Mass Spectrometry

Mass Spectrometry


Core Facilities Seminar

Dominique Alfandari, Prof. VASCI–Proteomics 101 A practical guide to preparing samples for proteomic analysis.

Replay on YouTube

Matthew Stone, PhD, AB SCIEX–Handle with care: Ensuring lipid nanoparticle quality for better genetic medicines

Replay on YouTube

Located on the 5th floor in the Life Science Laboratories the Mass Spectrometry Core houses a suite of state-of-the-art instrumentation for characterizing elements and compounds across the entire mass range from small (metal ions) to large (macromolecular assemblies). Specialized mass spectrometers encompass a variety of ionization techniques and separation devices to cover a wide range of analytical capabilities.

The facility accepts samples and will perform requested analysis. We offer training to users to conduct experimentation for use on a fee for service basis to both internal and external researchers, academic or industry based. Following an initial consultation, covering experimental parameters training and access is arranged through the director.

  • Perkin-Elmer NexION 350D ICP-MS

    Inductively coupled plasma mass spectrometry enables sensitive simultaneous quantitative measurement of most metals and many non-metals in a variety of samples, including biological matrices. Examples include environmental analysis (water contamination), metals in biological tissues and fluids, quantitation of metals in plant material. Quantitation levels in the sub-part per billion range can be achieved for the majority of elements. Laser ablation is also available for spatial imaging of metals in tissues and other sample types. HPLC can also be coupled for quantitative measurement of metal speciation.

  • Agilent 6890/5973 GC-MS and 7890B/7000C GC-QQQ MS

    Gas chromatography is a powerful tool for separation of volatile small molecule analytes. Samples are volatilized in the injector and then separate based on hydrophobicity and boiling point in the GC column, followed by mass determination in the MS. Results can be searched against the NIST MS libraries to identify compounds. Coupled to triple quadrupole mass spectrometry this enables quantitation of e.g. metabolites. Robotic auto-sampler can perform normal liquid-phase sample injection as well as headspace and SPME pretreatments.

  • Waters UPLC/Xevo TQD QQQ-MS

    Tandem quadrupole mass spectrometer coupled to UPLC rapid separation of complex mixtures. Separation and quantitation of a broad range of small molecules from metabolites to peptides.
    UPLC for separation of compounds at high resolution due to small stationary phase particle size. High sensitivity and selectivity of triple quadrupole enables quantitation at low levels even in a complex matrix background.
    Multi-mode ESCI ion source allows simultaneous ESI and APCI modes of ionization, together with rapid polarity switching for maximal compound detection. >1000 MRMs can be monitored per sample run for quantitation, with optional triggered full scan for compound confirmation and spectral interference determination.

  • Waters Synapt G2Si Q-TOF with IMS and HDX Automation

    Q-TOF instruments have a wide range of capabilities for characterization of small and large biomolecules. Ion mobility separation capabilities add an orthogonal separation based on gas-phase collisional cross-section (CCS).
    This instrument is primarily used in two modes, namely nanospray ionization for measurement of proteins under native conditions. IMS can be employed to measure changes in CCS in response to e.g. ligand binding or oligomerization state.
    Hydrogen-deuterium exchange is a powerful technique for measurement of protein-protein, protein-ligand interactions and protein dynamics. HDX automation enables experiments to be performed in an automated and highly reproducible fashion. Adding IMS enables complex mixtures of peptides to be separated in the HDX system based on HPLC elution time, gas phase structure, and peptide molecular weight. This orthogonal separation increases peak capacity for HDX measurement, allowing for more confident identification and deuterium uptake measurement, leading to increased protein coverage.

  • Bruker UltrafleXtreme MALDI-TOF/TOF

    State of the art MALDI-TOF instrument for high sensitivity measurement of limited sample quantity (routinely low fmol amounts).
    2 kHz laser repetition rate (1 kHz in TOF/TOF mode) enables very rapid data acquisition at high resolution and mass accuracy. Smartbeam IITM laser technology enables focus to 10 μm for high resolution spatial imaging applications. Applications include rapid top-down sequence confirmation of biopharmaceuticals, high speed tissue imaging for biodistribution and biomarker discovery, proteomics and glycoproteomics. LC-MALDI capabilities for high sensitivity measurement and offline interrogation of samples at greater depth than conventional online LC-MS proteomics.

  • Thermo Orbitrap Fusion

    This instrument combines supremely high sensitivity with high resolution and high mass accuracy to probe complex sample mixtures. Combined with Ultimate 3000 RSLC or Easy nLC 1000 nanoLC systems for metabolomics or proteomics workflows. The Orbitrap Fusion tribrid mass spectrometer combines the best of quadrupole, orbitrap, and ion trap mass analysis in a revolutionary architecture that delivers unprecedented depth of analysis. It enables life scientists analyzing even the most challenging low-abundance, high-complexity, or difficult samples to identify more compounds more quickly, quantify more accurately, and elucidate structures more thoroughly.

Other instrumentation in the Mass Spectrometry Center:

  Campus Users Other Academic Institutions Industry
Mass Spectrometry Service Analysis
Simple Sample Analysis (MSI) $55/sample $60/sample $110/sample
LC-MS Analysis $110/sample $132/sample $220/sample
ICP-MS  Analysis $22/sample $55/sample $110/sample
Proteomics Analysis $110/sample $132/Sample $220/sample
TMT Proteomic Analysis $165/sample $220/sample $330/sample
Mass Spectrometry Hourly Usage
Daytime Usage $50/hour $61/hour $110/hour
ICP-MS Usage $22/hour $33/hour $110/hour
GC-MS Usage $22/hour $33/hour $110/hour
MicroTOF II Usage $39/hour $50/hour $110/hour
MicroFlex Usage $39/hour $50/hour $110/hour
Advanced Data Acquisition/Analysis
Staff $110/hour $110/hour $220/hour
Rates are subject to change, contact facility to verify current fees.

FY24 Specialized Service Center Approved Fees


Training for new users consists of:

  • lab safety training,
  • operation of the instrument and associated software,
  • use of data analysis software,
  • exporting or presenting data,
  • clean up and shutdown of the instrumentation.

Once the training is complete, researchers may schedule their experiments through the director of Mass Spectrometry (Stephen Eyles) or online through CORUM at

The Mass Spectrometry Core Facility: Instrumentation includes UPLC-ESI-triple quadrupole for quantitative small molecule studies, a Solarix 4.7T FTMS, AB Sciex QStarXL Q-TOF, Bruker MicroTOF II ESI-TOF and Bruker MicroFlex MALDI-TOF mass spectrometers. Recent acquisitions include a Thermo Orbitrap Fusion tribrid mass spectrometer, equipped with both nanoLC and UPLC chromatography systems and a Waters Synapt G2Si quadrupole-time of flight instrument with ion mobility capabilities. The Synapt instrument is equipped with hydrogen-deuterium exchange automation robotics for performing HDX experiments.

FY24 Specialized Service Center Approved Fees

Updated July 2023

CORUM (access and reservations)

Steve has been Director of the Mass Spectrometry Core Facility at UMass Amherst since 2000. He has been involved in mass spectrometry and other biophysical and analytical techniques since grad school, working on developing novel methodologies to study biomolecular structure and dynamics. He has co-authored a book on Mass Spectrometry in Biophysics. Steve holds an undergraduate degree and D.Phil. in Chemistry from the University of Oxford. 

Publications resulting from use of the IALS Mass Spectrometry Facility at UMass Amherst


Kuhlmann NJ, Doxsey D, Chien P. Cargo competition for a dimerization interface restricts and stabilizes a bacterial protease adaptor. Proc Natl Acad Sci U S A. 2021 Apr 27;118(17):e2010523118. PMID: 33875581; PMCID: PMC8092595.

Özcan E, Rozycki MR, Sela DA. Cranberry Proanthocyanidins and Dietary Oligosaccharides Synergistically Modulate Lactobacillus plantarum Physiology. Microorganisms. 2021 Mar 22;9(3):656. PMID: 33810188; PMCID: PMC8004764.


Zhao Y, Kaltashov IA. Evaluation of top-down mass spectrometry and ion-mobility spectroscopy as a means of mapping protein-binding motifs within heparin chains. Analyst. 2020 Apr 14;145(8):3090-3099. PMID: 32150181; PMCID: PMC7160044.!divAb...

Yang Y, Du Y, Kaltashov IA. The Utility of Native MS for Understanding the Mechanism of Action of Repurposed Therapeutics in COVID-19: Heparin as a Disruptor of the SARS-CoV-2 Interaction with Its Host Cell Receptor. Anal Chem. 2020 Aug 18;92(16):10930-10934. Epub 2020 Jul 27. PMID: 32678978; PMCID: PMC7384394.

Sikora KN, Hardie JM, Castellanos-García LJ, Liu Y, Reinhardt BM, Farkas ME, Rotello VM, Vachet RW. Dual Mass Spectrometric Tissue Imaging of Nanocarrier Distributions and Their Biochemical Effects. Anal Chem. 2020 Jan 21;92(2):2011-2018. Epub 2019 Dec 30. PMID: 31825199; PMCID: PMC7086473.

Deol KK, Eyles SJ, Strieter ER. Quantitative Middle-Down MS Analysis of Parkin-Mediated Ubiquitin Chain Assembly. J Am Soc Mass Spectrom. 2020 May 6;31(5):1132-1139. Epub 2020 Apr 28. PMID: 32297515; PMCID: PMC7333183.

Deol KK, Crowe SO, Du J, Bisbee HA, Guenette RG, Strieter ER. Proteasome-Bound UCH37/UCHL5 Debranches Ubiquitin Chains to Promote Degradation. Mol Cell. 2020 Dec 3;80(5):796-809.e9.  Epub 2020 Nov 5. PMID: 33156996; PMCID: PMC7718437.

Tremblay CY, Vass RH, Vachet RW, Chien P. The Cleavage Profile of Protein Substrates by ClpXP Reveals Deliberate Starts and Pauses. Biochemistry. 2020 Nov 10;59(44):4294-4301. Epub 2020 Nov 2. PMID: 33135889; PMCID: PMC7658057.

Niu C, Yang Y, Huynh A, Nazy I, Kaltashov IA. Platelet Factor 4 Interactions with Short Heparin Oligomers: Implications for Folding and Assembly. Biophys J. 2020 Oct 6;119(7):1371-1379. Epub 2020 Apr 21. PMID: 32348723; PMCID: PMC7567982.

Niu C, Zhao Y, Bobst CE, Savinov SN, Kaltashov IA. Identification of Protein Recognition Elements within Heparin Chains Using Enzymatic Foot-Printing in Solution and Online SEC/MS. Anal Chem. 2020 Jun 2;92(11):7565-7573. Epub 2020 May 13. PMID: 32347711; PMCID: PMC8095033.

Martin CJ, Datta A, Littlefield C, Kalra A, Chapron C, Wawersik S, Dagbay KB, Brueckner CT, Nikiforov A, Danehy FT Jr, Streich FC Jr, Boston C, Simpson A, Jackson JW, Lin S, Danek N, Faucette RR, Raman P, Capili AD, Buckler A, Carven GJ, Schürpf T. Selective inhibition of TGFβ1 activation overcomes primary resistance to checkpoint blockade therapy by altering tumor immune landscape. Sci Transl Med. 2020 Mar 25;12(536):eaay8456. PMID: 32213632.

Liu T, Marcinko TM, Vachet RW. Protein-Ligand Affinity Determinations Using Covalent Labeling-Mass Spectrometry. J Am Soc Mass Spectrom. 2020 Jul 1;31(7):1544-1553. Epub 2020 Jun 22. PMID: 32501685; PMCID: PMC7332385.

Fernandez, K; Spielbauer, K. K.; Rusheen, A; Wang, L; Baker, T. G.; Eyles, S; Cunningham, L. L.  Lovastatin Protects Against Cisplatin-Induced Hearing Loss in. Elsevier, Volume 389, April 2020.

Duan Q, Liu MJ, Kita D, Jordan SS, Yeh FJ, Yvon R, Carpenter H, Federico AN, Garcia-Valencia LE, Eyles SJ, Wang CS, Wu HM, Cheung AY. FERONIA controls pectin- and nitric oxide-mediated male-female interaction. Nature. 2020 Mar;579(7800):561-566. Epub 2020 Mar 18. PMID: 32214247.

Dagbay KB, Treece E, Streich FC Jr, Jackson JW, Faucette RR, Nikiforov A, Lin SC, Boston CJ, Nicholls SB, Capili AD, Carven GJ. Structural basis of specific inhibition of extracellular activation of pro- or latent myostatin by the monoclonal antibody SRK-015. J Biol Chem. 2020 Apr 17;295(16):5404-5418. Epub 2020 Feb 19. PMID: 32075906; PMCID: PMC7170532.

Bednarskia, D. M,; Lantzb, E. E; Bobstc, C. E; Eisenhuta, A. R.; Eyles, S. J.; Fey, J. P. Sterilization of Epidermal Growth Factor with Supercritical Carbon Dioxide and Peracetic Acid; Analysis of Changes at the Amino Acid and Protein Level. Elsevier, Volume 1868, Issue 2, February 2020.


Deramos King, C. M.; Dozier, C. S.; Campbell, J. L.; Curry, E. D.; Godri Pollitt, K. J. Long-term Leaching of Arsenic from Pressure Treated Playground Structures in the Northeastern United States. Elsevier, Volume 656, 15 March 2019, pp 834-842

Limpikirati, P; Pan, X; Vachet, R. W. Covalent Labeling with Diethylpyrocarbonate: Sensitive to the Residue Microenvironment, Providing Improved Analysis of Protein Higher Order Structure by Mass Spectrometry. Anal. Chem., Volume 91, Issue 13, 21 May 2019, pp 8516-8523

Martin, C. B.; Chaplin, V. D.; Eyles, S. J.; Knapp, M. J. Protein Flexibility of the α‑Ketoglutarate-Dependent Oxygenase Factor-Inhibiting HIF-1: Implications for Substrate Binding, Catalysis, and Regulation. Biochemistry, Volume 58, Issue 39, 9 September 2019, pp 4047-4057

Liang, C; Savinov, S. N.; Fejzo, J; Eyles, S. J.; Chen, J. Modulation of Amyloid-β42 Conformation by Small Molecules Through Nonspecific Binding. Journal of Chemistry and Computation, Volume 15, Issue 10, 2 September 2019, pp 5169-5174

Liu, J; Li, Y; Deol, K. K.; Strieter, E. R. Synthesis of Branched Triubiquitin Active-Site Directed Probes. Organic Letters, Volume 21, Issue 17, 9 August 2019, pp 6790-6794.

Huang, M; Liu, Y; Yang, G; Klier, J; Schiffman, J. D. Anionic Polymerization of Methylene Malonate for High Performance Coatings. ACS Applied Polymer Materials, Volume 1, Issue 4, 21 February 2019, pp 657-663


Puffal J, Mayfield JA, Moody DB, Morita YS. Demethylmenaquinone Methyl Transferase Is a Membrane Domain-Associated Protein Essential for Menaquinone Homeostasis in Mycobacterium smegmatis. Front Microbiol. 2018 Dec 18;9:3145. PMID: 30619211; PMCID: PMC6305584.

Limpikirati P, Liu T, Vachet RW. Covalent labeling-mass spectrometry with non-specific reagents for studying protein structure and interactions. Methods. 2018 Jul 15;144:79-93.  Epub 2018 Apr 7. PMID: 29630925; PMCID: PMC6051898.

Liu, J; Zeinert, R; Francis, L; Chien, P. Lon Recognition of the Replication Initiator DnaA Requires a Bipartite Degron. Molecular Microbiology, Volume 111, Issue 1, 4 October 2018, pp 176-186.

Fahie, M.A., Liang, L., Avelino, A.R. et al. Disruption of the open conductance in the β-tongue mutants of Cytolysin A. Sci Rep 8, 3796 (2018).

Flanagan, M. L.; Arguello, E; Colman, D. E.; Kim, J; Krejci, J. N.; Liu, S; Yao, Y; Zhang, Y; Gorin, D. J. A DNA-Conjugated Small Molecule Catalyst Enzyme Mimic for Site-Selective Ester Hydrolysis. Chem. Sci., Volume 9, Issue 8, 10 January 2018, pp 2105-2112.

Stansfield, H.E., Kulczewski, B.P., Lybrand, K.E. et al. Identifying protein interactions with metal-modified DNA using microarray technology. J Biol Inorg. Chem 14, 193–199 (2009).

Morshedlooa, M. R.; Salamib, S. A.; Nazerib, V; Maggic, F; Craker, L. Essential Oil Profile of Oregano (Origanum vulgare L.) Populations Grown Under Similar Soil and Climate Conditions. Elsevier, Volume 119, 1 September 2018, pp 183-190

Matthew Skinner, Brandon M. Johnston, Yalin Liu, Brenton Hammer, Ryan Selhorst, Ioanna Xenidou, Sarah L. Perry, and Todd Emrick. Biomacromolecules,  Volume19, Issue 8, 19 July 2018, pp 3377-3389.

Kato, F; Kittilstved, K. R. Site-Specific Doping of Mn2+ in a CdS-Based Molecular Cluster. Chemistry of Materials, Volume 30, Issue 14, 13 June 2018, pp 4720-4727.

Huang, H; Dillon, S; Ryan, K. C.; Campecino, J. O.; Watkins, O. E.; Cabelli, D. E.;Brunold, T. C.; Maroney, M. J. The Role of Mixed Amine/Amide Ligation in Nickel Superoxide Dismutase. Inorgnaic Chemistry, Volume 57, Issue 20, 3 October 2018, pp 12521-12535.

Ward, S. M.; Skinner, M; Saha, B; Emrick, T. Polymer−Temozolomide Conjugates as Therapeutics for Treating Glioblastoma. Molecular Pharmaceutics, Volume15, Issue 11, 15 October 2018, pp 5263-5276.


Liu, T; Marcinko, T. M.; Kiefer, P. A.; Vachet, R. W. Using Covalent Labeling and Mass Spectrometry To Study Protein Binding Sites of Amyloid Inhibiting Molecules. Anal. Chem., Volume 89, Issue 21, 13 October 2017, pp 11583-11591.

Han, J; Qiu, W; Campbell, E. C.; White, J. C.; Xing, B. Nylon Bristles and Elastomers Retain Centigram Levels of Triclosan and Other Chemicals from Toothpastes: Accumulation and Uncontrolled Release. Enviorn. Sci. Technol., Volume 51, Issue 21, 25 October 2017, pp 12264-12273.

Smith, C. E.; Xie, Z; Bâldea, I; Frisbie, C. D. Work Function and Temperature Dependence of Electron Tunneling Through an N-type Perylene Diimide Molecular Junction with Isocyanide Surface Linkers. Nanoscale, 2018, Volume 10, Issue 3, 24 November 2017, pp 964-975.

Dagbay, K. B.; Hardya, J. A. Multiple Proteolytic Events in Caspase-6 Self-Activation Impact Conformations of Discrete Structural Regions. Proceedings of the National Academy of Science 2017, Volume 114, Issue 38, 19 September 2017, E7977-E7986.

C. C. Neto, K. A. Penndorf, M. Feldman, S. Meron-Sudai, Z. Zakay-Rones, D. Steinberg, M. Fridman, Y. Kashman, I. Ginsburg, I. Ofek; E. I. Weiss. Characterization of Non-Dialyzable Constituents from Cranberry Juice that Inhibit Adhesion, Co-Aggregation and Biofilm Formation by Oral Bacteria. Food Funct. 2017, Volume 8, Issue 5, 21 April 2017, pp 1955-1965.

Kwasny, M. T.; Zhu, L; Hickner, M. A.; Tew, G. N. Utilizing Thiol–Ene Chemistry for Crosslinked Nickel Cation-Based Anion Exchange Membranes. Polymer Chemistry, Volume 56, Issue 3, 14 November 2017, pp 328–339.


Gupta, P; Song, B; Neto, C; Camesano, T. A. Atomic Force Microscopy-Guided Fractionation Reveals the Influence of Cranberry Phytochemicals on Adhesion of Escherichia Coli. Food and Function, Volume 7, Issue 6, 9 May 2016, pp 2655-2666.


Borotto, N. B.; Zhou, Y; Hollingsworth, S. R.; Hale, J. E.; Graban, E. M.; Vaughan, R. C.; Vachet, R. W. Investigating Therapeutic Protein Structure with Diethylpyrocarbonate Labeling and Mass Spectrometry. Anal. Chem., Volume 87, Issue 20, 23 September 2015, pp 10627-10634

He, T; Gershenson, A; Eyles, S. J.; Lee, Y-J; Liu, W. R.; Wang, J; Gao, J; Roberts, M. F. Fluorinated Aromatic Amino Acids Distinguish Cation- Interactions from Membrane Insertion. The American Society for Biochemistry and Molecular Biology, Inc. The Journal of Biological Chemistry, Volume 290, Issue 31,  July 31, 2015, pp. 19334 –19342.


Carpenter, J. L.; Caruso, F. L.; Tata, A; Vorsac, N; Neto, C. C. Variation in Proanthocyanidin Content and Composition Among Commonly Grown North American Cranberry Cultivars (Vaccinium Macrocarpon). J Sci Food Agric 2014; Volume 94, Issue 13, 14 February 2014, pp 2738-2745

Koshy, S. S.; Li, X; Eyles, S. J.; Weis, R. M.; Thompson, L. K. Hydrogen Exchange Differences between Chemoreceptor Signaling Complexes Localize to Functionally Important Subdomains. Biochemistry, Volume 53, Issue 49, 24 November 2014, pp 7755-7764


Koshy, S. S.; Eyles, S. J.; Weis, R. M.; Thompson, L. K. Hydrogen Exchange Mass Spectrometry of Functional Membrane-Bound Chemotaxis Receptor Complexes. Biochemistry 2013, Volume52, Issue 49, 6 November 2013, pp 8833-8842.

Nguyen, S. N.; Bobst, C. E.; Kaltashov, I. A. Mass Spectrometry-Guided Optimization and Characterization of a Biologically Active Transferrin−Lysozyme Model Drug Conjugate. Molecular Pharmaceutics, Volume 10, Issue 5, 27 March 2013, pp 1998-2007


Lienkamp, K; Madkour, A. E.; Kumar, K-N; Nsslein, K; Tew, G. N. Antimicrobial Polymers Prepared by Ring-Opening Metathesis Polymerization: Manipulating Antimicrobial Properties by Organic Counterion and Charge Density Variation. Chemistry A European Journal 2009, Voulme 15, Issue 43, 23 October 2009, pp 11715-11722

Please acknowledge the Mass Spectrometry Center in all publications which include mass spectral data in the following manner or similar: Mass spectral data were obtained at the University of Massachusetts Mass Spectrometry Core Facility, RRID:SCR_019063

Work that includes data generated on the Orbitrap Fusion instrument should acknowledge NIH support: Research reported in this publication was supported by the Office Of The Director, National Institutes Of Health of the National Institutes of Health under Award Number S10OD010645. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Work that includes data generated on the Synapt G2 instrument (in LSL S220) should acknowledge that this instrument was purchased with support from the Massachusetts Life Sciences Center.

Research Resource IDentifiers (RRID) are unique identifiers used as a means of identifying and tracking key resources used in research and to generate publications, and to improve transparency of research methods.

They are important for adherence to Rigor and Transparency requirements in NIH funded research, and are essential metrics to ensure continued institutional funding of core facilities.
For more information, please visit

The Association of Biomolecular Resource Facilities (ABRF) has published a guideline to use when considering whether or not to include core laboratory members on their publications, and we ask our users to consider this guide when publishing data generated by the Mass Spectrometry Center. ABRF guideline: