Translational Metabolomics Shared Resource (TraMSR)

The Translational Metabolomics Shared Resource (TraMSR) uses advanced analytical techniques to uncover molecular changes that drive cancer development and progression. These insights enable new strategies for cancer prevention, early detection, and offer personalized treatment plans for patients.

Scheduling, Location, and Hours of Operation

Mass Spectrometry: Translational and Biomedical Research Center, 2nd floor
Redox and Bioenergetics: MACC Fund Research Center, 2nd floor
Preclinical and Clinical Imaging: Medical Imaging Research Center, 1st floor
Monday–Friday from 8 a.m.-5 p.m.
Submit a TraMSR iLab request

Services and Technologies

The TraMSR advances cancer research by identifying, quantifying, and imaging molecular metabolic profiles of cancer cells and tumors. Combining expertise in mass spectrometry and bioenergetics, preclinical imaging, and clinical trial response assessment using artificial intelligence (AI), TraMSR supports both preclinical research and patient monitoring in clinical trials.

View the FY25 TraMSR price sheet (PDF)

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Mass Spectrometry

View Mass Spectrometry Instrumentation and Examples. (PDF)

The Mass Spectrometry core offers advanced multi-omics services for the identification and quantification of biomolecules, including proteins, lipids, metabolites, small molecules, and complex carbohydrates. Utilizing cutting-edge technologies such as Liquid Chromatography-Mass Spectrometry (LC-MS/MS) and Imaging Mass Spectrometry (IMS), we provide comprehensive analytical capabilities to support a wide range of research needs, including the following areas:

Proteomics
Proteomics services provide identification, characterization, and quantification of proteins from complex biological samples and purified materials. We offer both in-solution and in-gel protein identification, utilizing trypsin or other proteolytic enzymes for digestion before mass spectrometry analysis. We support protein analysis from various enrichment techniques, including pull-down assays and co-immunoprecipitation (co-IP) for interaction studies, as well as proximity labeling techniques such as TurboID and APEX for interaction-based proteomics. For quantitative proteomics, we offer TMT-labeling, SILAC, and other advanced workflows to compare protein expression levels across multiple conditions. Additionally, we provide comprehensive post-translational modification (PTM) analysis, including phosphoproteomics, glycoproteomics, and S-S bond analysis to study disulfide bond formation and protein structural integrity.

Lipidomics
Lipidomics services enable the identification, characterization, and quantification of lipid molecules from various biological samples, including biofluids, tissues, and cell cultures. We analyze a wide range of lipid classes, including glycerolipids, sphingolipids, cholesterol, and fatty acids, using high-resolution mass spectrometry. Lipid extraction is performed using optimized protocols, followed by LC-MS/MS analysis. Lipid identification and annotation are conducted using advanced software tools such as LipidSearch and Compound Discoverer, ensuring high-confidence data interpretation. Additionally, we offer both targeted and untargeted lipidomics approaches, allowing for comprehensive profiling of lipid species and enabling studies on lipid metabolism, biomarker discovery, and disease mechanisms.

Metabolomics/small molecule analysis
Metabolomics and small molecule analysis services provide comprehensive identification, characterization, and quantification of metabolites and other small molecules from various biological samples, including biofluids, tissues, and cell cultures. We offer both targeted and untargeted metabolomics approaches using advanced mass spectrometry techniques. Targeted metabolomics focuses on the precise quantification of known metabolites using reference standards, ensuring high accuracy and reproducibility. Untargeted metabolomics enables the discovery of novel or unexpected metabolic changes by profiling a wide range of metabolites without prior knowledge. Data analysis is performed using Compound Discoverer, m/zCloud, and ChemSpider software, providing accurate compound identification and metabolic pathway insights.

Glycomics
Glycomics services provide identification, characterization, and quantification of glycans from various biological sources, including glycoproteins, glycolipids, free oligosaccharides, lipid-linked oligosaccharides, and sugar nucleotides. Using advanced mass spectrometry techniques, we analyze both N-linked and O-linked glycans, offering insights into their composition, structure, and modifications. Glycans are released through enzymatic or chemical methods, followed by purification for MS analysis. Data interpretation is conducted through both manual curation and software-based analysis to ensure precise glycan identification and structural annotation. Additionally, we offer glycoproteomics services to investigate site-specific glycosylation, providing a comprehensive understanding of glycan function in health and disease.

Mass Spectrometry Common Services:

LC-MS/MS

  • Proteomics
    • Protein ID
    • Quantitative proteomics
    • Protein post-translational modification (PTM) analysis (glycosylation, phosphorylation, etc)
  • Lipidomics
  • Metabolomics/Small Molecule
  • Glycomics
    • N-glycan
    • O-Glycan
    • Glycolipid

IMS

  • Lipidomics (glycerolipid, sphingolipid, etc.)
  • Small Molecule
  • Glycomics (N-glycan, Glycolipid)

MALDI

  • Molecular weight analysis

 

Redox and Bioenergetics

The Redox and Bioenergetics core provides state-of-the-art instrumentation, cutting-edge techniques, and sophisticated expertise dedicated to investigating cancer cell metabolism and redox signaling, and to design custom probes for reactive oxygen species (ROS) for MCWCC members.

View Redox and Bioenergetics Instrumentation and Scientific Examples. (PDF)

Major services support analyses of:

  • Cell bioenergetic function
    • Mitochondrial stress assay
    • Glycolytic stress assay
    • Fatty acid oxidation
    • ATP production rates
    • T-cell metabolic profiling
    • Bioenergetic substrate dependency
    • Bioenergetic profile dependency
    • Real-time monitoring of the effect of treatment on mitochondrial respiration
    • Analyses of mitochondrial complex I-IV activity in permeabilized cells
    • Analyses of respiration rates of isolated mitochondria
  • Cell redox status
    • Redox status of GSH/GSSG redox couple
    • Redox status of NAD(P)H/NAD(P) redox couple
    • Redox status of cellular peroxiredoxins (redox blotting)
  • ROS production
    • Superoxide production
    • Hydrogen peroxide production
    • Peroxynitrite production
    • Oxygen consumption (oxidative burst)
  • Extra/Intracellular levels of selected metabolites
    • Monitoring uptake and efflux of bioenergetic substrates and products
    • Monitoring cellular levels of metabolic intermediates and products
  • Uptake dynamics and retention of metabolism-modulating agents
    • Monitoring uptake and efflux of metabolism-modulating agents
    • Monitoring cellular levels of metabolism-modulating agents 

 

Preclinical Imaging

View Preclinical Imaging Instrumentation. (PDF)

  • IVIS SpectrumCT: small animal bioluminescence and fluorescence, low dose X ray microCT and Cherenkov Luminescence imaging
  • Small animal near-infrared (NIR) and short-wave infrared imaging (SWIR)
Clinical Imaging
  • Patient tumor and lymph node measurements and volumetrics
  • Clinical trial level reporting and audit support
  • Cloud-based image repository and tools
Biomedical Imaging Shared Resource

iLab Requests and Support

Access the links below to learn how to register for iLab and submit requests.

Researcher at Monitor

Shared Resource Acknowledgement

A condition for using MCW Cancer Center supported Shared Resources is that each Shared Resource is acknowledged in the publication. These acknowledgments enable the Cancer Center to measure and document Shared Resource productivity, impact, and service to members.

View Shared Resource acknowledgement instructions. (PDF)


Director

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Karin Hoffmeister, MD

Director, Translational Metabolomics Shared Resource

khoffmeister@mcw.edu

Technical Directors

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Kazuhiro Aoki, PhD

Technical Director, Mass Spectrometry

kaoki@mcw.edu

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Amit Joshi, PhD

Technical Director, Preclinical Imaging

ajoshi@mcw.edu

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Peter S. LaViolette, PhD, MS

Technical Director, Quantitative Clinical Imaging

plaviole@mcw.edu

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Jacek Zielonka, PhD

Technical Director, Redox & Bioenergetics

jzielonk@mcw.edu

Mass Spectrometry Staff Members

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Mayumi Ishihara-Aoki, MS

Research Scientist

maoki@mcw.edu

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Md Al Mamun, PhD

Research Scientist

amamun@mcw.edu

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Michaela Pereckas, BS

Research Associate

mpereckas@mcw.edu

Quantitative Clinical Imaging Staff Members

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Allison Lowman

Research Associate I

alowman@mcw.edu

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Savannah Duenweg, PhD

Research Scientist I

sduenweg@mcw.edu

Preclinical Imaging Staff Members

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Shayan Shafiee

Postdoctoral Researcher

sshafiee@mcw.edu

Redox & Bioenergetics Staff Members

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Monika Zielonka, MSc

Research Technologist III

mzielonka@mcw.edu

Notable Publications

Lysosomal enzyme binding to the cation-independent mannose 6-phosphate receptor is regulated allosterically by insulin-like growth factor 2. (Bohnsack RN, Misra SK, Liu J, Ishihara-Aoki M, Pereckas M, Aoki K, Ren G, Sharp JS, Dahms NM) Sci Rep 2024 Nov 06;14(1):26875. PMID: 39505925; PMCID: PMC11541866; DOI: 10.1038/s41598-024-75300-9; Scopus ID: 2-s2.0-85208688601

Glycosphingolipids and their impact on platelet activity in a murine model of fabry disease. (Kanack AJ, Prodoehl E, Ishihara-Aoki M, Aoki K, Dahms NM) Sci Rep 2024 Nov 27;14(1):29488. PMID: 39604471; PMCID: PMC11603304; DOI: 10.1038/s41598-024-80633-6; Scopus ID: 2-s2.0-85210527022

Radio-pathomic maps of glioblastoma identify phenotypes of non-enhancing tumor infiltration associated with bevacizumab treatment response. (Bobholz SA, Hoefs A, Hamburger J, Lowman AK, Winiarz A, Duenweg SR, Kyereme F, Connelly J, Coss D, Krucoff M, Banerjee A, LaViolette PS) J Neurooncol 2024 Apr;167(2):243. PMID: 38498261; PMCID: PMC11023959; DOI: 10.1007/s11060-024-04641-2; Scopus ID: 2-s2.0-85187929260

Regulation of immunomodulatory networks by Nrf2-activation in immune cells: Redox control and therapeutic potential in inflammatory diseases. (Pant T, Uche N, Juric M, Zielonka J, Bai X) Redox Biol 2024 Apr;70:103077. PMID: 38359749; PMCID: PMC10877431; DOI: 10.1016/j.redox.2024.103077; Scopus ID: 2-s2.0-85185554817

Noninvasive Autopsy-Validated Tumor Probability Maps Identify Glioma Invasion Beyond Contrast Enhancement. (Bobholz SA, Lowman AK, Connelly JM, Duenweg SR, Winiarz A, Nath B, Kyereme F, Brehler M, Bukowy J, Coss D, Lupo JM, Phillips JJ, Ellingson BM, Krucoff MO, Mueller WM, Banerjee A, LaViolette PS) Neurosurgery 2024 Mar 19. PMID: 38501824; DOI: 10.1227/neu.0000000000002898

Health position paper and redox perspectives - Disease burden by transportation noise. (Sørensen M, Pershagen G, Thacher JD, Lanki T, Wicki B, Röösli M, Vienneau D, Cantuaria ML, Schmidt JH, Aasvang GM, Al-Kindi S, Osborne MT, Wenzel P, Sastre J, Fleming I, Schulz R, Hahad O, Kuntic M, Zielonka J, Sies H, Grune T, Frenis K, Münzel T, Daiber A) Redox Biol 2024 Feb;69:102995. PMID: 38142584; PMCID: PMC10788624; DOI: 10.1016/j.redox.2023.102995; Scopus ID: 2-s2.0-85180606610

Quantitative Histomorphometric Features of Prostate Cancer Predict Patients Who Biochemically Recur Following Prostatectomy. (Duenweg SR, Brehler M, Lowman AK, Bobholz SA, Kyereme F, Winiarz A, Nath B, Iczkowski KA, Jacobsohn KM, LaViolette PS) Lab Invest 2023 Dec;103(12):100269. PMID: 37898290; PMCID: PMC10872376; DOI: 10.1016/j.labinv.2023.100269; Scopus ID: 2-s2.0-85181176849

T2-Weighted MRI Radiomic Features Predict Prostate Cancer Presence and Eventual Biochemical Recurrence. (Duenweg SR, Bobholz SA, Barrett MJ, Lowman AK, Winiarz A, Nath B, Stebbins M, Bukowy J, Iczkowski KA, Jacobsohn KM, Vincent-Sheldon S, LaViolette PS) Cancers (Basel) 2023 Sep 06;15(18). PMID: 37760407; PMCID: PMC10526331; DOI: 10.3390/cancers15184437; Scopus ID: 2-s2.0-85172781879

Carvedilol Phenocopies PGC-1α Overexpression to Alleviate Oxidative Stress, Mitochondrial Dysfunction and Prevent Doxorubicin-Induced Toxicity in Human iPSC-Derived Cardiomyocytes. (Uche N, Dai Q, Lai S, Kolander K, Thao M, Schibly E, Sendaydiego X, Zielonka J, Benjamin IJ) Antioxidants (Basel) 2023 Aug 09;12(8). PMID: 37627583; PMCID: PMC10451268; DOI: 10.3390/antiox12081585; Scopus ID: 2-s2.0-85169136890

Antiproliferative effects of mitochondria-targeted N-acetylcysteine and analogs in cancer cells. (Cheng G, Hardy M, Kalyanaraman B) Sci Rep 2023 May 04;13(1):7254. PMID: 37142668; PMCID: PMC10160116; DOI: 10.1038/s41598-023-34266-w; Scopus ID: 2-s2.0-85158068757

Developing small-diameter vascular grafts with human amniotic membrane: long-term evaluation of transplantation outcomes in a small animal model. (Wang B, Wang X, Kenneth A, Drena A, Pacheco A, Kalvin L, Ibrahim ES, Rossi PJ, Thatcher K, Lincoln J) Biofabrication 2023 Jan 30;15(2). PMID: 36626826; DOI: 10.1088/1758-5090/acb1da; Scopus ID: 2-s2.0-85147095444

Mitigation of gastrointestinal graft-versus-host disease with tocilizumab prophylaxis is accompanied by preservation of microbial diversity and attenuation of enterococcal domination. (Chhabra S, Szabo A, Clurman A, McShane K, Waters N, Eastwood D, Samanas L, Fei T, Armijo G, Abedin S, Longo W, Hari P, Hamadani M, Shah NN, Runaas L, Jerkins JH, Van den Brink M, Peled JU, Drobyski WR) Haematologica 2023 Jan 01;108(1):250-256. PMID: 36106394; PMCID: PMC9827178; DOI: 10.3324/haematol.2022.281309; Scopus ID: 2-s2.0-85145424654

Fluorinated triphenylphosphonium analogs improve cell selectivity and in vivo detection of mito-metformin. (AbuEid M, Keyes RF, McAllister D, Peterson F, Kadamberi IP, Sprague DJ, Chaluvally-Raghavan P, Smith BC, Dwinell MB) iScience 22 December 2022;25(12). DOI: 10.1016/j.isci.2022.105670; Scopus ID: 2-s2.0-85143723525

Corrigendum to ‘Ixazomib for chronic Graft-Versus-Host Disease prophylaxis following allogeneic hematopoietic cell transplantation.’ (Chhabra S, Visotcky A, Pasquini MC, Zhu F, Tang X, Zhang MJ, Thompson R, Abedin S, D'Souza A, Dhakal B, Drobyski WR, Fenske TS, Jerkins JH, Rizzo JD, Runaas L, Saber W, Shah NN, Shaw BE, Horowitz MM, Hari PN, Hamadani M) [Biology of Blood and Marrow Transplantation 26/10 (2020) 1876-1885, (S1083879120304146), (10.1016/j.bbmt.2020.07.005)] Transplantation and Cellular Therapy October 2022;28(10):717. PMID: 36202527; DOI: 10.1016/j.jtct.2021.01.005; Scopus ID: 2-s2.0-85101258094

Multi-Site Concordance of Diffusion-Weighted Imaging Quantification for Assessing Prostate Cancer Aggressiveness.(McGarry SD, Brehler M, Bukowy JD, Lowman AK, Bobholz SA, Duenweg SR, Banerjee A, Hurrell SL, Malyarenko D, Chenevert TL, Cao Y, Li Y, You D, Fedorov A, Bell LC, Quarles CC, Prah MA, Schmainda KM, Taouli B, LoCastro E, Mazaheri Y, Shukla-Dave A, Yankeelov TE, Hormuth DA 2nd, Madhuranthakam AJ, Hulsey K, Li K, Huang W, Huang W, Muzi M, Jacobs MA, Solaiyappan M, Hectors S, Antic T, Paner GP, Palangmonthip W, Jacobsohn K, Hohenwalter M, Duvnjak P, Griffin M, See W, Nevalainen MT, Iczkowski KA, LaViolette PS) J Magn Reson Imaging 2022 Jun;55(6):1745-1758. PMID: 34767682; PMCID: PMC9095769; DOI: 10.1002/jmri.27983; Scopus ID: 2-s2.0-85118887092

Prevention of Tumor Growth and Dissemination by In Situ Vaccination with Mitochondria-Targeted Atovaquone. (Huang M, Xiong D, Pan J, Zhang Q, Wang Y, Myers CR, Johnson BD, Hardy M, Kalyanaraman B, You M) Adv Sci (Weinh) 2022 Apr;9(12):e2101267. PMID: 35243806; PMCID: PMC9036031; Scopus ID: 2-s2.0-85125564839 

Oncostatin M Receptor-Targeted Antibodies Suppress STAT3 Signaling and Inhibit Ovarian Cancer Growth. (Geethadevi A, Nair A, Parashar D, Ku Z, Xiong W, Deng H, Li Y, George J, McAllister DM, Sun Y, Kadamberi IP, Gupta P, Dwinell MB, Bradley WH, Rader JS, Rui H, Schwabe RF, Zhang N, Pradeep S, An Z, Chaluvally-Raghavan P) Cancer Res 2021 Oct 15;81(20):5336-5352. PMID: 34380633; PMCID: PMC8530981; Scopus ID: 2-s2.0-85116424540

Pertuzumab and trastuzumab for HER2-positive, metastatic biliary tract cancer (MyPathway): a multicentre, open-label, phase 2a, multiple basket study. (Javle M, Borad MJ, Azad NS, Kurzrock R, Abou-Alfa GK, George B, Hainsworth J, Meric-Bernstam F, Swanton C, Sweeney CJ, Friedman CF, Bose R, Spigel DR, Wang Y, Levy J, Schulze K, Cuchelkar V, Patel A, Burris H) Lancet Oncol 2021 Sep;22(9):1290-1300. PMID: 34339623; DOI: 10.1016/S1470-2045(21)00336-3; Scopus ID: 2-s2.0-85113412076

Nuclear PFKP promotes CXCR4-dependent infiltration by T cell acute lymphoblastic leukemia. (Gao X, Qin S, Wu Y, Chu C, Jiang B, Johnson RH, Kuang D, Zhang J, Wang X, Mehta A, Tew KD, Leone GW, Yu XZ, Wang H) J Clin Invest 2021 Aug 16;131(16). PMID: 34255748; PMCID: PMC8363288; Scopus ID: 2-s2.0-85113146308 

WDR26 and MTF2 are therapeutic targets in multiple myeloma. (Sun F, Cheng Y, Riordan JD, Dupuy A, Dubois W, Pisano M, Dong J, Mock B, Zhan F, Hari P, Janz S) J Hematol Oncol 2021 Dec 07;14(1):203. PMID: 34876184; PMCID: PMC8650373; Scopus ID: 2-s2.0-85120899924 

AMPK-deficiency forces metformin-challenged cancer cells to switch from carbohydrate metabolism to ketogenesis to support energy metabolism. (Palma FR, Ratti BA, Paviani V, Coelho DR, Miguel R, Danes JM, Zaichik SV, de Abreu AL, Silva SO, Chen Y, Silverstein RL, Karan U, Jones DP, Bonini MG) Oncogene 2021 Sep;40(36):5455-5467. PMID: 34290400; PMCID: PMC8669831; DOI: 10.1038/s41388-021-01943-x; Scopus ID: 2-s2.0-85110982210