB Sciex 5600+ and Thermo Finnigan Fusion) have been installed within the facility as part of faculty hire program. We anticipate use of these instruments to expand our services. OneThermo-Finnigan LCQ ion trap MS, an AB-Sciex QStar XL MS, and an AB-Sciex 4800 Maldi tof/tof MS were retired from operations. As a result, services from these instruments will not be offered to researchers. What opportunities for training and professional development has the project provided? The CMSP staff provided training for undergraduate, graduate and post doctoral students with hands-on instructions on sample preparation, instrument usage and data interpretation. A series of three workshops were presented on proteomics with attendees coming from both the University and outside agencies (http://z.umn.edu/cmspworkshopaug2014). A one-day workshop was also provided to an undergraduate minority group on mass spectrometry. Visiting students from local colleges were also given tours of the facilities. The undergraduate teaching labs also made use of the facility. CMSP Staff also present scientific posters, oral presentations at the University and at scientific conferences (z.umn.edu/cmspresentations). How have the results been disseminated to communities of interest? Scientific knowledge was transferred through journal articles (See z.umn.edu/cmsppublications), presentations at scientific meetings (z.umn.edu/cmspresentations), and individual communication with scientists throughout the country and across th world. What do you plan to do during the next reporting period to accomplish the goals? The center will continue to provide high quality data to researchers. New cutting-edge instrumentation has been added to the facility. A new Q-Exactive (Thermo Finnigan) has been installed and in use for metabolomics research (Tim Griffin, PI). Two new instruments (AB Sciex 5600+ and Thermo Finnigan Fusion) have been installed within the facility as part of faculty hire program. We anticipate use of these instruments to expand our services.

Impacts
What was accomplished under these goals? The Center for Mass Spectrometry and Proteomics (CMSP) functions as a core facility for researchers throughout the University of Minnesota. Numerous research projects in the area of proteomics and metabolomics are dependent on the analytical information obtained with use of the available instrumentation. This information is given to the users and the results published in many scientific journals (See: z.umn.edu/cmsppublications). A total of over 110 principal investigators from over 45 different University areas as well as investigators from 25 other Universities or government agencies made use of the facility. Plant sciences, Microbiology, Biofuels, Natural product identification, Microbial degradation of fracking waters, Obesity studies, Flavor and Food science, Nutrition, Cancer research, Animal health, Diabetic studies, metaproteomics, proteogenomics and differential protein expression were just some of the areas impacted by making use of this instrumentation. In addition to supplying high-level scientific data, the CMSP also trained many users through both a series of workshops and undergraduate classroom instruction (See z.umn.edu/cmspworkshopaug2014 and z.umn.edu/cmspeducation). Numerous tours were given to students from other colleges and lectures given on the techniques and instrumentation (See z.umn.edu/cmspresentations) . National scientific meetings such as Association of Biomolecular and Research Facilities (ABRF), US HUPO, American Society of Mass Spectrometry (ASMS), Galaxy Community Conference (GCC) were attended and results presented at them. Instructional training was given to graduate students and post doctoral fellows.

Publications

  • Type: Journal Articles Status: Accepted Year Published: 2014 Citation: Tan DT, Temme HR, Arnold WA, Novak PJ. (2014) Estrone degradation: Does organic matter (quality), matter? Environ Sci Technol. 2014 Dec 2. \ Svensson B, Oda T, Nitu FR, Yang Y, Cornea I, Chen-Izu Y, Fessenden JD, Bers DM, Thomas DD, Cornea RL. (2014) FRET-Based Trilateration of Probes Bound within Functional Ryanodine Receptors. Biophys J.107(9):2037-48. Lamont EA, Janagama HK, Ribeiro-Lima J, Vulchanova L, Seth M, Yang M, Kurmi K, Waters WR, Thacker T, Sreevatsan S. (2014) Circulating Mycobacterium bovis peptides and host response proteins as biomarkers for unambiguous detection of subclinical infection. J Clin Microbiol. 52(2):536-43. Xiaofei Zhang; Lee R. DeHaan; LeeAnn Higgins; Todd W. Markowski; Donald L. Wyse; James A. Anderson (2014) New insights into high-molecular-weight glutenin subunits and sub-genomes of the perennial crop Thinopyrum intermedium (Triticeae) Journal of Cereal Science. 59(2):203-210. Li Y, Fiers WD, Bernard SM, Smith JL, Aldrich CC, Fecik RA. (2014) Polyketide Intermediate Mimics as Probes for Revealing Cryptic Stereochemistry of Ketoreductase Domains. ACS Chem Biol. 2014 Oct 9. Jagtap PD , Johnson JE, Onsongo G, Sadler FW, Murray K, Wang Y, Sheynkman GM, Bandhakavi S, Smith LM, and Griffin TJ (2014) Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework.J. Proteome Res., J 10.1021/pr500812t Bhargava M, Becker TL, Viken KJ, Jagtap PD, Dey S, Steinbach MS, Wu B, Kumar V, Bitterman PB, Ingbar DH, Wendt CH. (2014) Proteomic Profiles in Acute Respiratory Distress Syndrome Differentiates Survivors from Non-Survivors. PLoS One.9(10):e109713. Bloch SE and Schmidt-Dannert C. (2014) Construction of a Chimeric Biosynthetic Pathway for the De Novo Biosynthesis of Rosmarinic Acid in Escherichia coli ChemBioChem 10.1002/cbic.201402275 Liu LK, Finzel B. (2014) High-resolution crystal structures of alternate forms of the human CD44 hyaluronan-binding domain reveal a site for protein interaction. Acta Crystallogr F Struct Biol Commun.70(Pt 9):1155-61. Ablorh NA, Dong X, James ZM, Xiong Q, Zhang J, Thomas DD, Karim CB. (2014) Synthetic Phosphopeptides Enable Quantitation of the Content and Function of Phospholamban's four Phosphorylation States in Cardiac Muscle. J Biol Chem. 2014 Sep 4. pii: jbc.M114.556621.
  • Type: Journal Articles Status: Accepted Year Published: 2014 Citation: Van Gough D, Wheeler JS, Cheng S, Stevens MJ, Spoerke ED. (2014) Supramolecular assembly of asymmetric self-neutralizing amphiphilic Peptide wedges. Langmuir.(30):9201-9. doi: Sheynkman GM, Johnson JE, Jagtap PD, Shortreed MR, Onsongo G, Frey BL, Griffin TJ, Smith LM. (2104) Using galaxy-P to leverage RNA-Seq for the discovery of novel protein variations. BMC Genomics. 22;15(1):703. Lin-Moshier Y, Keebler MV, Hooper R, Boulware MJ, Liu X, Churamani D, Abood ME, Walseth TF1, Brailoiu E, Patel S, Marchant JS. (2014) The Two-pore channel (TPC) interactome unmasks isoform-specific roles for TPCs in endolysosomal morphology and cell pigmentation. Proc Natl Acad Sci U S A.. pii: 201407004. Thacker T, Sreevatsan S. (2014) Circulating Mycobacterium bovis Peptides and Host Response Proteins as Biomarkers for Unambiguous Detection of Subclinical Infection. J Clin Microbiol. 52(2):536-43. Stone MD, Harvey SB, Nelsestuen GL, Reilly C, Hertz MI, Wendt CH. (2014) Elevated peptides in lung lavage fluid associated with bronchiolitis obliterans syndrome. PLoS One. 2;9(1):e84471. Baldridge GD, Baldridge AS, Witthuhn BA, Higgins L, Markowski TW, Fallon AM. (2014) Proteomic profiling of a robust Wolbachia infection in an Aedes albopictus mosquito cell line. Mol Microbiol.. doi: 10.1111/mmi.12768. Boylan KL, Afiuni-Zadeh S, Geller MA, Hickey K, Griffin TJ, Pambuccian SE, Skubitz AP (2014) A feasibility study to identify proteins in the residual Pap test fluid of women with normal cytology by mass spectrometry-based proteomics. Clin Proteomics.11(1):30. 11-30. Fallon AM, Baldridge GD, Carroll EM, Kurtz CM. (2014) Depletion of host cell riboflavin reduces Wolbachia levels in cultured mosquito cells. In Vitro Cell Dev Biol Anim. 2014 May 2. Frohnert BI, Long EK, Hahn WS, and Bernlohr DA (2014) Glutathionylated Lipid Aldehydes Are Products of Adipocyte Oxidative Stress and Activators of Macrophage Inflammation. Diabetes 63:1 89-100 Lund TC, Patrinostro X, Kramer AC, Stadem P, Higgins L, Markowski TW, Wroblewski MS, Lidke DS, Tolar J, Blazar BR. (2014) sdf1 expression reveals a source of perivascular-derived mesenchymal stem cells in zebrafish. Stem Cells. Jun 6. doi: 10.1002/stem.1758.
  • Type: Journal Articles Status: Accepted Year Published: 2014 Citation: Dong X, Thomas DD. (2014) Time-resolved FRET Reveals the Structural Mechanism of SERCA-PLB Regulation. Biochem Biophys Res Commun. (14)00846-8. Yang Y, Rhodus NL, Ondrey FG, Wuertz BR, Chen X, Zhu Y, Griffin TJ. (2014) Quantitative proteomic analysis of oral brush biopsies identifies secretory leukocyte protease inhibitor as a promising, mechanism-based oral cancer biomarker. PLoS One. 2014 Apr 18;9(4):e95389. Lewis AK, James ZM, McCaffrey JE, Braun AR, Karim CB, Thomas DD, Sachs JN. (2014) Open and closed conformations of the isolated transmembrane domain of death receptor 5 support a new model of activation. Biophys J. 18;106(6):L21-4. Yerramsetty V, Gallaher DD, Ismail B (2014) Malonylglucoside Conjugates of Isoflavones Are Much Less Bioavailable Compared with Unconjugated ?-Glucosidic Forms in Rats. J Nutr. May 2014 jn.114.190801 Liu LK, Finzel BC. (2014) Fragment-Based Identification of an Inducible Binding Site on Cell Surface Receptor CD44 for the Design of Protein-Carbohydrate Interaction Inhibitors. J Med Chem. 2014 Mar 7. Palsuledesai CC, Ochocki JD, Markowski TW, Distefano MD. (2014) A combination of metabolic labeling and 2D-DIGE analysis in response to a farnesyltransferase inhibitor facilitates the discovery of new prenylated proteins. Mol Biosyst. 2014 Feb 28. Van Riper SK, de Jong EP , Higgins LA , Carlis JV, Griffin TJ. (2014) Improved intensity-based label free quantification via proximity-based intensity normalization (PIN) J. Proteome Res., Gnanandarajah JS, Gillis PA, Hernandez-Alvarado N, Higgins L, Markowski TW, Sung H, Lumley S, Schleiss MR (2014) .Identification by Mass Spectrometry and Immune Response Analysis of Guinea Pig Cytomegalovirus (GPCMV) Pentameric Complex Proteins GP129, 131 and 133.Viruses 13;6(2):727-51.. Lamont EA, Janagama HK, Ribeiro-Lima J, Vulchanova L, Seth M, Yang M, Kurmi K, Waters WR, Vermillion KL, Lidberg KA, Gammill LS. (2014) Cytoplasmic protein methylation is essential for neural crest migration. J Cell Biol. 2013 Dec 30.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2014 Citation: October 2013 "ProteoInformatics: Bioinformatic Approaches to Proteomics" by Pratik Jagtap for GERO 8021 Application of Proteomics to Aging November 2013 "Protein Mass Spectrometry" by LeeAnn Higgins for BIOC 4025 Laboratory in Biochemistry and BIOC 4125 Laboratory in Molecular Biology "Introduction to Galaxy-P" by Tim Griffin and Pratik Jagtap for Andrews Lab at University of Minnesota Duluth Campus. December 2013 "Protein Mass Spectrometry" by LeeAnn Higgins for BIOC 4125 Laboratory in Molecular Biology "Current Status of Proteomics Data Respositories & CPTAC Symposium Updates" by Pratik Jagtap at the Biological Mass Spectrometry Meeting Group (Griffin Lab). January 2014 "Large-scale multi-omic data integration and analysis: challenges and opportunities " by Tim Griffin at the Biomedical Informatics and Computational Biology Research Symposium. February 2014 "Metaproteomics: an opportunity-rich complement to metagenomics " by Tim Griffin at the Metagenomics Supergroup Meeting. March 2014 "The Galaxy framework as a unifying bioinformatics solution for 'omics' core facilities" by Pratik Jagtap at the "Association of BioMolecular Resource Facilities 2014 Conference" at Albuquerque, NM. See award winning poster here. April 2014 "Learnings from Albuquerque: Summary of the Association of Biomolecular Resource Facilities Conference" by Pratik Jagtap at Biological Mass Spectrometry Meeting Group (Griffin Lab). June 2014 "Public sharing of complex MS-based qualitative and quantitative proteomic data analysis workflows: adding value to big data repositories" by Tim Griffin at the 61st Annual Conference of American Society for Mass Spectrometry at Baltimore, MD. July 2014 See Video of "The Galaxy framework as a unifying bioinformatics solution for multi-omicdata analysis" by Pratik Jagtap at the Galaxy Community Conference at Baltimore, MD. Also on slideshare. September 2014 "Introduction to CMSP" by Pratik Jagtap at the Biodale Science Salon organized by Minnesota Academy of Sciences and Biotechnology Institute at St. Paul, MN.


Progress 01/01/13 to 09/30/13

Outputs
Target Audience: The CMSP staff provided training for undergraduate, graduate and post doctoral students with hands on instructions on instrument usage and data interpretation. A series of three workshops were presented on proteomics with attendees coming from both the University and outside agencies. A one day workshop was also provided to an undergraduate minority group on mass spectrometry. Visiting students from local colleges were also given tours of the facilities. The undergraduate teaching labs also made use of the facility. Scientific knowledge was transferred through journal articles, presentations at scientific meetings, and individual communication with scientists throughout the country. Changes/Problems: No major changes What opportunities for training and professional development has the project provided? The CMSP staff provided training for undergraduate, graduate and post doctoral students with hands on instructions on instrument usage and data interpretation. A series of three workshops were presented on proteomics with attendees coming from both the University and outside agencies. A one day workshop was also provided to an undergraduate minority group on mass spectrometry. Visiting students from local colleges were also given tours of the facilities. The undergraduate teaching labs also made use of the facility. How have the results been disseminated to communities of interest? Scientific knowledge was transferred through journal articles, presentations at scientific meetings, and individual communication with scientists throughout the country. What do you plan to do during the next reporting period to accomplish the goals? The center will continue to provide high quality data to researchers.New cutting-edge instrumentationwill be addedto the facility

Impacts
What was accomplished under these goals? The Center for Mass Spectrometry and Proteomics (CMSP) functions as a core facility for researchers throughout the University. Numerous research projects are dependent on the analytical information obtained with use of the availableinstrumentation. This information is given to the users and the results published in many scientific journals. A total of over 110 principal investigators from over 45 different University areas as well as investigators from 25 other Universities or government agencies made use of the facility. Plant sciences, microbiology, biofuels, natural product identification, microbial degradation of fracking waters,obesity studies, flavor and food science, nutrition, cancer research, animal health, diabetic studies, and differential protein expression were just some of the areas impacted by making use of this instrumentation. In addition to supplying high level scientific data, the CMSP also trained many users through both a series of workshops and undergraduate classroom instruction. Numerous tours were given to students from other colleges and lectures given on the techniques and instrumentation. National scientific meeting were attended and results presented at them. Instructional training was given to graduate students and post doctoral fellows.

Publications

  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Yu L1, O'Sullivan DJ2. (2013) Production of galactooligosaccharides using a hyperthermophilic ?-galactosidase in permeabilized whole cells of Lactococcus lactis. J Dairy Sci. S0022-0302(13)00867-9.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Makris TM, Knoot CJ, Wilmot CM, Lipscomb JD. (2013) Structure of a dinuclear iron cluster-containing ?-hydroxylase active in antibiotic biosynthesis. Biochemistry. 24;52(38):6662-71.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Satori CP, Henderson MM, Krautkramer EA, Kostal V, Distefano MD, Arriaga EA. (2013) Bioanalysis of eukaryotic organelles. Chem Rev. 10;113(4):2733-811.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Thumbigere-Math V, Michalowicz B, de Jong E, Griffin T, Basi D, Hughes P, Tsai M, Swenson K, Rockwell L, Gopalakrishnan R. (2013) Salivary proteomics in bisphosphonate-related osteonecrosis of the jaw. Oral Dis. 2013 Oct 31. doi: 10.1111/odi.12204. [Epub ahead of print]
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Wilson MB, Spivak M, Hegeman AD, Rendahl A, Cohen JD. (2013) Metabolomics reveals the origins of antimicrobial plant resins collected by honey bees.PLoS One. 18;8(10):e77512. doi: 10.1371/journal.pone.0077512.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Vostrikov VV, Mote KR, Verardi R, Veglia G. (2013) Structural Dynamics and Topology of Phosphorylated Phospholamban Homopentamer Reveal Its Role in the Regulation of Calcium Transport. Structure 0969-2126(13)00358-4.
  • Type: Journal Articles Status: Accepted Year Published: 2013 Citation: Moen RJ, Klein JC, Thomas DD. (2013) Electron Paramagnetic Resonance Resolves Effects of Oxidative Stress on Muscle Proteins.Exerc Sport Sci Rev. 2013 Nov 1.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Sharpe KM, Premsukh MD, Townsend D. (2013) Alterations of dystrophin-associated glycoproteins in the heart lacking dystrophin or dystrophin and utrophin.J Muscle Res Cell Motil.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Dodge AG, Preiner CS, Wackett LP. (2013) Expanding the Cyanuric Acid Hydrolase Protein Family to the Fungal Kingdom. J Bacteriol. 2013 Sep 13.
  • Type: Journal Articles Status: Accepted Year Published: 2013 Citation: Rashidian M, Kumarapperuma SC, Gabrielse K, Fegan A, Wagner CR, Distefano MD. (2013) Simultaneous Dual Protein Labeling Using a Triorthogonal Reagent.J Am Chem Soc. 2013 Oct 17.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Wendt CH, Tram KV, Price AP, England KA, Stiehm A, Panoskaltsis-Mortari A. (2013) Club Cell Secretory Protein improves Survival in a Murine Obliterative Bronchiolitis Model. Am J Physiol Lung Cell Mol Physiol. 2013 Aug 30. [Epub ahead of print]
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Lund TC, Kobs AJ, Kramer A, Nyquist M, Kuroki MT, Osborn J, Lidke DS, Low-Nam ST, Blazar BR, Tolar J. (2013) Bone marrow stromal and vascular smooth muscle cells have chemosensory capacity via bitter taste receptor expression.PLoS One. 2013;8(3):e58945.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Ochocki JD, Igbavboa U, Wood WG, Arriaga EA, Wattenberg EV, Distefano MD.Evaluation of prenylated peptides for use in cellular imaging and biochemical analysis.Methods Mol Biol. 2014;1088:213-23.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Gustavsson M, Verardi R, Mullen DG, Mote KR, Traaseth NJ, Gopinath T, Veglia G. (2013) Allosteric regulation of SERCA by phosphorylation-mediated conformational shift of phospholamban. Proc Natl Acad Sci U S A. 2013 Oct 7
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Tran PV, Dakoji S, Reise KH, Storey KK, Georgieff MK. (2013) Fetal iron deficiency alters proteome of adult rat hippocampal synaptosomes. Am J Physiol Regul Integr Comp Physiol. 2013 Oct 2.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Robinson SR, Abrahante JE, Johnson CR, Murtaugh MP. (2013) Purifying selection in Porcine reproductive and respiratory syndrome virus ORF5a protein influences variation in envelope glycoprotein 5 glycosylation. Infect Genet Evol. 2013 Sep 28. doi:pii: S1567-1348(13)00363-8. 10.1016
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2013 Citation: Frohnert BI, Long EK, Hahn WS, Bernlohr DA. (2013) Glutathionylated Lipid Aldehydes are Products of Adipocyte Oxidative Stress and Activators of Macrophage Inflammation.Diabetes. 2013 Sep 23. [Epub ahead of print]Frohnert BI, Long EK, Hahn WS, Bernlohr DA. (2013) Glutathionylated Lipid Aldehydes are Products of Adipocyte Oxidative Stress and Activators of Macrophage Inflammation.Diabetes. 2013 Sep 23. [Epub ahead of print]
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Long EK, Hellberg K, Foncea R, Hertzel AV, Suttles J, Bernlohr DA. (2013) Fatty acids induce leukotriene C4 synthesis in macrophages in a fatty acid binding protein-dependent manner. Biochim Biophys Acta.1831(7):1199-207.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2013 Citation: Bhargava M, Dey S, Becker TL, Steinbach MS, Wu B, Lee SM, Higgins L, Kumar V, Bitterman PB, Ingbar DH, Wendt CH. (2013) Protein Expression Profile of Rat Type Two Alveolar Epithelial Cells During Hyperoxic Stress and Recovery. Am J Physiol Lung Cell Mol Physiol. 2013 Sep 6. [Epub ahead of print]
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Satish Tammana TV, Tammana D, Diener DR, Rosenbaum J. (2013) Centrosomal protein CEP104/Chlamydomonas FAP256 moves to the ciliary tip during cilia assembly. J Cell Sci. Aug
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Beckmann JF, Fallon AM. (2013) Detection of the Wolbachia Protein WPIP0282 in Mosquito Spermathecae: Implications for Cytoplasmic Incompatibility. Insect Biochem Mol Biol. (13)00125-2.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Mahmoodi MM, Rashidian M, Dozier JK, Distefano MD. (2013) Chemoenzymatic site-specific reversible immobilization and labeling of proteins from crude cellular extract without prior purification using oxime and hydrazine ligation. Curr Protoc Chem Biol.5(2):89-109.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: De la Mora-Rey T, Guenther BD, Finzel BC. (2013) The structure of the TOG-like domain of Drosophila melanogaster Mast/Orbit. Acta Crystallogr Sect F Struct Biol Cryst Commun. 69(Pt 7):723-9.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Cabrera JA, Butterick TA, Long EK, Ziemba EA, Anderson LB, Duffy C, Sluiter W, Duncker DJ, Zhang J, Chen Y, Ward HB, Kelly RF, McFalls EO. (2013) Reduced Expression of Mitochondrial Electron Transport Chain Proteins from Hibernating Hearts Relative to Ischemic Preconditioned Hearts in the Second Window of Protection. J Mol Cell Cardiol.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Yukl ET, Jensen LM, Davidson VL, Wilmot CM. (2013) Structures of MauG in complex with quinol and quinone MADH. Acta Crystallogr Sect F Struct Biol Cryst Commun. 69(Pt 7):738-43.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Long EK, Olson DM, Bernlohr DA. (2013) High Fat Diet Induces Changes in Adipose Tissue trans-4-Oxo-2-Nonenal and trans-4-Hydroxy-2-Nonenal Levels in a Depot-Specific Manner.Free Radic Biol Med. 2013.05.030.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Ran Q, Badgley BD, Dillon N, Dunny GM, Sadowsky MJ. (2013) Occurrence, genetic diversity, and persistence of enterococci in a lake superior watershed. Appl Environ Microbiol. 79(9):3067-75.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Bower R, Tritschler D, Vanderwaal K, Perrone CA, Mueller J, Fox L, Sale WS, Porter ME. (2013) The N-DRC forms a conserved biochemical complex that maintains outer doublet alignment and limits microtubule sliding in motile axonemes. Mol Biol Cell.24(8):1134-52.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Wirschell M, Olbrich H, Werner C, Tritschler D, Bower R, Sale WS, Loges NT, Pennekamp P, Lindberg S, Stenram U, Carl�n B, Horak E, K�hler G, N�rnberg P, N�rnberg G, Porter ME, Omran H. (2013) The nexin-dynein regulatory complex subunit DRC1 is essential for motile cilia function in algae and humans. Nat Genet.45(3):262-8.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Margatan W, Ruud K, Wang Q, Markowski T, Ismail B. (2013) Angiotensin Converting Enzyme Inhibitory Activity of Soy Protein Subjected to Selective Hydrolysis and Thermal Processing. J Agric Food Chem. 2013 Mar 29. [Epub ahead of print]
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Eberle CA, Anderson NO, Clasen BM, Hegeman AD, Smith AG. (2013) PELPIII: the class III pistil-specific extensin-like Nicotiana tabacum proteins are essential for interspecific incompatibility. Plant J. Jun;74(5):805-14.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Lund TC, Kobs AJ, Kramer A, Nyquist M, Kuroki MT, Osborn J, Lidke DS, Low-Nam ST, Blazar BR, Tolar J. (2013) Bone Marrow Stromal and Vascular Smooth Muscle Cells Have Chemosensory Capacity via Bitter Taste Receptor Expression. PLoS One 8(3):e58945. doi:
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Yukl ET, Liu F, Krzystek J, Shin S, Jensen LM, Davidson VL, Wilmot CM, Liu A. (2013) Diradical intermediate within the context of tryptophan tryptophylquinone biosynthesis. Proc Natl Acad Sci U S A. 2013 Mar 4.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Wilmot CM, Yukl ET. (2013) MauG: a di-heme enzyme required for methylamine dehydrogenase maturation. Dalton Trans.42(9):3127-35.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Jagtap P, Goslinga J, Kooren JA, McGowan T, Wroblewski MS, Seymour SL, Griffin TJ. (2013) A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies. Proteomics. doi: 10.1002/pmic.201200352P. [Epub ahead of print]
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Van Riper SK, de Jong EP, Carlis JV, Griffin TJ.( 2013) Mass spectrometry-based proteomics: basic principles and emerging technologies and directions. Adv Exp Med Biol. 990:1-35.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Yin DT, Purpero VM, Fujii R, Jing Q, Kazlauskas RJ. (2013) New Structural Motif for Carboxylic Acid Perhydrolases. Chemistry. doi: 10.1002/chem.201202027. [Epub ahead of print]
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Hamilton MJ, Weingarden AR, Unno T, Khoruts A, Sadowsky MJ. (2013) High-throughput DNA sequence analysis reveals stable engraftment of gut microbiota following transplantation of previously frozen fecal bacteria. Gut Microbes.;4(2). [Epub ahead of print]
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Wilson DJ, Shi C, Teitelbaum AM, Gulick AM, Aldrich CC. (2013) Characterization of AusA: A Dimodular Nonribosomal Peptide Synthetase Responsible for Production of Aureusimine Pyrazinones. Biochemistry. 52(5):926-37.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Kumar N, Ippel H, Weber C, Hackeng T, Mayo KH. (2013) Protein lysine-N? alkylation and O-phosphorylation mediated by DTT-generated reactive oxygen species. Protein Sci. 12. doi: 10.1002/pro.2214.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Fallon AM, Baldridge GD, Higgins LA, Witthuhn BA (2013) Wolbachia from the planthopper Laodelphax striatellus establishes a robust, persistent, streptomycin-resistant infection in clonal mosquito cells. In Vitro Cell Dev BiolAnimal 49:6673
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Beckmann JF, Markowski TW, Witthuhn BA, Fallon AM. (2013) Detection of the Wolbachia-encoded DNA binding protein, HU beta, in mosquito gonads. Insect Biochemistry and Molecular Biology 43 (2013) 272-279
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Lin-Moshier Y, Sebastian PJ, Higgins L, Sampson ND, Hewitt JE, Marchant JS. (2013) Re-evaluation of the role of calcium homeostasis endoplasmic reticulum protein (CHERP) in cellular calcium signaling. J Biol Chem.:288(1):355-67.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Lamont EA, Janagama HK, Ribeiro-Lima J, Vulchanova L, Seth M, Yang M, Kurmi K, Waters WR, Thaker T, Sreevatsan S. (2013) Circulating Mycobacterium bovis peptides and host response proteins as biomarkers for unambiguous detection of subclinical infection. J Clin Microbiol. 2013 Dec 4. [Epub ahead of print]


Progress 01/01/12 to 12/31/12

Outputs
OUTPUTS: The Center for Mass Spectrometry and Proteomics (CMSP) is the core biological mass spectrometry facility at the University of Minnesota. The following mass spectrometric instrumentation is maintained in the facility: an AB Sciex QTrap 5500 quadrupole-ion trap mass spectrometer, a Thermo-Fischer Velos orbitrap LC/MS, an Agilent 6130 quadrupole LC/MS with mass based fraction collection capabilities, a Bruker Biflex III Maldi-tof, two Thermo-Fisher LCQ ion traps, a Thermo-Fisher LTQ linear ion trap,, a LECO Pegasus IV GC/GC-tof MS, one AB-Sciex QStar quadrupole-tof, a QTrap4000 quadrupole-ion trap mass spectrometers, a Varian Saturn 3 GC/MS, a Waters LCT Premier XE LC/MS and an AB-Sciex 4800 maldi tof/tof mass spectrometer. There are also twelve liquid chromatographs and several gas chromatographs. This analytical instrumentation allows users to identify, quantify or characterize small volatile compounds, metabolites, environmental contaminents and proteins. The overall objective of the facility is to provide expertise and equipment to analyze the chemical makeup of biological samples for University and external researchers. The results of these mass spectrometric analyses are made available to the investigators to further their research needs. In addition to reporting results to the users, the Center also takes part in the instruction of students and advanced users. These would consist of a series of proteomic workshops as well as for credit classroom instruction. During 2012, over 10,000 sample sets were run by mass spectrometry. These came from 45 different University Departments as well as from other Universities, government agencies and local industries. Over 100 principal investigators used mass spectrometry, and their units included: Biochemistry, Molecular Biology and Biophysics, Microbiology, Neuroscience, Genomics, Biotechnical Institute, Obesity Center, Ecology,Evolution and Behavior, Genetics, Cell Biology, Plant Biology, Entomology, Fisheries and Wildlife, Soil, Water and Climate, Food Science and Nutrition, Horticulture, Bioprocess and Biosystems Engineering, Geology, Cancer Center, Equine Medicine, Veterinary Biomedical Science, Plant Pathology and Veterinary Pathobiology. PARTICIPANTS: The CMSP staff provided mass spectrometric analytical data to users within and without the University. Over 100 principal investigators used the facility. Data interpretation was also provided. A series of four advanced workshops were presented on proteomics with attendees coming from both the University and outside agencies. TARGET AUDIENCES: The CMSP staff provided training for undergraduate, graduate and post doctoral students with hands on instructions on instrument usage and data interpretation. A series of three workshops were presented on proteomics with attendees coming from both the University and outside agencies. A one day workshop was also provided to an undergraduate minority group on mass spectrometry. Visiting students from local colleges were also given tours of the facilities. The undergraduate teaching labs also made use of the facility. Scientific knowledge was transferred through journal articles, presentations at scientific meetings, and individual communication with scientists throughout the country. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
The Center for Mass Spectrometry and Proteomics (CMSP) functions as a core facility for researchers throughout the University. Numerous research projects are dependent on the analytical information obtained with use of the available instrumentation. This information is given to the users and the results published in many scientific journals. A total of over 100 principal investigators from over 45 different University areas as well as investigators from 25 other Universities or government agencies made use of the facility. Plant sciences, microbiology, biofuels, natural product identification, microbial degradation of fracking waters,obesity studies, flavor and food science, nutrition, cancer research, animal health, diabetic studies, and differential protein expression were just some of the areas impacted by making use of this instrumentation. In addition to supplying high level scientific data, the CMSP also trained many users through both a series of workshops and undergraduate classroom instruction. Numerous tours were given to students from other colleges and lectures given on the techniques and instrumentation. National scientific meeting were attended and results presented at them. Instructional training was given to graduate students and post doctoral fellows.

Publications

  • Seffernick JL, Erickson JS, Cameron SM, Cho S, Dodge AG, Richman JE, Sadowsky MJ, Wackett LP. (2012) Defining Sequence Space and Reaction Products within the Cyanuric Acid Hydrolase (AtzD)/Barbiturase Protein Family. J Bacteriol. 194(17):4579-88.
  • de Jong EP, Griffin TJ. (2012) Online Nanoscale ERLIC-MS Outperforms RPLC-MS for Shotgun Proteomics in Complex Mixtures. J Proteome Res. 2012 Sep 14.
  • Templeton DL, Mosser KH, Chen CN, Stone MD, John R, Dengel DR, Thompson LV (2012) Effects of Left Ventricular Assist Device (LVAD) Placement on Myocardial Oxidative Stress Markers. Heart Lung Circ.
  • Duckworth BP, Wilson DJ, Nelson KM, Boshoff HI, Barry CE, and Aldrich CC. (2012) Development of a Selective Activity-Based Probe for Adenylating Enzymes: Profiling MbtA Involved in Siderophore Biosynthesis from Mycobacterium tuberculosis ACS Chem. Biol. 10.1021
  • Jagtap P, McGowan T, Bandhakavi S, Tu ZJ, Seymour S, Griffin TJ, Rudney JD. (2012) Deep metaproteomic analysis of human salivary supernatant. Proteomics 12(7):992-1001.
  • Kim YM, Stone M, Hwang TH, Kim YG, Dunlevy JR, Griffin TJ, Kim DH (2012)SH3BP4 Is a Negative Regulator of Amino Acid-Rag GTPase-mTORC1 Signaling. Mol Cell. 29;46(6):833-46.
  • Yoder AR, Robinson JW, Dickey DM, Andersland J, Rose BA, Stone MD, Griffin TJ, Potter LR.(2012) A functional screen provides evidence for a conserved, regulatory, juxtamembrane phosphorylation site in guanylyl cyclase a and B. PLoS One. 2012;7(5).
  • Jagtap P, Bandhakavi S, Higgins L, McGowan T, Sa R, Stone MD, Chilton J, Arriaga EA, Seymour SL, Griffin TJ. (2012) Workflow for analysis of high mass accuracy salivary data set using MaxQuant and ProteinPilot search algorithm. Proteomics. 12(11):1726-30.
  • Curtis JM, Hahn WS, Stone MD, Inda JJ, Droullard DJ,. Kuzmicic JP, Donoghue MA, Long EK, Armien AG, Lavandero S, Arriaga E, Griffin TJ, and Bernlohr, DA. (2012) Protein carbonylation and adipocyte mitochondria function. J Biol Chem. 10.1074
  • Feng M, Jensen LM, Yukl ET, Wei X, Liu A, Wilmot CM, Davidson VL. (2012) Proline 107 Is a Major Determinant in Maintaining the Structure of the Distal Pocket and Reactivity of the High-Spin Heme of MauG. Biochemistry 51(8):1598-606.
  • Song KY, Choi HS, Law PY, Wei LN, Loh HH. (2012) Post-transcriptional regulation of mu-opioid receptor: role of the RNA-binding proteins heterogeneous nuclear ribonucleoprotein H1 and F. Cell Mol Life Sci. 69(4):599-610.
  • Kang DH, Song KY, Choi HS, Law PY, Wei LN, Loh HH.(2012) Novel dual-binding function of a poly (C)-binding protein 3, transcriptional factor which binds the double-strand and single-stranded DNA sequence. Gene. 10;501(1):33-8.
  • Cabrera JA, Ziemba EA, Colbert R, Anderson LB, Sluiter W, Duncker DJ, Butterick TA, Sikora J, Ward HB, Kelly RF, McFalls EO. (2012) Altered expression of mitochondrial electron transport chain proteins and improved myocardial energetic state during late ischemic preconditioning. Am J Physiol Heart Circ Physiol. 302(10):H1974-82.
  • Pravetoni M, Le Naour M, Harmon TM, Tucker AM, Portoghese PS, Pentel PR. (2012) An oxycodone conjugate vaccine elicits drug-specific antibodies that reduce oxycodone distribution to brain and hot-plate analgesia. J Pharmacol Exp Ther. 341(1):225-32
  • Yin DT, Kazlauskas RJ. (2012) Revised molecular basis of the promiscuous carboxylic acid perhydrolase activity in serine hydrolases. Chemistry 18(26):8130-9.
  • Valley CC, Lewis AK, Mudaliar DJ, Perlmutter JD, Braun AR, Karim CB, Thomas DD, Brody JR, Sachs JN. (2012) Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) induces death receptor 5 networks that are highly organized. J Biol Chem 287(25):21265-78.
  • Abate-Pella D, Zeliadt NA, Ochocki JD, Warmka JK, Dore TM, Blank DA, Wattenberg EV, Distefano MD. (2012) Photochemical modulation of Ras-mediated signal transduction using caged farnesyltransferase inhibitors: activation by one- and two-photon excitation. Chembiochem. 13(7):1009-16.
  • Lei T, Yang J, Zheng L, Markowski T, Witthuhn BA, Ji Y, (2012) The essentiality of staphylococcal Gcp is independent of its repression of branched-chain amino acids biosynthesis. PLOS ONE in press
  • Shi C, Geders TW, Park SW, Wilson DJ, Boshoff HI, Abayomi O, Barry CE 3rd, Schnappinger D, Finzel BC, Aldrich CC. (2011) Mechanism-based inactivation by aromatization of the transaminase BioA involved in biotin biosynthesis in Mycobaterium tuberculosis. J Am Chem Soc.133(45):18194-201.
  • Yang L, Rudser KD, Higgins L, Rosen HR, Zaman A, Corless CL, David L, Gourley GR. (2011) Novel biomarker candidates to predict hepatic fibrosis in hepatitis C identified by serum proteomics. Dig Dis Sci.56(11):3305-15. Zhang J, Wang L, Zhang Y, Li L,
  • Ha KN, Masterson LR, Hou Z, Verardi R, Walsh N, Veglia G, Robia SL. (2011) Lethal Arg9Cys phospholamban mutation hinders Ca2+-ATPase regulation and phosphorylation by protein kinase A. Proc Natl Acad Sci 15;108(7):2735-40.
  • Kyro K, Manandhar SP, Mullen D, Schmidt WK, Distefano MD (2001) Photoaffinity labeling of Ras converting enzyme using peptide substrates that incorporate benzoylphenylalanine (Bpa) residues: Improved labeling and structural implications. Bioorganic & Medicinal Chemistry 19 (24)7559-7569.
  • Cao Y, Posokhova E, and Martemyanov KA. (2011) TRPM1 Forms Complexes with Nyctalopin In Vivo and Accumulates in Postsynaptic Compartment of ON-Bipolar Neurons in mGluR6-Dependent Manner. The Journal of Neuroscience 31(32):11521-11526.
  • Tarboush NA, Jensen LM, Yukl ET, Geng J, Liu A, Wilmot CM, Davidson VL, (2011) Mutagenesis of tryptophan199 suggests that hopping is required for MauG-dependent tryptophan tryptophylquinone biosynthesis. Proc Natl Acad Sci U S A. 108(41):16956-61
  • Klein JC, Moen RJ, Smith EA, Titus MA, and Thomas DD. (2011) Structural and Functional Impact of Site-Directed Methionine Oxidation in Myosin Biochemistry.50(47):10318-27
  • Moen RJ, Johnsrud DO, Thomas DD, Titus MA. (2012) Characterization of a myosin VII MyTH/FERM domain. J Mol Biol. 413(1):17-23.
  • Liang X, Hall JW, Yang J, Yan M, Doll K, Bey R, Ji Y (2011) Identification of Single Nucleotide Polymorphisms Associated with Hyperproduction of Alpha-Toxin in Staphylococcus aureus. PLoS One 6(4):e18428.
  • Posokhova E, Song H, Belcastro M, Higgins L, Bigley LR, Michaud NA, Martemyanov KA, Sokolov M. (2011) Disruption of the chaperonin containing TCP-1 function affects protein networks essential for rod outer segment morphogenesis and survival. Mol Cell Proteomics. 10(1): M110.000570
  • Hellestad VJ, Witthuhn BA, Fallon AM. (2011) The insect repellent DEET (N,N-diethyl-3-methylbenzamide) increases the synthesis of glutathione S-transferase in cultured mosquito cells. Cell Biol Toxicol. (2):149-57.
  • Bandhakavi S, Markowski TW, Xie H, Griffin TJ. (2011) Three-dimensional peptide fractionation for highly sensitive nanoscale LC-based shotgun proteomic analysis of complex protein mixtures. Methods Mol Biol. 790:47-56.
  • Griffin TJ, Bandhakavi S. (2011) Dynamic range compression: a solution for proteomic biomarker discovery Bioanalysis. (18):2053-6.
  • Kooren JA, Rhodus NL, Tang C, Jagtap PD, Horrigan BJ, Griffin TJ. (2011)Evaluating the potential of a novel oral lesion exudate collection method coupled with mass spectrometry-based proteomics for oral cancer biomarker discovery. Clin Proteomics. 13;8:13.
  • de Jong EP, van Riper SK, Koopmeiners JS, Carlis JV, Griffin TJ. (2011) Sample collection and handling considerations for peptidomic studies in whole saliva; implications for biomarker discovery. Clin Chim Acta. 412(23-24):2284-8.


Progress 01/01/11 to 12/31/11

Outputs
OUTPUTS: The Center for Mass Spectrometry and Proteomics (CMSP) is the core biological mass spectrometry facility at the University of Minnesota. During 2011 an AB Sciex QTrap 5500 and a Thermo-Electron LTQ Velos Orbitrap mass spectrometers were added to the facility. The AB Sciex QStar pulsar, the AB Sciex QTrap 2000 and Thermo-Electron Orbitrap mass spectrometers were retired and traded in for the previous mentioned instruments. The following additional mass spectrometric instrumentation is maintained in the facility: an Agilent 6130 quadrupole LC/MS with mass based fraction collection capabilities, a Bruker Biflex III Maldi-tof, two Thermo-Electron LCQ ion traps, a Thermo-Electron LTQ linear ion trap,, a LECO Pegasus IV GC/GC-tof MS, one AB-Sciex QStar quadrupole-tof, a QTrap4000 quadrupole-ion trap mass spectrometers, a Varian Saturn 3 GC/MS, a Waters LCT Premier XE LC/MS and an AB-Sciex 4800 maldi tof/tof mass spectrometer. There are also twelve liquid chromatographs and several gas chromatographs. This analytical instrumentation allows users to identify, quantify or characterize small volatile compounds, metabolites, environmental contaminents and proteins. The overall objective of the facility is to provide expertise and equipment to analyze the chemical makeup of biological samples for University and external researchers. The results of these mass spectrometric analyses are made available to the investigators to further their research needs. In addition to reporting results to the users, the Center also takes part in the instruction of students and advanced users. These would consist of a series of proteomic workshops as well as for credit classroom instruction. During 2011, over 10,000 sample sets were run by mass spectrometry. These came from 45 different University Departments as well as from other Universities, government agencies and local industries. Over 100 principal investigators used mass spectrometry, and their units included: Biochemistry, Molecular Biology and Biophysics, Microbiology, Neuroscience, Genomics, Biotechnical Institute, Obesity Center, Ecology,Evolution and Behavior, Genetics, Cell Biology, Plant Biology, Entomology, Fisheries and Wildlife, Soil, Water and Climate, Food Science and Nutrition, Horticulture, Bioprocess and Biosystems Engineering, Geology, Cancer Center, Equine Medicine, Veterinary Biomedical Science, Plant Pathology and Veterinary Pathobiology. PARTICIPANTS: he CMSP staff provided mass spectrometric analytical data to users within and without the University. Over 100 principal investigators used the facility. Data interpretation was also provided. A series of four advanced workshops were presented on proteomics with attendees coming from both the University and outside agencies. TARGET AUDIENCES: The CMSP staff provided training for undergraduate, graduate and post doctoral students with hands on instructions on instrument usage and data interpretation. A series of three workshops were presented on proteomics with attendees coming from both the University and outside agencies. A one day workshop was also provided to an undergraduate minority group on mass spectrometry. Visiting students from local colleges were also given tours of the facilities. The undergraduate teaching labs also made use of the facility. Scientific knowledge was transferred through journal articles, presentations at scientific meetings, and individual communication with scientists throughout the country. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
The Center for Mass Spectrometry and Proteomics (CMSP) functions as a core facility for researchers throughout the University. Numerous research projects are dependent on the analytical information obtained with use of the available instrumentation. This information is given to the users and the results published in many scientific journals. A total of over 100 principal investigators from over 45 different University areas as well as investigators from 25 other Universities or government agencies made use of the facility. Plant sciences, microbiology, biofuels, natural product identification, obesity studies, flavor and food science, nutrition, cancer research, animal health, diabetic studies, and differential protein expression were just some of the areas impacted by making use of this instrumentation. In addition to supplying high level scientific data, the CMSP also trained many users through both a series of workshops and undergraduate classroom instruction. Numerous tours were given to students from other colleges and lectures given on the techniques and instrumentation. National scientific meeting were attended and results presented at them. Instructional training was given to graduate students and post doctoral fellows.

Publications

  • Mahoney DW, Therneau TM, Heppelmann CJ, Higgins L, Benson LM, Zenka RM, Jagtap P, Nelsestuen GL, Bergen HR, Oberg AL. (2011) Relative Quantification: Characterization of bias, variability and fold changes in mass spectrometry data from iTRAQ labeled peptides. J Proteome Res. Jul 14
  • Rollefson JB, Stephen CS, Tien M, Bond DR. (2011) Identification of an extracellular polysaccharide network essential for cytochrome anchoring and biofilm formation in Geobacter sulfurreducens. J Bacteriol. 193(5):1023-33.
  • Masterson LR, Yu T, Shi L, Wang Y, Gustavsson M, Mueller MM, Veglia G. (2011) cAMP-Dependent Protein Kinase A Selects the Excited State of the Membrane Substrate Phospholamban. J Mol Biol.
  • Rodriguez Estrada AE, Hegeman A, Corby Kistler H, May G. (2011) In vitro interactions between Fusarium verticillioides and Ustilago maydis through real-time PCR and metabolic profiling. Fungal Genet Biol. Jun 15
  • Lei Y, Zhang Y, Guenther BD, Kreth J, Herzberg MC. (2011) Mechanism of adhesion maintenance by methionine sulphoxide reductase in Streptococcus gordonii. Mol Microbiol. 80(3):726-38.
  • Mullen DG, Kyro K, Hauser M, Gustavsson M, Veglia G, Becker JM, Naider F, Distefano MD. (2011) Synthesis of a-factor peptide from Saccharomyces cerevisiae and photoactive analogues via Fmoc solid phase methodology. Bioorg Med Chem.19(1):490-7.
  • Levesque HM, Scaffidi D, Polkinghorne CN, Sorensen PW. (2011) A multi-component species identifying pheromone in the goldfish. J Chem Ecol. 37(2):219-27.
  • Frias JA, Richman JE, Erickson JS, Wackett LP. (2011) Purification and characterization of OleA from Xanthomonas campestris and demonstration of a non-decarboxylative Claisen condensation reaction. J Biol Chem. 286(13):10930-8
  • Lin YC, Anderson MJ, Kohler PL, Strandberg KL, Olson ME, Horswill AR, Schlievert PM, Peterson ML. (2011) Pro-inflammatory exoprotein characterization of toxic shock syndrome Staphylococcus aureus Biochemistry. Jul 12.
  • Zu T, Gibbens B, Doty NS, Gomes-Pereira M, Huguet A, Stone MD, Margolis J, Peterson, M, Markowski TW, Ingram MA, Nan Z, Forster C, Low WC, Schoser B, Somia NV, Clark HB, Schmechel S, Bitterman PB, Gourdon G, Swanson MS, Moseley M, Ranum LP. (2011) Non-ATG-initiated translation directed by microsatellite expasnsions. PNAS 108(1):260-5
  • Lim H, Sorensen PW. (2011) Polar metabolites synergize the activity of prostaglandin f(2α) in a species-specific hormonal sex pheromone released by ovulated common carp. J Chem Ecol.37(7):695-704.
  • Brickman TJ, Cummings CA, Liew SY, Relman DA, Armstrong SK. (2011) Transcriptional profiling of the iron starvation response in Bordetella pertussis provides new insights into siderophore utilization and virulence gene expression. J Bacteriol. Jul 8.
  • Frohnert BI, Sinaiko AR, Serrot FJ, Foncea RE, Moran A, Ikramuddin S, Choudry U, Bernlohr DA. (2011) Increased Adipose Protein Carbonylation in Human Obesity. Obesity 2011 May 19.
  • Kelly RF, Cabrera JA, Ziemba EA, Crampton M, Anderson LB, McFalls EO, Ward HB. (2011) Continued depression of maximal oxygen consumption and mitochondrial proteomic expression despite successful coronary artery bypass grafting in a swine model of hibernation. J Thorac Cardiovasc Surg. 1(1):261-8.
  • Zhang J, Wang L, Li G, Anderson LB, Xu Y, Witthuhn B, Lu J. (2011) Mouse Prostate Proteomes Are Differentially Altered by Supranutritional Intake of Four Selenium Compounds. Nutr Cancer. May 24:1
  • Kim YC, Udeshi ND, Balsbaugh JL, Shabanowitz J, Hunt DF, Olszewski NE. (2011) O-GlcNAcylation of the Plum pox virus capsid protein catalyzed by SECRET AGENT: characterization of O-GlcNAc sites by electron transfer dissociation mass spectrometry. Amino Acids. 40(3):869-76
  • Chen WP, Yang XY, Harms GL, Gray WM, Hegeman AD, Cohen JD. (2011) An automated growth enclosure for metabolic labeling of Arabidopsis thaliana with 13C-carbon dioxide - an in vivo labeling system for proteomics and metabolomics research. Proteome Sci. 9(1):9.
  • Johnson CR, Griggs TF, Gnanandarajah JS, Murtaugh MP, (2011),Novel Structural Protein in Porcine Reproductive and Respiratory Syndrome Virus Encoded in an Alternative Open Reading Frame 5 Present in All Arteriviruses. J Gen Virol. 2011 Feb 9.
  • Stone MD, Chen XB, McGowan T, Bandhakavi S, Cheng B, Rhodus N, Griffin TJ. (2011) Large-Scale Phosphoproteomics Analysis of Whole Saliva Reveals a Distinct Phosphorylation Pattern. J Proteome Res. 10(4):1728-36


Progress 01/01/10 to 12/31/10

Outputs
OUTPUTS: The Center for Mass Spectrometry and Proteomics (CMSP) is the core biological mass spectrometry facility at the University of Minnesota. The following mass spectrometric instrumentation is maintained in the facility: an Agilent 6130 quadrupole LC/MS with mass based fraction collection capabilities, a Bruker Biflex III Maldi-tof, two Thermo-Electron LCQ ion traps, a Thermo-Electron LTQ linear ion trap, a Thermo-Electrom LTQ orbitrap, a LECO Pegasus IV GC/GC-tof MS, two ABI-Sciex QStar quadrupole-tofs, an ABI-Sciex QTrap2000 and a QTrap4000 quadrupole-ion trap mass spectrometers, a Varian Saturn 3 GC/MS, a Waters LCT Premier XE LC/MS and an ABI-Sciex 4800 maldi tof/tof mass spectrometer. There are also twelve liquid chromatographs and several gas chromatographs. This analytical instrumentation allows users to identify, quantify or characterize small volatile compounds, metabolites, environmental contaminents and proteins. The overall objective of the facility is to provide expertise and equipment to analyze the chemical makeup of biological samples for University and external researchers. The results of these mass spectrometric analyses are made available to the investigators to further their research needs. In addition to reporting results to the users, the Center also takes part in the instruction of students and advanced users. These would consist of a series of proteomic workshops as well as for credit classroom instruction. During 2010, well over 10,000 sample sets were run by mass spectrometry. These came from 50 different University Departments as well as from other Universities, government agencies and local industries. Over 100 principal investigators used mass spectrometry, and their units included: Biochemistry, Molecular Biology and Biophysics, Microbiology, Neuroscience, Genomics, Biotechnical Institute, Obesity Center, Ecology,Evolution and Behavior, Genetics, Cell Biology, Plant Biology, Entomology, Fisheries and Wildlife, Soil, Water and Climate, Food Science and Nutrition, Horticulture, Bioprocess and Biosystems Engineering, Geology, Cancer Center, Equine Medicine, Veterinary Biomedical Science, Plant Pathology and Veterinary Pathobiology. PARTICIPANTS: The CMSP staff provided mass spectrometric analytical data to users within and without the University. Over 100 principal investigators used the facility. Data interpretation was also provided. A series of four advanced workshops were presented on proteomics with attendees coming from both the University and outside agencies. TARGET AUDIENCES: The CMSP staff provided training for undergraduate, graduate and post doctoral students with hands on instructions on instrument usage and data interpretation. A series of four workshops were presented on proteomics with attendees coming from both the University and outside agencies. A one day workshop was also provided to an undergraduate minority group on mass spectrometry. Visiting students from local colleges were also given tours of the facilities. The undergraduate teaching labs also made use of the facility. Scientific knowledge was transferred through journal articles, presentations at scientific meetings, and individual communication with scientists throughout the country. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
The Center for Mass Spectrometry and Proteomics (CMSP) functions as a core facility for researchers throughout the University. Numerous research projects are dependent on the analytical information obtained with use of the available instrumentation. This information is given to the users and the results published in many scientific journals. A total of over 100 principal investigators from over 50 different University areas as well as investigators from 25 other Universities or government agencies made use of the facility. Plant sciences, microbiology, biofuels, natural product identification, obesity studies, flavor and food science, nutrition, cancer research, animal health, diabetic studies, and differential protein expression were just some of the areas impacted by making use of this instrumentation. In addition to supplying high level scientific data, the CMSP also trained many users through both a series of workshops and undergraduate classroom instruction. Numerous tours were given to students from other colleges and lectures given on the techniques and instrumentation. National scientific meeting were attended and results presented at them. Instructional training was given to graduate students and post doctoral fellows.

Publications

  • Andersen JD, Jemmerson R, Geller MA, Miseme B, Boylan KLM, Harrington KM, Weivoda S, Witthuhn BA, Argenta P, Vogel RI and Skubitz APN (2010) Leucine-rich alpha-2-glycoprotein-1 is Upregulated in Sera and Tumors of Ovarian Cancer Patients. J Ovarian Res.3:21
  • Yoder A, Stone MD, Griffin TJ, Potter LR. Mass spectrometric identification of phosphorylation sites in guanylyl cyclase A and B. (2010) Biochemistry 49(47) 10137-45. PMID: 20977274
  • Onsongo G, Stone MD, Van Riper SK, Chilton J, Wu B, Higgins L, Lund TC, Carlis JV, Griffin TJ. LTQ-iQuant: A freely available software pipeline for automated and accurate protein quantification of isobaric tagged peptide data from LTQ instruments. (2010) Proteomics 10(19) 3533-8. PMID: 20821806
  • de Jong EP, Xie H, Onsongo G, Stone MD, Chen XB, Kooren JA, Refsland EW, Griffin RJ, Ondrey FG, Wu B, Le CT, Rhodus NL, Carlis JV, Griffin TJ. (2010) Quantitative proteomics reveals myosin and actin as promising saliva biomarkers for distinguishing pre-malignant and malignant oral lesions. PLoS One. (6): 11148.
  • Serrano J, Higgins L, Witthuhn BA, Anderson LB, Markowski T, Holcombe GW, Kosian PA, Korte JJ, Tietge JE, Degitz SJ. (2010) In vivo assessment and potential diagnosis of xenobiotics that perturb the thyroid pathway: Proteomic analysis of Xenopus laevis brain tissue following exposure to model T4inhibitors. Comp Biochem Physiol Part D Genomics Proteomics. 5(2):138-50.
  • Roe MR, McGowan TF, Thompson LV, Griffin TJ. (2010) Targeted 18O-labeling for improved proteomic analysis of carbonylated peptides by mass spectrometry. J Am Soc Mass Spectrom. 21(7):1190-203.
  • Anderson JD, Boylan KL, Xue FS, Anderson LB, Witthuhn BA, Markowski TW, Higgins L, and Skubitz AP. (2010) Identification of candidate biomarkers in ovarian cancer serum by depletion of highly abundant proteins and differential in-gel electrophoresis. Electrophoresis. (4):599-610.
  • Boyce M, Malone ED, Anderson LB, Park S, Godden SM, Jenner F, and Trumbel TN, (2010), Evaluation of diffusion of triamcinolone acetonide from the distal interphalangeal joint into the navicular bursa in horses. Am J Vet Res. Feb;71(2):169-75.
  • Canales BK, Anderson L, Higgins L, Ensrud-Bowlin K, Roberts KP, Wu B, Kim IW, Monga M, (2010) Proteome of Human Calcium Kidney Stones. Urology. Aug 13.
  • Zykova TA, Zhu F, Vakorina TI, Zhang J, Higgins L, Urusova DV, Bode AM, Dong Z. (2010)T-LAK cell-originated protein kinase (TOPK)phosphorylation of Prx1 at Ser32 prevents UVB-induced apoptosis in RPMI7951 melanoma cells through the regulation of Prx1 peroxidase activity. J Biol Chem. 285(38):29138-46
  • Boylan KL, Andersen JD, Anderson LB, Higgins L, Skubitz AP. (2010) Quantitative proteomic analysis by iTRAQ(R) for the identification of candidate biomarkers in ovarian cancer serum. Proteome Sci. 14;8:31
  • Gourley GR, Yang L, Higgins L, Riviere MA, David LL. (2010) Proteomic analysis of biopsied human colonic mucosa. J Pediatr Gastroenterol Nutr. 51(1):46-54.
  • Reilly SM, Krick T, Dass A. (2010) Surfactant-free Synthesis of Ultrasmall Gold Nanoclusters J. Phys. Chem. C. 114 (2), pp 741-745
  • Rudney JD, Xie H, Rhodus NL, Ondrey FG, Griffin TJ. A metaproteomic analysis of the human salivary microbiota by three-dimensional peptide fractionation and tandem mass spectrometry. (2010) Mol Oral Microbiol. 25 (1) 38-49
  • Bandhakavi S, Kim YM, Ro SH, Xie H, Onsongo G, Jun CB, Kim DH, Griffin TJ. Quantitative nuclear proteomics identifies mTOR regulation of DNA damage response. (2010) Mol Cell Proteomics 9 (2) 403-14
  • Zu T, Gibbens B, Doty NS, Gomes-Pereira M, Huguet A, Stone MD, Margolis J, Peterson, M, Markowski TW, Ingram MA, Nan Z, Forster C, Low WC, Schoser B, Somia NV, Clark HB, Schmechel S, Bitterman PB, Gourdon G, Swanson MS, Moseley M, Ranum LP. Non-ATG-initiated translation directed by microsatellite expasnsions. (2010) Proc Natl Acad Sci (in press) PMID: 21173221
  • Jayapal KP, Sui S, Philp RJ, Kok YJ, Yap MG, Griffin TJ, Hu WS. Multitagging proteomic strategy to estimate protein turnover rates in dynamic systems. (2010) J Proteome Res 9 (5) 2087-97
  • Posokhova E, Song H, Belcastro M, Higgins L, Bigley LR, Michaud NA, Martemyanov KA, Sokolov M. (2010) Disruption of the chaperonin containing TCP-1 function affects protein networks essential for Rod outer segment morphogenesis and survival. Mol Cell Proteomics. 2 (in press)
  • Bandhakavi S, Van Riper SK, Tawfik, PN, Stone MD, Haddad T, Rhodus N, Carlis J, Griffin TJ. Hexapeptide libraries for enhanced protein PTM identification and relative abundance profiling in whole human saliva. (2010) J Proteome Res (in press) PMID: 21142092
  • Yee JC, Jacob NM, Jayapal KP, Kok YJ, Philp R, Griffin TJ, Hu WS. Global assessment of protein turnover in recombinant antibody producing myeloma cells. (2010) J Biotechnol 148 (4) 182-93
  • Heilmann SM, Jader LR, Harned LA, Sadowsky MJ, Schendel FJ, Lefebvre PA, von Keitz MG, Valentas KJ. (2010) Hydrothermal carbonization of microalgae II. Fatty acid, char, and algal nutrient products. Applied Energy.(in press)
  • Hellestad VJ, Witthuhn BA, Fallon AM. (2010) The insect repellent DEET (N,N-diethyl-3-methylbenzamide) increases the synthesis of glutathione S-transferase in cultured mosquito cells. Cell Biol Toxicol
  • Salinas K, Hemmer MJ, Serrano J, Higgins L, Anderson LB, Benninghoff AD, Williams DE, Walker C. (2010) Identification of estrogen-responsive vitelline envelope protein fragments from rainbow trout (Oncorhynchus mykiss) plasma using mass spectrometry. Mol Reprod Dev.
  • Stone MD, Odland RM, McGowan T, Onsongo G, Tang C, Rhodus NL, Jagtap P, Bandhakavi S, Griffin TJ.(2010) Novel In Situ Collection of Tumor Interstitial Fluid from a Head and Neck Squamous Carcinoma Reveals a Unique Proteome with Diagnostic Potential. Clin Proteomics.6(3):75-82
  • Janagama HK, Senthilkumar TMA, Bannantine JP, Kugudas A, Jagtap P, Higgins L, Witthuhn B, Sreevatsan S. (2010) Iron-sparing Response of Mycobacterium avium subsp. paratuberculosis is strain dependent. BMC Microbiology
  • Pozo-Bayon MA, Pimenta P, Pilch S, Masters JG, Martin-Alvarez PJ, Reineccius G. (2010) API-IT-MS for measuring aroma release from dentifrice products using a device to simulate tooth brushing. J Agric Food Chem. 2010 Apr 28;58(8):5034-41.
  • Kast D, Espinoza-Fonseca LM, Yi C, Thomas DD. (2010) Phosphorylation-induced structural changes in smooth muscle myosin regulatory light chain. Proc Natl Acad Sci U S A. May 4;107(18):8207-12.


Progress 01/01/09 to 12/31/09

Outputs
OUTPUTS: The Center for Mass Spectrometry and Proteomics (CMSP) is the core biological mass spectrometry facility at the University of Minnesota. The following mass spectrometric instrumentation is maintained in the facility: an Agilent 6130 quadrupole LC/MS with mass based fraction collection capabilities, a Bruker Biflex III Maldi-tof, two Thermo-Electron LCQ ion traps, a Thermo-Electron LTQ linear ion trap, a Thermo-Electrom LTQ orbitrap, a LECO Pegasus IV GC/GC-tof MS, two ABI-Sciex QStar quadrupole-tofs, an ABI-Sciex QTrap2000 and a QTrap4000 quadrupole-ion trap mass spectrometers, a Varian Saturn 3 GC/MS, a Waters LCT Premier XE LC/MS and an ABI-Sciex 4800 maldi tof/tof mass spectrometer. There are also twelve liquid chromatographs and several gas chromatographs. This analytical instrumentation allows users to identify, quantify or characterize small volatile compounds, metabolites, environmental contaminents and proteins. The overall objective of the facility is to provide expertise and equipment to analyze the chemical makeup of biological samples for University and external researchers. The results of these mass spectrometric analyses are made available to the investigators to further their research needs. In addition to reporting results to the users, the Center also takes part in the instruction of students and advanced users. These would consist of a series of proteomic workshops as well as for credit classroom instruction. During 2009, well over 10,000 sample sets were run by mass spectrometry. These came from 52 different University Departments as well as from other Universities, government agencies and local industries. Over 120 principal investigators used mass spectrometry, and their units included: Biochemistry, Molecular Biology and Biophysics, Microbiology, Neuroscience, Genomics, Biotechnical Institute, Obesity Center, Ecology,Evolution and Behavior, Genetics, Cell Biology, Plant Biology, Entomology, Fisheries and Wildlife, Soil, Water and Climate, Food Science and Nutrition, Horticulture, Bioprocess and Biosystems Engineering, Geology, Cancer Center, Equine Medicine, Veterinary Biomedical Science, Plant Pathology and Veterinary Pathobiology. PARTICIPANTS: The CMSP staff provided mass spectrometric analytical data to users within and without the University. Over 120 principal investigators used the facility. Data interpretation was also provided. A series of five advanced workshops were presented on proteomics with attendees coming from both the University and outside agencies. TARGET AUDIENCES: The CMSP staff provided training for undergraduate, graduate and post doctoral students with hands on instructions on instrument usage and data interpretation. A series of five workshops were presented on proteomics with attendees coming from both the University and outside agencies. A one day workshop was also provided to an undergraduate minority group on mass spectrometry. Visiting students from local colleges were also given tours of the facilities. The undergraduate teaching labs also made use of the facility. Scientific knowledge was transferred through journal articles, presentations at scientific meetings, and individual communication with scientists throughout the country. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
The Center for Mass Spectrometry and Proteomics (CMSP) functions as a core facility for researchers throughout the University. Numerous research projects are dependent on the analytical information obtained with use of the available instrumentation. This information is given to the users and the results published in many scientific journals. A total of over 120 principal investigators from over 50 different University areas as well as investigators from 20 other Universities or government agencies made use of the facility. Plant sciences, microbiology, natural product identification, obesity studies, flavor and food science, nutrition, cancer research, animal health, diabetic studies, and differential protein expression were just some of the areas impacted by making use of this instrumentation. In addition to supplying high level scientific data, the CMSP also trained many users through both a series of workshops and undergraduate classroom instruction. Numerous tours were given to students from other colleges and lectures given on the techniques and instrumentation. National scientific meeting were attended and results presented at them. Instructional training was given to graduate students and post doctoral fellows.

Publications

  • 1: Bandhakavi S, Kim YM, Ro SH, Xie H, Onsongo G, Jun CB, Kim DH, Griffin TJ. Quantitative nuclear proteomics identifies mTOR regulation of DNA damage response. Mol Cell Proteomics. 2009 Nov 23. [Epub ahead of print] PubMed PMID: 19955088.
  • 2: Yan W, Apweiler R, Balgley BM, Boontheung P, Bundy JL, Cargile BJ, Cole S, Fang X, Gonzalez-Begne M, Griffin TJ, Hagen F, Hu S, Wolinsky LE, Lee CS, Malamud D, Melvin JE, Menon R, Mueller M, Qiao R, Rhodus NL, Sevinsky JR, States D, Stephenson JL, Than S, Yates JR, Yu W, Xie H, Xie Y, Omenn GS, Loo JA, Wong DT. Systematic comparison of the human saliva and plasma proteomes. Proteomics Clin Appl. 2009 Jan 1;3(1):116-134. PubMed PMID: 19898684; PubMed Central PMCID: PMC2773554.
  • 3: Bandhakavi S, Stone MD, Onsongo G, Van Riper SK, Griffin TJ. A dynamic range compression and three-dimensional peptide fractionation analysis platform expands proteome coverage and the diagnostic potential of whole saliva. J Proteome Res. 2009 Dec;8(12):5590-600. PubMed PMID: 19813771; PubMed Central PMCID: PMC2789208.
  • 4: Wiczer BM, Bernlohr DA. A novel role for fatty acid transport protein 1 in the regulation of tricarboxylic acid cycle and mitochondrial function in 3T3-L1 adipocytes. J Lipid Res. 2009 Dec;50(12):2502-13. Epub 2009 Jun 17. PubMed PMID: 19535819; PubMed Central PMCID: PMC2781321.
  • 5: Canales BK, Anderson L, Higgins L, Frethem C, Ressler A, Kim IW, Monga M. Proteomic analysis of a matrix stone: a case report. Urol Res. 2009 Sep 4. [Epub ahead of print] PubMed PMID: 19730843.
  • 6: Canales BK, Higgins L, Markowski T, Anderson L, Li QA, Monga M. Presence of five conditioning film proteins are highly associated with early stent encrustation. J Endourol. 2009 Sep;23(9):1437-42. PubMed PMID: 19698053.
  • 7: Ge X, Qiu Y, Loh HH, Law PY. GRIN1 regulates micro-opioid receptor activities by tethering the receptor and G protein in the lipid raft. J Biol Chem. 2009 Dec 25;284(52):36521-34. Epub 2009 Oct 27. PubMed PMID: 19861419; PubMed Central PMCID: PMC2794768.
  • 8. Riedl MS, Braun PD, Kitto KF, Roiko SA, Anderson LB, Honda CN, Fairbanks CA, Vulchanova L. Proteomic analysis uncovers novel actions of the neurosecretory protein VGF in nociceptive processing. J Neurosci. 2009 Oct 21;29(42):13377-88
  • 9. A. C. Dharmaratne, T. Krick, A. Dass, Nanocluster Size Evolution Studied by Mass Spectrometry in Room Temperature Au25(SR)18 Synthesis, J. Am. Chem. Soc. 2009, 131,13604-13605.
  • 10. Fallon AM, Witthuhn BA, Proteasome activity in a naive mosquito cell line infected with Wolbachia pipientis wAlbB. In Vitro Cell Dev Biol Anim. 2009 Sep;45(8):460-6. Epub 2009 Mar 19


Progress 01/01/08 to 12/31/08

Outputs
OUTPUTS: The Center for Mass Spectrometry and Proteomics (CMSP) is the core biological mass spectrometry facility at the University of Minnesota. During 2008 four new mass spectrometers were added to the facility and one was retired. The new instrumentation include an Thermo-Electron LTQ orbitrap LC/MS, a Waters LCT tof LC/MS, a LECO GC/GC-tof MS and an Agilent quadrupole LC/MS with a mass based fraction collector. The Kratos MS-25 RFA magnetic sector mass spectrometer was retired. The remaining instrumentation include: a Bruker Biflex III Maldi-tof, two Thermo-Electron LCQ ion traps, a Thermo-Electron LTQ linear ion trap, three ABI-Sciex QStar quadrupole-tofs, an ABI-Sciex QTrap2000 and a QTrap4000 quadrupole-ion trap mass spectrometers, a Varian Saturn 3 GC/MS and an ABI-Sciex 4800 maldi tof/tof mass spectrometer. There are also twelve liquid chromatographs and several gas chromatographs. This analytical instrumentation allows users to identify, quantify or characterize chemical compounds with molecular weight from those of small volatile compounds to large proteins. So the overall objective is to analyze the chemical makeup of biologically derived samples for researchers both within and outside the University. The results of these mass spectrometric analyses are given to the investigators to further their research needs. Specifically, these objectives include: analysis by EI,CI,ESI, APCI, DESI and Maldi ionization mass spectrometry, assist in the interpretation of the acquired spectra for structure elucidation, identification and quantification of organic molecules. Differential protein expression of various biological or disease states is one of the many functions of the lab. In addition to reporting results to the users, the Center also takes part in the instruction of students and advanced users. These would consist of a series of proteomic workshops as well as for credit classroom instruction. During 2008, over 10,000 sample sets were run by mass spectrometry. These came from over 50 different University Departments as well as from other Universities, government agencies and local industries. Over 100 principle investigators used mass spectrometry and their units included: Biochemistry, Molecular Biology and Biophysics, Microbiology, Neuroscience, Genomics, Biotechnical Institute, Obesity Center, Ecology,Evolution and Behavior, Genetics, Cell Biology, Plant Biology, Entomology, Fisheries and Wildlife, Soil, Water and Climate, Food Science and Nutrition, Horticulture, Bioprocess and Biosystems Engineering, Geology, Cancer Center, Equine Medicine, Veterinary Biomedical Science, Plant Pathology and Veterinary Pathobiology. PARTICIPANTS: The CMSP staff provided mass spectrometric analytical data to users within and without the University. Over 100 principal investigators used the facility. Data interpretation was also provided. A series of five advanced workshops were presented on proteomics with attendees coming from both the University and outside agencies. TARGET AUDIENCES: The CMSP staff provided training for undergraduate, graduate and post doctoral students with hands on instructions on instrument usage and data interpretation. A series of five workshops were presented on proteomics with attendees coming from both the University and outside agencies. A one day workshop was also provided to an undergraduate minority group on mass spectrometry. Visiting students from local colleges were also given tours of the facilities. A class was presented to Medical School Fellows. The undergraduate teaching labs also made use of the facility. Scientific knowledge was transferred through journal articles, presentations at scientific meetings, and individual communication with scientists throughout the country. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
The Center for Mass Spectrometry and Proteomics (CMSP) functions as a core facility for researchers throughout the University. Numerous research projects are dependent on the analytical information obtained with use of the available instrumentation. This information is given to the users and the results published in many scientific journals. A total of over 100 principal investigators from over 50 different University areas as well as investigators from 20 other Universities or government agencies made use of the facility. Plant sciences, microbiology, natural product identification, obesity studies, flavor and food science, nutrition, cancer research, animal health, diabetic studies, and differential protein expression were just some of the areas impacted by making use of this instrumentation. In addition to supplying high level scientific data, the CMSP also trained many users through both a series of workshops and undergraduate classroom instruction. Numerous tours were given to students from other colleges and lectures given on the techniques and instrumentation. National scientific meeting were attended and results presented at them. Hands on training was also given to graduate students and post doctoral fellows.

Publications

  • Prochniewicz, E., D. A. Lowe, D. J. Spakowicz, L. Higgins, K. OConor, L. V. Thompson, D. A. Ferrington, and D. D. Thomas. 2008. Functional, structural and chemical changes in myosin associated with hydrogen peroxide treatment of skeletal muscle fibers. Am J Physiol Cell Physiol, 294: C613-26. PMID: 18003749
  • Prochniewicz, E., D. J. Spakowicz, and D. D. Thomas. 2008. Changes in actin structural transitions associated with oxidative inhibition of muscle contraction. Biochemistry, 47:11811-11817. PMID: 18855423
  • Harvey SB, Zhang Y, Wilson-Grady J, Monkkonen T, Nelsestuen GL, Kasthuri RS, Verneris MR, Lund TC, Ely EW, Bernard GR, Zeisler H, Homoncik M, Jilma B, Swan T, Kellogg TA. O-Glycoside Biomarker of Apolipoprotein C3: Responsiveness to Obesity, Bariatric Surgery, and Therapy with Metformin, to Chronic or Severe Liver Disease and to Mortality in Severe Sepsis and Graft vs Host Disease. J Proteome Res. 2008 Dec 5. [Epub ahead of print]PMID: 19055479
  • Akkina SK, Zhang Y, Nelsestuen GL, Oetting WS, Ibrahim HN. Temporal Stability of the Urinary Proteome after Kidney Transplant: More Sensitive than Protein Composition J Proteome Res. 2008 Nov 14. [Epub ahead of print] PMID: 19012427
  • Chen CN, Ferrington DA, Thompson LV. Carbonic anhydrase III and four-and-a-half LIM protein 1 are preferentially oxidized with muscle unloading. J Appl Physiol. 2008 Nov;105(5):1554-61. Epub 2008 Aug 28.
  • Decanini A, Karunadharma PR, Nordgaard CL, Feng X, Olsen TW, Ferrington DA.Human retinal pigment epithelium proteome changes in early diabetes. Diabetologia. 2008 Jun;51(6):1051-61. Epub 2008 Apr 15.
  • Ferrington DA, Hussong SA, Roehrich H, Kapphahn RJ, Kavanaugh SM, Heuss ND, Gregerson DSImmunoproteasome responds to injury in the retina and brain. J Neurochem. 2008 Jul;106(1):158-69. Epub 2008 Jul 1.
  • Nordgaard CL, Karunadharma PP, Feng X, Olsen TW, Ferrington DA.Mitochondrial proteomics of the retinal pigment epithelium at progressive stages of age-related macular degeneration. Invest Ophthalmol Vis Sci. 2008 Jul;49(7):2848-55. Epub 2008 Mar 14.
  • Grimsrud PA, Xie H, Griffin TJ, Bernlohr DA.Oxidative stress and covalent modification of protein with bioactive aldehydes. J Biol Chem. 2008 Aug 8;283(32):21837
  • Feng J, Xie H, Meany DL, Thompson LV, Arriaga EA, Griffin TJ. Quantitative proteomic profiling of muscle type-dependent and age-dependent protein carbonylation in rat skeletal muscle mitochondria. J Gerontol A Biol Sci Med Sci. (2008) 63, 11, 1137-1152.
  • Grimsrud PA, Xie H, Griffin TJ, Bernlohr DA. Oxidative stress and covalent modification of protein with bioactive aldehydes. J Biol Chem. (2008) 283, 32, 21837-21841.
  • Gnanandarajah JS, Dvorak CM, Johnson CR, Murtaugh MP. Presence of free haptoglobin alpha 1S-subunit in acute porcine reproductive and respiratory syndrome virus infection. J Gen Virol. 2008 Nov;89(Pt 11):2746-53
  • Kassie, F., Anderson, L.B. , Higgins, L., Pan, Y., Matise, I., Negia, M., Upadhyaya, P., Wang, M. and Hech, S. S., (2008) Chemopreventive agents modulate the protein expression profile of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone plus benzo[a]pyrene-induced lung tumors in A/J mice. Carcinogenesis, 29:610-619
  • Jayapal KP, Philp RJ, Kok YJ, Yap MG, Sherman DH, Griffin TJ, Hu WS. Uncovering genes with divergent mRNA-protein dynamics in Streptomyces coelicolor. PLoS ONE (2008) 3, 5: e2097
  • Bandhakavi S, Xie H, O'Callaghan B, Sakurai H, Kim DH, Griffin TJ. Hsf1 activation inhibits rapamycin resistance and TOR signaling in yeast revealed by combined proteomic and genetic analysis. PLoS ONE (2008) 13, 3: e1598.
  • Xie H, Onsongo G, Popko J, de Jong EP, Cao J, Carlis JV, Griffin RJ, Rhodus NL, Griffin TJ. Proteomics analysis of cells in whole saliva from oral cancer patients via value-added three-dimensional peptide fractionation and tandem mass spectrometry. Mol Cell Proteomics (2008) 7, 3, 486-498
  • Agger SA, Lopez-Gallego F, Hoye TR, Schmidt-Dannert C. Identification of sesquiterpene synthases from Nostoc punctiforme PCC 73102 and Nostoc sp. strain PCC 7120. J Bacteriol. 2008 Sep;190(18):6084-96. Epub 2008 Jul 25.
  • Marasco EK, Schmidt-Dannert C. Identification of bacterial carotenoid cleavage dioxygenase homologues that cleave the interphenyl alpha,beta double bond of stilbene derivatives via a monooxygenase reaction. Chembiochem. 2008 Jun 16;9(9):1450-61.


Progress 01/01/07 to 12/31/07

Outputs
The primary objective of the Center for Mass Spectrometry and Proteomics (MSP) is the analysis of biologically derived samples for researchers within and outside the University of Minnesota. The core instrumentation consists of 11 mass spectrometers: a Varian Saturn 3, two Thermo-Electron LCQs and one LTQ, a Bruker Biflex III, 3 ABI QStars, two QTraps and a 4800 Maldi tof/tof). The facility also has 10 HPLCs and 4 GCs. The instrumentation was used for the structural elucidation and quantification of a wide variety of organic molecules. Protein identification and structure as it applies to looking at biological state was the greatest area of growth. During 2007 over 8000 sample sets were run by mass spectrometry and over 500 by gas chromatography. These came from 50 different University areas and included over 180 principal investigators. Departments using the instrumentation include: Biochemistry, Molecular Biology and Biophysics; Fisheries, Wildlife and Conservation Biology; Biotechnical Institute; Microbiology; Soil Water and Climate; Veterinary Medicine; Plant Biology; Plant Pathology; Horticulture; Agronomy and Plant Genetics; Bio-Based Products; Entomology; Ecology, Evolution and Behavior; USDA; USEPA; and Genetics,Cell and Development.

Impacts
The Center for Mass Spectrometry and Proteomics (MSP) has functioned as a core facility for researchers at the University of Minnesota. Numerous research projects are dependant upon use of the advanced analytical capabilities of its instrumentation. A total of 180 principal investigators from 50 University departments as well as researchers from 20 other Universities or government agencies made use of the instrumentation. Research areas included: nutrition, flavor compounds, fish pheromones, plant and animal diseases, plant growth, soil contaminants, biomarkers, differential protein expression, and cancer research to name a few. Training was provided to 75 faculty, researchers and students in five proteomic workshops given in 2007.

Publications

  • Gnanandarajah J, Dvorak CMT, Johnson CR, Murtaugh MP. (2007) Presence of alpha 1S subunit of haptoglobin in serum is associated with PRRSV infection. In preparation for J Biol Chem.
  • Roe MR, Xie H, Bandhakavi S, Griffin TJ. (2007) Proteomic mapping of 4-hydroxynonenal protein modification sites by solid-phase hydrazide chemistry and mass spectrometry. Anal Chem.79(10):3747-56.
  • Lund TC, Anderson LB, McCullar V, Higgins LA, Yun GH, Grzywacz B, Verneris MR, and Miller JS. (2007) iTRAQ is a useful method to screen for membrane-bound proteins differentially expressed in human natural killer cell types. J Proteome Res.(2):644-53
  • Huq MD, Tsai NP, Lin YP, Higgins L, Wei LN. (2007) Vitamin B6 conjugation to nuclear corepressor RIP140 and its role in gene regulation. Nat Chem Biol. 3(3):161-5.
  • Xie H, Bandhakavi S, Roe MR, Griffin TJ. (2007) Preparative Peptide isoelectric focusing as a tool for improving the identification of lysine-acetylated peptides from complex mixtures. J Proteome Res (5):2019-26.
  • Meany DL, Xie H, Thompson LV, Arriaga EA, Griffin TJ. (2007) Identification of carbonylated proteins from enriched rat skeletal muscle mitochondria using affinity chromatography stable isotope labeling and tandem mass spectrometry. Proteomics (7):1150-63.
  • Vander Haar E, Lee SI, Bandhakavi S, Griffin TJ, Kim DH. (2007) Insulin signalling to mTOR mediated by the Akt/PKB substrate PRAS40. Nat Cell Biol (3):316-23.
  • Kasthuri RS, Wroblewski M, Jilma B, Key NS, Nelsestuen GL. (2007),Potential biomarkers of an exaggerated response to endotoxemia. Biomarkers. May-Jun;12(3):287-302.
  • Kasthuri RS, McMillan KR, Flood-Urdangarin C, Harvey SB, Wilson-Grady JT, Nelsestuen GL. (2007)Correlation of a T45S variant of apolipoprotein C1 with elevated BMI in persons of American Indian and Mexican ancestries. Int J Obes Feb. 20(Lond).
  • Grimsrud, P.A., Griffen, T.J., Picklo, M.J., and Bernlohr, D.D., (2007) Aldehyde Modification of Proteins in Obesity and Insulin Resistance, Mol Cellular Proteomics, 6, 624-637


Progress 01/01/06 to 12/31/06

Outputs
The primary objective of the Center for Mass Spectrometry and Proteomics (MSP) is the analysis of biologically derived samples for reasearchers within and outside the University of Minnesota. The core instrumentation consists of 12 mass spectrometers ( a Kratos MS-25RFA, a Varian Saturn 3, two Therom-Electron LCQs and one LTQ, a Bruker Biflex III, 3 ABI Qstars, two QTraps and a 4800 Maldi tof/tof). The facility also has 10 HPLCs and 4 GCs.. During 2006 a ABI 4800 Maldi tof/tof instrument was added to the facility. The instrumentation was used for the structural elucidation and quantification of a wide variety of organic molecules. Protein identification and structure as it applies to looking at biological state was the greatest area of growth. During 2006 over 15000 samples were run by mass spectrometry and over 1300 by gas chromatography. These came from 50 different University areas and included over 130 principal investigators. Departments using the instrumentation include: Biochemistry, Molecular Biology and Biophysics, Fisheries, Wildlife and Conservation Biology,, Biotechnical Institute, Microbiology, Soil Water and Climate, Veternary Medicine, Plant Biology, Plant Pathology, Horticulture, Agronomy and Plant Genetics, Bio-Based Products, Entomology, Ecology, Evolution and Behavior, USDA, USEPA, and Genetics and Cell Development.

Impacts
The Center for Mass Spectrometry and Proteomics (MSP) has functioned as a core facility for researchers at the University of Minnesota. Numerous research projects are dependant upon use of the advanced analytical capabilities of its instrumentation. A total of 133 principal investigators from 50 University departments as well as researchers from 14 other Universities or government agencies made use of the instrumentation. Reasearch areas included: nutrition, flavor compounds, insect pheremones, plant and animal diseases, plant growth, soil contaminants, biomarkers, differential protein expression, cancer research to name a few. Training was provided to students and five proteomic workshops were given in 2006.

Publications

  • K. Okrasa, R. J. Kazlauskas,Manganese carbonic anhydrase as an enantioselective epoxidation of olefins with hydrogen peroxide,Chem. Eur. J. 2006, 11, 1587-1596.
  • Pearson, A.R., Marimanikkuppam, S., Li, X., Davidson, V.L. & Wilmot, C.M. Isotope labelling studies reveal the order of oxygen incorporation into the tryptophan tryptophylquinone cofactor of methylamine dehydrogenase. J. Am. Chem. Soc. (2006) 128: 12416-12417
  • Oetting WS, Rogers TB, Krick TP, Matas AJ, Ibrahim HN., Urinary beta2-microglobulin is associated with acute renal allograft rejection. Am J Kidney Dis. 2006 May;47(5):898-904.
  • Smith JA, Blanchette RA, Burnes TA, Jacobs JJ, Higgins L, Witthuhn BA, David AJ, Gillman JH., Proteomic comparison of needles from blister rust-resistant and susceptible Pinus strobus seedlings reveals upregulation of putative disease resistance proteins., Mol Plant Microbe Interact. 2006 Feb;19(2):150-60
  • Zykova TA, Zhu F, Lu C, Higgins L, Tatsumi Y, Abe Y, Bode AM, Dong Z., Lymphokine-activated killer T-cell-originated protein kinase phosphorylation of histone H2AX prevents arsenite-induced apoptosis in RPMI7951 melanoma cells., Clin Cancer Res. 2006 Dec 1;12(23):6884-93.
  • Russeth KP, Higgins L, Andrews MT., Identification of proteins from non-model organisms using mass spectrometry: application to a hibernating mammal., J Proteome Res. 2006 Apr;5(4):829-39.
  • Wroblewski MS, Wilson-Grady JT, Martinez MB, Kasthuri RS, McMillan KR, Flood-Urdangarin C, Nelsestuen GL., A functional polymorphism of apolipoprotein C1 detected by mass spectrometry.FEBS J. 2006 Oct;273(20):4707-15.
  • Kasthuri RS, Verneris MR, Ibrahim HN, Jilma B, Nelsestuen GL., Studying multiple protein profiles over time to assess biomarker validity. Expert Rev Proteomics. 2006 Aug;3(4):455-64
  • Zhang Y, Wroblewski M, Hertz MI, Wendt CH, Cervenka TM, Nelsestuen GL., Analysis of chronic lung transplant rejection by MALDI-TOF profiles of bronchoalveolar lavage fluid., Proteomics. 2006 Feb;6(3):1001-10.
  • Grimsrud PA, Picklo Sr MJ, Griffin TJ, Bernlohr DA., Carbonylation of adipose proteins in obesity and insulin resistance: Identification of adipocyte fatty acid-binding protein as a cellular target of 4-hydroxynonenal.,Mol Cell Proteomics. 2007 Jan 6
  • Xie H, Griffin TJ., Trade-off between high sensitivity and increased potential for false positive peptide sequence matches using a two-dimensional linear ion trap for tandem mass spectrometry-based proteomics., J Proteome Res. 2006 Apr;5(4):1003-9.


Progress 01/01/05 to 12/31/05

Outputs
The primary objective of the Center for Mass Spectrometry and Proteomics (MSP) is the analysis of biologically derived samples from researchers within and outside the University. The core instrumenttion consist of eleven mass spectrometers ( a Kratos MS-25RFA, a Varian Saturn 3, two Thermo Electron LCQs and one LTQ, a Bruker Biflex III, three ABI QStars and two QTraps). The facility also has 10 HPLCs and 3 GCs. During 2005 an ABI QTrap 4000 LC/MS and three HPLCs were added to the facility. The instrumentation was used for structural elucidation and quantification of a wide range of organic molecules. Especially noteworthy was the extensive use in the field of proteomics. During 2005, over 15,000 samples were run by mass spectrometry and over 500 by gas chromatography. These came from over 50 University departments including: Biochemistry, Molecular Biology and Biophysics, Fisheries, Wildlife and Conservation Biology, Biotechnology Institute, Microbiology, Soil, Water and Climate, Veterinary Medicine, Plant Biology, Bio-Based Products, Plant Pathology, Agronomy and Plant Genetics, Biosystems andAgricultural Engineering, Entomology, Ecology, Evolution and Behavior, USDA, USEPA, Horticulture, Genetics Cell Development and Animal Science.

Impacts
The Center for Mass Spectrometry and Proteomics (MSP) has functioned as a core facility for researchers at the University of Minnesota. Numerous research projects are dependant upon the advanced analytical capabilities of the instrumentation. A total of 168 faculty from 53 University departmentsas well as researchers from 15 different Universities and government agencies made use of the instrumentation. The range of projects goes from small molecule insect pheromones to plant hormones to proteins. Assistance is given to users in experimental design and interpretation of data. Training is provided to students on use of the instrumentation. Workshops on proteomics are given five times a year.

Publications

  • Matsuda T, Feng J, Witthuhn BA, Sekine Y, Ihle JN. Related Articles, Determination of the transphosphorylation sites of Jak2 kinase. Biochem Biophys Res Commun. 2004 Dec 10;325(2):586-94.
  • Songon An and Karin Musier-Forsyth , Cys-tRNAPro Editing by Haemophilus influenzae YbaK via a Novel Synthetase YbaKRNA Ternary Complex* J. Biol. Chem., Vol. 280, Issue 41, 34465-34472, October 14, 2005
  • Park SW, Huq MD, Hu X, Wei LN Tyrosine nitration on p65: a novel mechanism to rapidly inactivate nuclear factor-kappaB. Mol Cell Proteomics. 2005 Mar;4(3):300-9
  • Shaukat Ali Khan, Sung Wook Park, M. D. Mostaqul Huq, Li-Na Wei, Dr. Ligand-independent orphan receptor TR2 activation by phosphorylation at the DNA-binding domain. Proteomics. 2005 Nov 30;6(1):123-130
  • Pawan Gupta,. Mostaqul Huq, Shaukat Ali Khan, Nien-Pei Tsai and Li-Na We, Regulation of Co-repressive Activity of and HDAC Recruitment to RIP140 by Site-specific Phosphorylation. Molecular & Cellular Proteomics 4:1776-1784, 2005
  • Smith JA, Blanchette RA, Burnes TA, Jacobs JJ, Higgins LA, Witthuhn BA, David AJ, and Gillman JH, Proteomic Comparison of Needles from Blister RustResistant and Susceptible Pinus strobus Seedlings Reveals Upregulation of Putative Disease Resistance Proteins. Molecular Plant-Microbe Interactions accepted on 10 October 2005
  • Shaukat Ali Khan, Sung Wook Park, Mostaqul Huq, Li-Na Wei, Protein kinase C-mediated phosphorylation of orphan nuclear receptor TR2: Effects on receptor stability and activity. PROTEOMICSVolume 5, Issue 15 , Pages 3885 - 3894, 2005
  • Mostaqul Huq and Li-Na Wei , Post-translational Modification of Nuclear Co-repressor Receptor-interacting Protein 140 by Acetylation, Molecular & Cellular Proteomics 4:975-983, 2005.
  • M. D. Mostaqul Huq*, Shaukat Ali Khan*, Sung Wook Park and Li-NaWei Mapping of phosphorylation sites of nuclear corepressor receptor interacting protein 140 by liquid chromatography-tandem mass spectroscopy. Proteomics 2005, 5, 2157 2166
  • Sung Wook Park, M. D.Mostaqul Huq, Xinli Hu and Li-Na Wei Tyrosine Nitration on p65:A Novel Mechanism to Rapidly Inactivate Nuclear Factor- B* Molecular & Cellular Proteomics 4:300-309, 2005.
  • Streitz, J. M.; Madden, M. T.; Marimanikkuppam, S. S.; Krick, T. P.; Salo, W. L.; Aufderheide, A. C. Analysis of protein expression patterns in Barrett's esophagus using MALDI mass spectrometry, in search of malignancy biomarkers Diseases of the Esophagus, 18, 3, p170-176, 7p (2005).


Progress 01/01/04 to 12/31/04

Outputs
The primary objective of the Mass Spectrometry Consortium for the Life Sciences (MSCLS) is the analysis of biologically derived samples from researchers within and outside the University. The core instruments consist of (a Kratos MS-25RFA, a Saturn 3, two ThermoElectrom LCQs, a Bruker Biflex III, three ABI QStars, an ABI QTrap and a ThermoElectron LTQ) mass spectrometers. Besides these 10 mass spectrometers, the facility has 7 HPLCs and 3 GCs. In year 2003 the LTQ mass spectrometer and 2 Agilent HPLCs were added to the facility. The instrumentation was used for structural elucidation and quantification of a wide range of organic moleculed as well as extensive use in the field of proteomics. During 2003, a total of 16277 samples were run by mass spectrometry and 1762 by gas chromatography. Samples were analyzed for the following Departments: Biochemistry, Biophysics and Molecular Biology, Fisheries and Wildlife, Biotechnology Institute, Microbiology, Soil Science, Veternary Medicine,Plant Biology, Agricultural Engineering,Plant Pathology, Agronomy and Plant Genetics, Food Science and Nutrition, Horticulture, USDA, USEPA, Genetics and Cell Development, Entomology, Ecology, Evolution and Behavior, Bio-Based Products and Animal Science.

Impacts
The MCLS has functioned as a core facility for researchers at the University of Minnesota. Numerious research projects are dependant upon the advanced analytical capabilities. Faculty from 42 University departments as well as researchers from 14 different Universities or government agencies have made use of the instrumentation. The range of projects goes from small molecule insect pheromones to plant hormones to large molecule protein identification. Assistance is given to users of the facility for experimental design and interpretation of data. Training is provided to students on use of the instrumentation.

Publications

  • Buffo, R.A., G. Zehentbauer and G.A. Reineccius, Determinination of Linear Response in the Detection of Aroma Compounds by Atmospheric Pressure Ionization * Mass Spectrometry (API*MS), J. Agric. Food Chem., (2004)
  • Buffo, R.A., J.A. Rapp, T. Krick, G.A. Reineccius, Persistance of Aroma Compounds in Human Breath after Consuming an Aqueous Model Mixture, Food Chem. 89:103-108 (2004)
  • H. Wang, G.M. Vath, K.J. Gleason, P.E. Hanna and C.R. Wagner, Probing the Mechanism of Hampster Arylamine N-Acetyltransferase 2 Acetylation by Active Site Modification, Site Directed Mutagenesis, and Pre-Steady State Kinetic Studies, Biochemistry, 43,8234-8246 (2004)
  • Z. Guo, C.R. Wagner and P.E. Hanna, Mass Spectrometric Investigation of the Mechanism of Inactivation of hampster Arylamine N-Acetyltransferase 1 by N-Hydroxy-2-Acetylaminoflourine, Chem. Res. Toxicol, 17,275-286 (2004)
  • A.R. Pearson, T. De la Mora-Rey, M.E. Graichen, Y. Wang, L.H. Jones, S. Marimanikkuppam, S.A. Agger, P.A. Grimsrud, V.L. Davidson and C.M. Wilmot, Further Insights into Quinone Cofactor Biogenesis: Probing the Role of mauG in methylamine dehydrogenase TTQ formation, Biochemistry 453, 5494-5502 (2004)


Progress 01/01/03 to 12/31/03

Outputs
The primary objective of the Mass Spectrometry Consortium for the Life Sciences (MSCLS) is the analysis of biologically derived samples using mass spectrometry for researchers within and outside the University. The core instrumentation consists of (a Kratos MS-25 , a Varian Saturn 3, two Thermo Finnigan LCQs, a Bruker Biflex III, three ABI QStars and An ABI QTrap) mass spectrometers. Besides these 9 mass spectrometer s there also are 4 HPLCs and 3 GCs. In year 2003 the 3rd QStar with Maldi and the QTrap mass spectrometers were added to the facility. The instrumentation was used for structure elucidation, identification and quantificationof a wide range of organic molecules as well as protein identification along their post translational modifications. During 2003, 10,387 samples were run by mass spectrometry and 805 by gas chromatography. Samples were analyzed for the following departments: Biochemistry, Biophysics and Molecular Biology (4547), Fisheries and Wildlife (707), Biotechnology Institute (543), Microbiology (460), Soil Science (409), Veternary Medicine (378), Plant Biology (174), Agricultural Engineering (150), Plant Pathology (128), Agronomy (91), Food Science and Nutrition (69), Horticulture (58), USDA (52), Genetics Cell Development (46), Agronomy and Plant Genetics (40), Entomology (20), Ecology,Evolution and Behavior (19), and Wood and Paper Science (14).

Impacts
The MCLS has functioned as a core facility for researchers at the University of Minnesota. Numerious research projects are dependant upon the advanced analytical capabilities. Faculty from 32 University departments as well as researchers from 14 different Universities or government agencies have made use of the instrumentation. The range of projects goes from small molecule insect pheromones to plant hormones to large molecule protein identification. Assistance is given to users of the facility for experimantal design and interpretation of data. Training is provided to students on use of the instrumentation.

Publications

  • Pearson, A.R., Jones, L.H.,Higgins,L.,Ashcroft. A.E., Wilmot,C.M.,and Davidson,V.L. (2003) Biochemistry 42,3224-30
  • Kapphahn,R.J., Ethen, C.M., Peters,E.A., Higgins, L., and Ferrington, D.A. (2003) Biochemistry
  • Hernandez, V.P., Higgins, L., and Fallon, A.M. (2003) Dev Comp Immunol 27, 11-20


Progress 01/01/02 to 12/31/02

Outputs
The primary objective of the Mass Spectrometry Consortium for the Life Sciences (MSCLS) is the analysis of biologically derived samples using mass spectrometry and gas chromatography for researchers within and outside the University. The core instrumentation consists of (a Kratos MS-25, a Varian Saturn 3, two Thermo Finnigan LCQs, a Bruker Biflex III, a QStar Pulsar and a Qstar) mass spectrometers and a HP 5890 GC. There are also three high pressure liquid chromatographs. The second QStar quadrupole time of flight mass spectrometer was added to the facility in 2002. This instrumentation was used for structure elucidation, identification and quantification of a wide variety of organic molecules as well as protein identification along with their post translational modifications. During 2002, 7031 samples were analyzed by mass spectrometry and 1453 samples by gas chromatography. Samples were analyzed by mass spectrometry for the following departments: Biochemistry, Molecular Biology and Biophysics (2454), Fisheries and Wildlife (640), Food Science and Nutrition (265), Agronomy (249), Veterinary Medicine (239), Microbiology (210), Biosystems and Agricultural Engineering (156), Biotechnology Institute (141), Wood and Paper Science (64), Plant Pathology (63), Plant Biology (58), Horticulture (41), Entomology (32), Soil Science (23), and Ecology (12).

Impacts
The MSCLS has functioned as a core facility for researchers at the University of Minnesota. Numerous research projects are dependent upon the advanced analytical capabilities with faculty from 34 different Departments making use of the instrumentation. The range of projects goes from small molecule insect pheromones and plant hormones to large molecule protein identification. Assistance is given to users for experimental design and the interpretation of the data.

Publications

  • Anderson LB, Maderia M, Ouellette AJ, Putnam-Evans C, Higgins L, Krick T, MacCoss MJ, Lim H, Yates JR 3rd, Barry BA Posttranslational modifications in the CP43 subunit of photosystem II.Proc Natl Acad Sci U S A. 2002 Nov 12;99(23):14676-81.
  • Bennaars-Eiden A, Higgins L, Hertzel AV, Kapphahn RJ, Ferrington DA, Bernlohr DA.Covalent Modification of Epithelial Fatty Acid-binding Protein by 4-Hydroxynonenal in Vitro and in Vivo. Evidence for a Role in Antioxidant Biology. J Biol Chem. 2002 Dec 27;277(52):50693-702
  • Rodrigues-Fo E, Mirocha CJ, Xie W, Krick TP, Martinelli JA . Electron ionization mass spectral fragmentation of deoxynivalenol and related tricothecenes. Rapid Commun Mass Spectrom. 2002;16(19):1827-35.
  • Hernandez VP, Higgins L, and Fallon AM. Characterization and cDNA cloning of an immune-induced lysozyme from cultured Aedes albopictus mosquito cells. Developmental and Comparative Immunology,. 2003 Jan;27(1):11-20.
  • Schwientek M, Higgins L, Fallon A. Cultured Aedes albopictus mosquito cells accumulate elongation factor 1-alpha (EF-1alpha) during serum starvation. Insect Biochemistry and Molecular Biology, 2002 32(9): 1055-1063.


Progress 01/01/01 to 12/31/01

Outputs
The primary objective of the Mass Spectrometry Consortium for the Life Sciences (MSCLS) is the analysis of biologically derived samples using mass spectrometry and gas chromatography for research projects within and outside the University. The analytical instrumentation consists of two Kratos MS-25's, a Varian Saturn 3, two Finnigan LCQ's, a Bruker Biflex III and a HP 5890 GC. In 2001, a new ABI Q-star Pulsar was acquired with a second one to be delivered in 2002. The primary advancement in mass spectrometry has been in the field of proteomics, which has allowed for the identification of proteins along with their post-translational modifications. Structure elucidation, identification and quantification of a wide variety of organic molecules were also provided to users. During 2001, 5440 samples were analyzed by mass spectrometry and 1477 samples by gas chromatography. The principle users of the GC were: BPTI, Biochemistry, Plant Pathology, Wood and Paper Science, Agricultural Engineering and Animal Science. Samples were analyzed by mass spectrometry for the following departments: Biochemistry(1829), Food Science(335), Plant Pathology(189), Fisheries and Wildlife(135), Veterinary Diagnostics(129), Veterinary Pathobiology(101), Agronomy(97), Microbiology(97), Horticulture(93), Entomology(67), USDA(19), Plant Biology(17), Wood and Paper Science(15), Soil Science (11), and Agricultural Engineering(4).

Impacts
The MSCLS has functioned as a core facility for researchers at the University. Numerous research projects are dependent upon the advanced analytical capabilities with faculty from 31 different Departments using the instrumentation. The range of project goes from small molecule insect pheromones and plant hormones to large molecule whole protein identification. Assistance is given to users for experimental design and interpretation of data.

Publications

  • S. Kim, J. S. Patzlaff, T. Krick, I. Ayala, R. Sachs, and B. A. Barry.(2000) "Isotope-based discrimination between infrared modes of plastoquinone and tyrosine radicals in photosystem II." Journal of Physical Chemistry B 104, 9720-9727.
  • M. R. Razeghifard, S. Kim, J. Patzlaff, R. S. Hutchison, T. Krick, I. Ayala, J. J. Steenhuis, S. Boesch, R. A. Wheeler, and B. A. Barry. (1999) "The in vitro, in vivo, and calculated vibrational spectrum of plastoquinone and plastosemiquinone anion radicals." Journal of Physical Chemistry B 103, 9790-9800.
  • Michael B. Martinez, Michael Flickinger, LeeAnn Higgins, Thomas Krick and Gary L. Nelsestuen (2001) "Reduced outer membrane permeability of Escherichia coli O157:H7: Suggested role of modified outer membrane porins and theoretical function in resistance to antimicrobial agents" Biochemistry, 40, 11965-11974.


Progress 01/01/00 to 12/31/00

Outputs
Objectives: The overall objective is to operate the seven mass spectrometers - Kratos MS-25, Kratos MS-25-RFA, HP 5790, Varian Saturn 3, two Finnigan LCQs and Bruker Biflex III - as well as the HP 5890 GC for the analysis of samples submitted by research staff within and outside the University. This analytical instrumentation together with the NMR allows users to identify, quantify or characterize chemical compounds for their research projects. Methodology will be developed to expand the scope and usefulness of the instrumentation to fit the research needs. New instrumentation and computer improvements will continue to be added. A second Finnnigan LCQ mass spectrometer was added to the facility. Near the end of the year the BioIon mass spectrometer was decommissioned. A Michron capillary HPLC was added to the new LCQ. An NSF grant was awarded for new data acquisition software and hardware for the KRATOS mass spectrometers. During 2000 4815 samples were analyzed by mass spectrometry - MS - and 1683 by gas chromatography - GC -. The purpose of these analyses was for structural elucidation, identification, and quantification of organic molecules and was provided as a service to reseachers on the St. Paul Campus. Examples of analyses include: peptide structure, identification of proteins, fungal toxins, drugs, agricultural chemials, determination of microbial pathways, flavor components, insect pheromones, naturally occurring biologically active compounds, carbohydrates, lipids and environmental contaminants. The principal users of the GC were: Bioprocess Technical Institute, Agronomy, Biochemistry, Fisheries and Wildlife, Plant Biology and Soil Science. Samples were analyzed by mass spectrometry for the following departments: Biochemistry 1252, Food Science 1197, Chemistry 489, Fisheries and Wildlife 385, Plant Biology 242, Medicinal Chemistry 159, Neuroscience 130, Plant Bioloy 89, Agronomy 62, Oral Science 60, Entomology 50, Horticulture 48, Veterinary Medcine 36, Microbiology 34, Wood and Paper Science 29, Agricultural Engineering 17 and Soil Science 9.

Impacts
Samples are submitted directly to the Mass Spectrometry Consortium for the Life Sciences in room 43 Gortner Lab. The analyses are carried out with the results reported to the individuals orally and accompanied with pertinent print-outs, spectra or chromatograms. Assistance is given for further experiment design or interpretation of the spectra data.

Publications

  • Data obtained from the lab were included in many publications and several theses in 2000.


Progress 01/01/99 to 12/31/99

Outputs
Objectives: The overall objective is to operate the seven mass spectrometers - Kratos MS-25, Kratos MS-25-RFA, BioIon 20R, HP 5790, Varian Saturn 3, Finnigan LCQ and Bruker Biflex III - as well as the HP 5890 GC for the analysis of samples submitted by research staff from within and outside the University. This analytical instrumentation together with the NMR allows users to identify, quantify or characterize chemical compounds for their research projects. Methodology will be developed to expand the scope and usefulness of the instrumentation to fit the research needs. New instrumentation and computer improvements will continue to be added. In 1998, a major expansion of the lab took place. Room 43 Gortner was added to the facility more than doubling the space. Three other mas spectrometers were added to the facility. Through an NSF grant the LC-MS Finnigan LCQ and the Bruker Biflex III maldi-Tof MS were added to the facility. This is especially important for research in the areas of proteomics. Also a Varian ion trap GC-MS was acquired which will add routine Cl GC-MS. During 1999, 2695 samples were analyzed by mass spectrometry - MS - and 2325 by gas chromatography - GC -. The purpose of these analyses was for structural elucidation, identification, and quantification of organic molecules and was provided as a service to researchers on the St. Paul Campus. Examples of analyses include: peptide structure, identification of proetins, fungal toxins, drugs, agricultural chemicals, determination of microbial pathways, flavor components, insect pheromones, naturally occurring biologically active compounds, carbohydrates, lipids and environmental contaminants. The principal users of the GC were: Bioprocess Technical Institute, Agronomy, Biochemistry, Fisheries and Wildlife, Plant Biology and Soil Science. Samples were analyzed by mass spectrometry for the following departments: Biochemistry, 731, Chemistry, 461, Plant Pathology, 328, Chemical Engineering, 179, Medicinal Chemistry, 158, Food Science, 137, BPTI, 116, Plant Biology, 86, USDA, 58, Entomology, 36, Forest Products, 35, Vet Medicine, 25, Agronomy, 21, and Soil Science, 13.

Impacts
Samples are submitted directly to the Mass Spectrometry Consortium for the Life Sciences in room 43 Gortner lab. The analyses are carried out with the results reported to the individuals orally and accompanied with pertinent print-outs, spectra or chromatograms. Assistance is given for further experiment design or interpretation of the spectra data.

Publications

  • Data obtained from the lab were included in many publications and several these in 1999.


Progress 01/01/98 to 12/31/98

Outputs
OBJECTIVES: The overall objective is to operate the KRATOS MS-25, KRATOS MS-25-RFA, BioIon 20R and Bruker maldi-TOF mass spectrometers as well as the HP 5890 GC for the analysis of samples submitted by research staff from within and outside the University. This analytical instrumentation together with the NMR allows users to identify, quantify, or characterize chemical compounds for their research projects. Methodology will be developed to expand the scope and usefulness of the instrumentation to fit the research needs. New instrumentation and computer improvements will continue to be added. APPROACH: Samples are submitted directly to the GC-MS lab in 76 Gortner lab. The analyses were carried out with the results reported to the individuals orally and accompanied with pertinent print-outs, spectra or chromatograms. Assistance is given for further experiment design or interpretation of the spectral data. PROGRESS: 1998-01 to 1998-12 A new Bruker maldi-TOF mass spectrometer has been added to the facility - funding from NSF. During 1998, over 1100 samples were analyzed by mass spectrometry - MS and 2400 by gas chromatography - GC. The purpose of these analyses was for structural elucidation, identification, and quantification of organic moelcules and was provided as a service to researchers on the St. Paul Campus. Examples of analyses include: peptide structure, identification of proteins, fungal toxins, drugs, agricultural chemicals, determination of microbial pathways, flavor components, pheromones, naturally occurring biologically active compounds, carbohydrates, lipids and environmental contaminants. The principal users of the GC were: Bioprocess Technical Institute, Agricultural Engineering, Food Science, Fisheries and Wildlife, Plant Biology and Ecology. Samples were analyzed by mass spectrometry for the following departments: Biochemistry - 306, BPTI - 204, Microchemical Facility - 125, Chemistry - 63, Soil Science - 53, Food Science - 41, Agricultural Engineering - 36, Plant Pathology - 23, Plant Biology - 18, USDA - 15, Fisheries and Wildlife - 10, and Entomology - 3.

Impacts
(N/A)

Publications

  • Data obtained from the lab were included in many publications and several theses in 1998.


Progress 01/01/97 to 12/31/97

Outputs
During 1997, over 1200 samples were analyzed by mass spectrometry (MS) and 3700 by gas chromatography (GC). The purpose of these analyses was for structural elucidation, identification and quantification of organic molecules and was provided as a service to researchers on the St. Paul Campus. Examples of analyses include: the identification of fungal toxins, drugs, agricultural chemicals, determination of microbial pathways, flavor components, plant hormones, pheromones, DNA adducts, naturally occurring biologically active compounds, environmental contaminants, proteins, peptides, carbohydrates and lipids. The principal users of the gas chromatograph were: Bioprocess Technical Institute, Agricultural Engineering, Entomology, Forestry, Soil Science and Plant Biology. Samples were analyzed by mass spectrometry for the following departments: Bioprocess Technology Institute (281), Medicinal Chemistry (241), Biochemistry (216), Food Science (141), Genetics (82), Agricultural Engineering (58), Fisheries and Wildlife (19), Forestry (13), Entomology (12), USDA (10), Plant Pathology (6), Plant Biology (5), North Dakota (3) and Agronomy (2).

Impacts
(N/A)

Publications

  • Data obtained from this lab were included in many publications as well as several theses in 1997.


Progress 01/01/96 to 12/30/96

Outputs
During 1996, over 1500 samples were analyzed by mass spectrometry (MS), 3200 by gas chromatography (GC) and 20 by FT-IR. The purpose of these analyses was for structural elucidation, identification and quantification of organic molecules and was provided as a service to researchers on the St. Paul Campus. Examples of analyses include: the identification of fungal toxins, drugs, agricultural chemicals, determination of microbial pathways, flavor components, plant hormones, pheromones, DNA adducts, naturally occurring biologically active compounds, environmental contaminants, proteins, peptides, carbohydrates and lipids. The principal users of the gas chromatograph were: Bioprocess Technology Institute, Aricultural Engineering, Biochemistry, Forestry, Soil Science and Plant Biology. Samples were analyzed by mass spectrometry for the following departments: Biochemistry (632), Medicinal Chemistry (145), Soil Science (130), Food Science (112), Bioprocess Technology Institute (73), Harvard University (63), Genetics (59), Radiology (45), Fisheries and Wildlife (42), USDA (27), Plant Biology (17), VA Hospital (13), Plant Pathology (12), Pharmacology (14), Agricultural Engineering (19), Horticulture (9), Geology (5), and Ecology (1).

Impacts
(N/A)

Publications

  • Data obtained from this lab were included in many publications as well as several theses.


Progress 01/01/95 to 12/30/95

Outputs
During 1995, over 2450 samples were analyzed by mass spectrometry (MS), 3300 by gas chromatography (GC) and 50 by FT-IR. The purpose of these analyses was for structural elucidation, identification and quantification of organic molecules and was provided as a service to researchers on the St. Paul Campus. Examples of analyses include: the identification of fungal toxins, drugs, agricultural chemicals, determination of microbial pathways, flavor components, plant hormones, DNA adducts, naturally occurring biologically active compounds, environmental contaminants, proteins, peptides, carbohydrates and lipids. The principal users of the gas chromatograph were the Bioprocess Technology Institute, Agricultural Engineering, Genetics/Cell Biology, Agronomy and Biochemistry. Samples were analyzed by mass spectrometry for the following department: Epidemiology (615) Biochemistry (435), Genetics/Cell Biology (340), Medicinal Chemistry (321), Food Science (155), Agronomy (61), USDA (58) Plant Biology (48), Bioprocess Technology Institute (38), VA Hospital (20), Plant Pathology (17), Pharmacology (12), Soil Science (11), Forest Products (7), Environmental Health (3), and Horticulture (4).

Impacts
(N/A)

Publications


    Progress 01/01/94 to 12/30/94

    Outputs
    During 1994, over 2000 samples were analyzed by mass spectrometry (MS), 3600 by gas chromatography (GC) and 40 by FT-IR. The purpose of these analyses was for structural elucidation,identification and quantification of organic molecules and was provided as a service to researchers on the St Paul Campus. Examples of analyses include: the identification of pheromones, fungal toxins,agricultural chemicals, determination of microbial pathways, flavor components, plant hormones, naturally occurring biologically active compounds, environmental contaminants, proteins, peptides and carbohydrates. The principal users of the GC were the Bioprocess Technical Institute, Agricultural Engineering and Genetics/Cell Biology, Microbiology and Biochemistry. Samples were analyzed by mass spectrometry for the following departments: Biochemistry (312), Genetics/Cell Biology (271), Medicinal Chemistry (257), Epidemiology (210), Bioprocess Technical Institute (205), Plant Biology (121), VA Hospital (113), Food Science (76), Plant Pathology (65), Soil Science (57), Fisheries and Wildlife (36), USDA (20), Horticulture (10), Forest Products (9), Gray Freshwater Biology (8), Microbiology (8), and Agricultural Engineering (3).

    Impacts
    (N/A)

    Publications


      Progress 01/01/93 to 12/30/93

      Outputs
      The work pertains to enzymatic digestion of forages which contain cellulose, hemiceluloses, and proteins. Enzymes are key in utilization of forages, on a very large scale in animal nutrition, and on a somewhat smaller scale in evaluating forages. The enzymes are cellulases, hemicellulases, and proteases. In addition to the ways they are used and produced now, in silage in cattle rumen, and in the soil (by microorganisms), these enzymes are of increasing interest as means for pretreatment of plant and forage materials to make forage carbohydrates and proteins more accessible. Cellulases and proteases are of sharply increasing use also in human food processing industries, in paper and even clothing industries. Our research pertains to two sectors of enzymes R and D:(i) How they can be best deployed, depending on the nature of the forage or biomass. (ii) Separations technology for them, because their main cost is in separations and purification after microorganisms have produced them as crudes. A number of fungi produce cellulases and hemicellulases. Feasibility of utilization of new forages, differing varieties of older forages and feeds such as alfalfa, sharply depend on enzyme catalysis of their degradation. The Current research aims at precipitative means for isolating such enzymes, to yield very active cellulases and companion enzymes such as xylanases. Precipitation of proteins out of alfalfa in a scaleable way was worked with. In the earlier work, synthetic agents were used.

      Impacts
      (N/A)

      Publications


        Progress 01/01/92 to 12/30/92

        Outputs
        Instrumentation available at this facility include mass spectrometers, an FT-IR,gas chromatographs and an NMR. Researchers from the St. Paul Campus are the primary users of this instrumentation. A second Kratos MS-25 mass spectrometer has been added to the facility this year. The FT-IR has been used to obtain spectra of approximately 200 samples with the majority coming from Biochemistry and Food Science. Well over a thousand samples have been run on the HP-5890 gas chromatograph principally from Genetics/Cell Biology, Food Science, Biochemistry, Ecology, BPTI and Microbiology. A total of 1135 samples were analyzed by mass spectrometry.

        Impacts
        (N/A)

        Publications


          Progress 01/01/91 to 12/30/91

          Outputs
          A 170SX Nicolet FT Infrared Spectrometer has been added to the facility this year. IR spectra of samples from Entomology, Biochemistry, BPTI and Food Science have been obtained from it. Well over a thousand samples have been run on the HP-5890 gas chromatograph with the majority coming from Genetics/Cell Biology, Food Science, Horticulture, Biochemistry, Gray FWBI, Plant Biology, BPTI and Entomology. A total of 946 samples were analyzed by mass spectrometry.

          Impacts
          (N/A)

          Publications


            Progress 01/01/90 to 12/30/90

            Outputs
            Improvements made to this facility include the interfacing of a Macintosh II computer to the Kratos mass spectrometer. This allows for high quality graphic output as well as the transferring of both text and graphical data into standard word processing documents. Fast atom bombardment ionization has become a routine technique. Over a thousand samples have been run on the HP gas chromatograph with Genetics/Cell Biology, Biochemistry and Entomology being the main users. A total of 1511 samples were analyzed by mass spectrometry.

            Impacts
            (N/A)

            Publications


              Progress 01/01/89 to 12/30/89

              Outputs
              Improvements made to the facility include the addition of a 73 mbyte disk drive and a second terminal to the KRATOS MS-25 GC/MS and the addition of an autosampler to the HP 5890 gas chromatograph. Over 2000 samples were run on the gas chromatograph with the majority coming from the Genetics/Cell Biology, Entomology, Plant Pathology and Biochemistry Departments. A total of 1638 samples were submitted for mass spectral analysis by various departments and institutions.

              Impacts
              (N/A)

              Publications


                Progress 01/01/88 to 12/30/88

                Outputs
                Improvements made to the facility this last year include both the addition of a heated inlet system to the LKB - 9000 GC/MS and the acquisition of a state-of-the-art HP 5890 gas chromatograph equipped with flame ionization, electron capture and thermal conductivity detectors. A total of 3710 samples were submitted for mass spectral analysis by the various departments and institutions.

                Impacts
                (N/A)

                Publications


                  Progress 01/01/87 to 12/30/87

                  Outputs
                  Improvements made to the facility this past year include: routine analyses by Fast Atom Bombardment (FAB) mass spectrometry, exact mass measurements with GC/MS and installation of a magabore column interface in the LKB-9000 GC/MN. A total of 1044 samples were submitted by various departments and institutions.

                  Impacts
                  (N/A)

                  Publications


                    Progress 01/01/85 to 12/30/85

                    Outputs
                    In the past year a total of 1535 samples were submitted and analyzed. This doesnot include the 2260 isotope ratio samples analyzed by Pharmacology on the KRATOS M.S. A new computer system was added to the LKM M.S.

                    Impacts
                    (N/A)

                    Publications


                      Progress 01/01/84 to 12/30/84

                      Outputs
                      The LKB 9000 GC-MS was moved to room 76 Gortner, thus placing it together with the newly installed KRATOS MS-25 double focussing GC-MS. A total of 1969 samples (including the 698 run by Pharmacology on the KRATOS) were run from Dec. 1983 through Dec. 1984.

                      Impacts
                      (N/A)

                      Publications


                        Progress 01/01/83 to 12/30/83

                        Outputs
                        A total of 1401 samples were submitted for analysis and were analyzed within thepast year. The numbers submitted by the various departments and institutions were as follows. A new Kratos MS-25 double focusing magnetic gas chromatograph mass spectrometer has been purchased and installation was completed in December, 1983. This new mass spectrometer will greatly enhance the analytical capabilities of the St. Paul campus departments.

                        Impacts
                        (N/A)

                        Publications


                          Progress 01/01/82 to 12/30/82

                          Outputs
                          A total of 1,481 samples were submitted for analysis and were analyzed within the past year. The numbers submitted by the various departments and institutions were as follows: Entomology, Biochemistry, V.A. Hospital, Food Science, Gray Freshwater Biological Inst., Pathology, Hormel Institute, Horticulture, Pediatrics, Plant Pathology, U.S. Davis (Cet), Mechanical Engineering, Soil Science, N. Central Forest Experiment Station, Vetinary Pathobiology, Lab Medicine, Microbiology, Environmental Health, U. of Illinois, Chicago Circle, Geology, Genetics and Cell Biology, Sci-Med Life, U. of Illinois (Vet), Forestry, U. of Manitoba.

                          Impacts
                          (N/A)

                          Publications


                            Progress 01/01/79 to 12/30/79

                            Outputs
                            A total of 2538 samples were submitted for analysis and were analyzed within thepast year.

                            Impacts
                            (N/A)

                            Publications


                              Progress 01/01/75 to 12/30/75

                              Outputs
                              A total of 2113 samples were submitted for analysis and were analyzed. This is an increase of 154 over the previous year. A PDP-8 computer was successfully interfaced to the mass spectrometer.

                              Impacts
                              (N/A)

                              Publications


                                Progress 01/01/74 to 12/30/74

                                Outputs
                                A total of 1959 samples were submitted for analysis and were analyzed. This is an increase of 780 over the previous year.

                                Impacts
                                (N/A)

                                Publications


                                  Progress 01/01/73 to 12/30/73

                                  Outputs
                                  A total of 1179 samples were submitted for analysis and were analyzed.

                                  Impacts
                                  (N/A)

                                  Publications


                                    Progress 01/01/72 to 12/30/72

                                    Outputs
                                    The LKB-9000 gas chromatograph-mass spectrometer was installed by the LKB Company during January 1972. An operator was hired and trained. Samples were accepted for analysis commencing the end of February 1972. Through November 1972 a total of 686 samples were received and mass spectral data obtained. These are broken down by requesting departments below. The operator gives help in interpretation of the spectral data and in the general indoctrination of potential users into the capabilities, and limitations, of the instruments. Groups of students from this and other departments are at infrequent intervals instructed in the theory and practice of mass spectrometry. The instrument has proven to be a rather delicate machine and rather considerable amounts of time are required to keep it functioning at a satisfactory level.

                                    Impacts
                                    (N/A)

                                    Publications