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Mass Spectrometry Facility

The MUSC Mass Spectrometry Facility provides expertise, services, and state-of-the-art instrumentation for proteomics and metabolomics.

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Proteomics Services:
Label free proteomics for protein profiling; Protein identification; characterization of post-translational modifications; TMT and SILAC- based quantitative proteomics; customized PTM-specific method development.

 

Metabolomics Services:

Metabolite profiling is available using the Biocrates platforms: MxP 500XL and p180 kits.  The MxP 1000 kit will be available after June, 2026.

 

Analyses include sample preparation, data acquisition, database searching, generation of reports, assistance with data interpretation, and preparation of grant applications and manuscripts.

 

Facility Resources and Equipment:
The MUSC Mass Spectrometry Facility, housed within the Proteomics Center, provides expertise, services, education, and state-of-the-art instrumentation to enhance biomedical research through proteomics and metabolomics. High resolution, accurate mass (HR/AM) mass spectrometers are available for protein identification, characterization of post-translational modifications, protein profiling, identification of protein interactions and drug targets, and biomarker discovery. The core also assists in the development of customized isolation, detection, and characterization of post-translationally modified peptides. Targeted metabolite profiling is available using Biocrates MxP Quant 500/500XL, MxP Quant 1000, or AbsoluteIDQ p180 platforms.

Equipment and Computing Infrastructure:

  • Quantitative proteomic experiments (LFQ, nDIA, TMT, SILAC, IS-PRM) can be performed on the Thermo Scientific Vanquish Neo UHPLC Orbitrap Astral Zoom LC-MS/MS with Biopharma and Faims; Easy 1200 nanoLC-Orbitrap Exploris 480 LC-MS/MS; or Easy 1200 nanoLC Orbitrap Fusion Lumos LC-MS/MS with CID, HCD, ETD, EThcD, and UVPD (213 nm) fragmentation capabilities.
  • For sample preparation a Kingfisher Apex, Opentrons OT-2, and Thermo Scientific Vanquish UPLC with diode array detector are available.
  • Software platforms available include MaxQuant, Spectronaut, Proteome Discoverer with Chimerys, Biopharma Finder, Fragpipe, and Skyline.
  • For database searches a 6 x Intel Xeon Gold 6238R processor (28 cores 56 threads 2.2 GHz up to 4 GHz) with 48GB RAM or a 2 x Intel Xeon E5-2695 processor (18 cores 36 threads 2.1 GHz up to 3.3 GHz) with 128GB RAM are available.
  • For Orbitrap Astral data, the Ardia Platform Server: Dell PowerEdge T550: 2 x Intel Xeon Platinum 8352M processor (64 cores 128 threads 2.3 GHz with 512GB RAM) and Precision 7960 Tower XCTO Base: Intel Xeon w9-3495X (105MB Cache, 56 cores, 112 threads, 1.9GHz to 4.8GHz) are available.
  • Statistical and bioinformatic analyses are performed with Perseus (Max Planck Institute), Graphpad Prism, as well as R-packages from Bioconductor.
  • Raw data are temporarily stored on high-speed servers with automated backup and deposited upon request in the PRIDE repository via the ProteomeXchange consortium.
  • Targeted, absolute quantification of metabolites using the Biocrates platform is available on the Thermo Scientific Vanquish Flex UPLC-TSQ Altis Plus MS and Vanquish Horizon HPLC-Exploris 480 MS.
  • Software used for metabolomic analysis include WebIDQ, Compound Discoverer, Skyline, and MetaboAnalyst.
     

Recent Publications

Wu Y, Tian L, Pugel A, Alimohammadi R, Cheng Q, Cui W, Nishimura MI, Ball LE, Lin CW, Mehrotra S, Kraft AS, Yu XZ. Targeting Pim2 Improves Antitumor Immunity through Promoting Effector Function and Persistence of CD8 T cells. J Clin Invest. 2026 Jan 27:e192928. doi: 10.1172/JCI192928. Epub ahead of print. PMID: 41592107. Phosphoproteomics

Wood DJ, Tsvetkov E, Comte-Walters S, Welsh CL, Bloyd M, Wood TG, Akiki RM, Anderson EM, Penrod RD, Madan LK, Ball LE, Taniguchi M, Cowan CW. Epigenetic Control of an Auxiliary Subunit of Voltage-Gated Sodium Channels Regulates the Strength of Drug-Cue Associations and Relapse-Like Cocaine Seeking. Biol Psychiatry. 2025 Oct 15;98(8):597-611. doi: 10.1016/j.biopsych.2025.01.027. Epub 2025 Feb 7. PMID: 39923817. Disulfide bonds and Cysteine modifications

Le Minh G, Merzy J, Esquea EM, Ahmed NN, Young RG, Sharp RJ, Dhameliya TT, Agana B, Lee MH, Bethard JR, Comte-Walters S, Ball LE, Reginato MJ. GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance. Cells. 2025 Mar 8;14(6):398. doi: 10.3390/cells14060398. PMID: 40136647; PMCID: PMC11941746. O-GlcNAc modification

Wang M, Grauzam S, Bayram MF, Dressman J, DelaCourt A, Blaschke C, Liang H, Scott D, Huffman G, Black A, Ochoa-Rios S, Lewin D, Angel PM, Drake RR, Ball L, Bethard J, Castellino S, Kono Y, Kubota N, Hoshida Y, Quirk L, Yopp A, Gopal P, Singal A, Mehta AS. Spatial omics-based machine learning algorithms for the early detection of hepatocellular carcinoma. Commun Med (Lond). 2024 Dec 3;4(1):258. doi: 10.1038/s43856-024-00677-7. PMID: 39627514; PMCID: PMC11614901. Core fucosylation

Oberholtzer N, Chakraborty P, Kassir MF, Dressman J, Das S, Mills S, Comte-Walters S, Gooz M, Choi S, Parikh RY, Hedley Z, Vaena S, DeMass R, Scurti G, Romeo M, Gangaraju VK, Berto S, Hill E, Ball LE, Mehta AS, Maldonado EN, Nishimura MI, Ogretmen B, Mehrotra S. H2S-Prdx4 axis mitigates Golgi stress to bolster tumor-reactive T cell immunotherapeutic response. Sci Adv. 2024 Nov 15;10(46):eadp1152. doi: 10.1126/sciadv.adp1152. Epub 2024 Nov 15. PMID: 39546607; PMCID: PMC11566994. Thiol status

Brobbey C, Yin S, Liu L, Ball LE, Howe PH, Delaney JR, Gan W. Autophagy dictates sensitivity to PRMT5 inhibitor in breast cancer. Sci Rep. 2023 Jul 3;13(1):10752. doi: 10.1038/s41598-023-37706-9. PMID: 37400460; PMCID: PMC10318021. Arginine Methylation

Yin S, Liu L, Ball LE, Wang Y, Bedford MT, Duncan SA, Wang H, Gan W. CDK5-PRMT1-WDR24 signaling cascade promotes mTORC1 signaling and tumor growth. Cell Rep. 2023 Apr 25;42(4):112316. doi: 10.1016/j.celrep.2023.112316. Epub 2023 Mar 29. PMID: 36995937; PMCID: PMC10539482. Phosphorylation

Zhang Z, Huang Z, Awad M, Elsalanty M, Cray J, Ball LE, Maynard JC, Burlingame AL, Zeng H, Mansky KC, Ruan HB. O-GlcNAc glycosylation orchestrates fate decision and niche function of bone marrow stromal progenitors. Elife. 2023 Mar 2;12:e85464. doi: 10.7554/eLife.85464. PMID: 36861967; PMCID: PMC10032655. O-GlcNAc Modification

Jensen CC, Clements AN, Liou H, Ball LE, Bethard JR, Langlais PR, Toth RK, Chauhan SS, Casillas AL, Daulat SR, Kraft AS, Cress AE, Miranti CK, Mouneimne G, Rogers GC, Warfel NA. PIM1 phosphorylates ABI2 to enhance actin dynamics and promote tumor invasion. J Cell Biol. 2023 Jun 5;222(6):e202208136. doi: 10.1083/jcb.202208136. Epub 2023 Apr 12. PMID: 37042842; PMCID: PMC10103708. Phosphoproteomics

Liu L, Lin B, Yin S, Ball LE, Delaney JR, Long DT, Gan W. Arginine methylation of BRD4 by PRMT2/4 governs transcription and DNA repair. Sci Adv. 2022 Dec 9;8(49):eadd8928. doi: 10.1126/sciadv.add8928. Epub 2022 Dec 7. PMID: 36475791; PMCID: PMC9728970. Arginine Methylation

Yin S, Liu L, Brobbey C, Palanisamy V, Ball LE, Olsen SK, Ostrowski MC, Gan W. PRMT5-mediated arginine methylation activates AKT kinase to govern tumorigenesis. Nat Commun. 2021 Jun 8;12(1):3444. doi: 10.1038/s41467-021-23833-2. PMID: 34103528; PMCID: PMC8187744. Arginine Methylation

Wu Y, Tian L, Pugel A, Alimohammadi R, Cheng Q, Cui W, Nishimura MI, Ball LE, Lin CW, Mehrotra S, Kraft AS, Yu XZ. Targeting Pim2 Improves Antitumor Immunity through Promoting Effector Function and Persistence of CD8 T cells. J Clin Invest. 2026 Jan 27:e192928. doi: 10.1172/JCI192928. PMID: 41592107. PhosphoTMT

Mulholland PJ, Berto S, Wilmarth PA, McMahan C, Ball LE, Woodward JJ. Adaptor protein complex 2 in the orbitofrontal cortex predicts alcohol use disorder. Mol Psychiatry. 2023 Nov;28(11):4766-4776. doi: 10.1038/s41380-023-02236-3. Epub 2023 Sep 7. PMID: 37679472; PMCID: PMC10918038. TMT-based proteomics

Jensen CC, Clements AN, Liou H, Ball LE, Bethard JR, Langlais PR, Toth RK, Chauhan SS, Casillas AL, Daulat SR, Kraft AS, Cress AE, Miranti CK, Mouneimne G, Rogers GC, Warfel NA. PIM1 phosphorylates ABI2 to enhance actin dynamics and promote tumor invasion. J Cell Biol. 2023 Jun 5;222(6):e202208136. doi: 10.1083/jcb.202208136. Epub 2023 Apr 12. PMID: 37042842; PMCID: PMC10103708. PhosphoSILAC

Griggs M, Daylor V, Petrucci T, Weintraub A, Huff M, Willey S, Byerly K, Loizzi B, Morningstar J, Ball LE, Bethard JR, Drake R, Sharma A, Eichinger JK, Nichols M, Kautz S, Shapiro S, Maitland A, Patel S, Norris RA, Gensemer C. Proteomic discoveries in hypermobile Ehlers-Danlos syndrome reveal insights into disease pathophysiology. Immunohorizons. 2025 Sep 17;9(10):vlaf044. doi: 10.1093/immhor/vlaf044. PMID: 40972649; PMCID: PMC12448790. Serum proteomics

Le Minh G, Merzy J, Esquea EM, Ahmed NN, Young RG, Sharp RJ, Dhameliya TT, Agana B, Lee MH, Bethard JR, Comte-Walters S, Ball LE, Reginato MJ. GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance. Cells. 2025 Mar 8;14(6):398. doi: 10.3390/cells14060398. PMID: 40136647; PMCID: PMC11941746. Proteomics, O-GlcNAcylated proteins, protein interactions

Hunt EG, Hurst KE, Riesenberg BP, Kennedy AS, Gandy EJ, Andrews AM, Del Mar Alicea Pauneto C, Ball LE, Wallace ED, Gao P, Meier J, Serody JJ, Coleman MF, Thaxton JE. Acetyl-CoA carboxylase obstructs CD8+ T cell lipid utilization in the tumor microenvironment. Cell Metab. 2024 May 7;36(5):969-983.e10. doi: 10.1016/j.cmet.2024.02.009. Epub 2024 Mar 14. PMID: 38490211; PMCID: PMC12010431. Profiling of tumor infiltrating lymphocytes

Badenetti L, Yu SH, Colonna MB, Hull R, Bethard JR, Ball L, Flanagan-Steet H, Steet R. Multi-omic analysis of a mucolipidosis II neuronal cell model uncovers involvement of pathways related to neurodegeneration and drug metabolism. Mol Genet Metab. 2024 Nov;143(3):108596. doi: 10.1016/j.ymgme.2024.108596. Epub 2024 Oct 22. PMID: 39461112; PMCID: PMC11569414. Cell surface glycoproteomics

Wei H, Green E, Ball L, Fan H, Lee J, Strange C, Wang H. Proteomic Analysis of Exosomes Secreted from Human Alpha-1 Antitrypsin Overexpressing Mesenchymal Stromal Cells. Biology (Basel). 2021 Dec 21;11(1):9. doi: 10.3390/biology11010009. PMID: 35053007; PMCID: PMC8773149. Exosomes

Burge RA, Bialousow L, McFall T, Bamonte L, Johnson G, Smith M, Vaena SG, Comte-Walters S, Ball LE, Berto S, O'Bryan JP, Hobbs GA. Pancreatic Cells Are Resistant to KRASQ61L Expression due to Hyperactive ERK/MAPK Signaling and Apoptosis Induction. Cancer Res Commun. 2025 Oct 1;5(10):1865-1878. doi: 10.1158/2767-9764.CRC-25-0281. PMID: 40951926; PMCID: PMC12541299.

Le Minh G, Merzy J, Esquea EM, Ahmed NN, Young RG, Sharp RJ, Dhameliya TT, Agana B, Lee MH, Bethard JR, Comte-Walters S, Ball LE, Reginato MJ. GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance. Cells. 2025 Mar 8;14(6):398. doi: 10.3390/cells14060398. PMID: 40136647; PMCID: PMC11941746.

Gerassimovich YA, Miladinovski-Bangall SJ, Bridges KM, Boateng L, Ball LE, Valafar H, Nag A. Proximity-dependent biotinylation detects associations between SARS coronavirus nonstructural protein 1 and stress granule-associated proteins. J Biol Chem. 2021 Dec;297(6):101399. doi: 10.1016/j.jbc.2021.101399. Epub 2021 Nov 11. PMID: 34774526; PMCID: PMC8580555.

Schuck PL, Ball LE, Stewart JA. The DNA-binding protein CST associates with the cohesin complex and promotes chromosome cohesion. J Biol Chem. 2021 Sep;297(3):101026. doi: 10.1016/j.jbc.2021.101026. Epub 2021 Jul 30. PMID: 34339741; PMCID: PMC8390553.

Please contact Peggi Angel, PhD for more information regarding Mass Spectrometry Imaging for peptides, lipids, and metabolites. Please contact Richard Drake, PhD for more information regarding MSI for glycans and glycoproteomics.

Womersley JS, Obellianne C, Padula AE, Lopez MF, Griffin WC, Ball LE, Berto S, Grant KA, Townsend DM, Uys JD, Mulholland PJ. Adaptations in glutathione-based redox protein signaling pathways and alcohol drinking across species. Biomed Pharmacother. 2024 Nov;180:117514. doi: 10.1016/j.biopha.2024.117514. Epub 2024 Oct 2. PMID: 39362067; PMCID: PMC11775667.

Hartig JP, Bejar K, Young LEA, Grimsley G, Bethard JR, Troyer DA, Hernandez J, Wu JD, Ippolito JE, Ball LE, Gelfond JAL, Johnson-Pais TL, Mehta AS, Leach RJ, Angel PM, Drake RR. Determining the N-Glycan and Collagen/Extracellular Matrix Protein Compositions in a Novel Outcome Cohort of Prostate Cancer Tissue Microarrays Using MALDI-MSI. Cancer Res Commun. 2024 Nov 1;4(11):3036-3048. doi: 10.1158/2767-9764.CRC-24-0152. PMID: 39347566; PMCID: PMC11600299.

Rujchanarong D, Lefler J, Saunders JE, Pippin S, Spruill L, Bethard JR, Ball LE, Mehta AS, Drake RR, Ostrowski MC, Angel PM. Defining the Tumor Microenvironment by Integration of Immunohistochemistry and Extracellular Matrix Targeted Imaging Mass Spectrometry. Cancers (Basel). 2021 Sep 1;13(17):4419. doi: 10.3390/cancers13174419. PMID: 34503228; PMCID: PMC8430776.

Clift CL, Su YR, Bichell D, Jensen Smith HC, Bethard JR, Norris-Caneda K, Comte-Walters S, Ball LE, Hollingsworth MA, Mehta AS, Drake RR, Angel PM. Collagen fiber regulation in human pediatric aortic valve development and disease. Sci Rep. 2021 May 7;11(1):9751. doi: 10.1038/s41598-021-89164-w. PMID: 33963260; PMCID: PMC8105334.

Mass Spectrometry Publication Acknowledgment

When you publish, please acknowledge the core and the appropriate funding source(s):

Proteomics performed in the MUSC Mass Spectrometry Facility, a University Research Resource Facility, was supported, in part, by NIH grants: Orbitrap Astral Zoom MS (HEI S10 OD038396); Orbitrap Exploris 480 MS (HEI S10 OD028692); Orbitrap Fusion Lumos ETD/UVPD MS (HEI S10 OD025126); MUSC Digestive Disease Research Core Center (P30 DK123704); SC COBRE in Oxidants, Redox Balance and Stress Signaling (P30 GM140964); South Carolina Clinical & Translational Research Institute (SCTR voucher program); (UM1TR005294); and the Hollings Cancer Center (P30CA138313).

Please let us know when you publish!

Mass Spectrometry Analysis Request

Staff is available for consultation during all stages of proteomics experiments (from experimental design to publication). First-time users of the resource should contact the facility to ensure their samples are compatible with mass spectrometry.

To schedule a consult, please click here. For sample submission and quote generation, please complete the Sample Submission Form.

Facility Administration

 

Director

Lauren E. Ball, Ph.D.

Associate Professor, Pharmacology & Immunology

Associate Director of University Shared Resources

ballle@musc.edu

843-792-4513

 

Core Manager

Jennifer R. Bethard, MS

bethard@musc.edu

 

Expertise:

Instrumentation

Phosphoproteomics

High throughput proteomics of biofluids

 

Staff Scientist

Yun Xiong, Ph.D.

xiongyu@musc.edu

 

Expertise:

High Throughput Proteomics

Computational Proteomics

Staff Scientist
 Mi-Hye Lee, Ph.D.
leemih@musc.edu

Expertise:
 Sample preparation

  • PTM
  • Omics
  • TMT-based proteomics
  • Automated sample processing
  • Protein interactions

 

Post-Doctoral Fellow

Jasmine Gill, Ph.D.

gillja@musc.edu

 

Expertise:

Metabolomics

Proteomics

We acknowledge support from the MUSC Vice President for Research, College of Medicine, P20 GM103542 (SC COBRE in Oxidants, Redox Balance and Stress Signaling ), S10 OD025126 (Orbitrap Elite), S10 OD010731 (Orbitrap Lumos), U01CA244303 (Reginato/Ball), P30CA138313 (Hollings Cancer Center).

Contact Us

Lauren E. Ball, Ph.D.
Director
843-792-4513
ballle@musc.edu

Jennifer R. Bethard, MS
Facility Manager
bethard@musc.edu

Mailing Address

173 Ashley Ave

BSB 358; MSC 509

Charleston, SC 29425

 

Address

Darby Children's Research Institute

Room CRI305

Medical University of South Carolina

171 Ashley Ave

Charleston, SC 29425

Overall Core Administration