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Shaw Lab at UNL Chemistry

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Cutting-edge bioanalytical technologies and methods to enable and inform chemical and structural biology approaches

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Selected Publications

Protein Complex Heterogeneity and Topology Revealed by Electron Capture Charge Reduction and Surface Induced Dissociation

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Shaw, J. B. [Co-Corresponding Author] et al. ACS Central Science DOI: 10.1021/acscentsci.4c00461

Here, we demonstrate the utility of native MS combined with gas phase charge reduction and surface induced dissociation for the characterization of protein complex topology and heterogeneity 

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Enhanced Top-Down Protein Characterization with Electron Capture Dissociation and Cyclic Ion Mobility Spectrometry

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Shaw, J. B. [Corresponding Author] et al. Anal. Chem. 2022, 94, 3888–3896.

In this study, we use ion mobility spectrometry to separate ECD product ions and decongest top-down MS/MS spectra for greatly increased protein sequence coverage and other figures of merit. 

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Charge Movement and Structural Changes in the Gas-Phase Unfolding of Multimeric Protein Complexes Captured by Native Top-Down Mass Spectrometry

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Zhou, M; Liu, W; Shaw, J. B. [Corresponding Author] Anal. Chem. 2020, 92, 1788-1795.

In this study, we use electron capture dissociation and ultraviolet photodissociation to track gas-phase unfolding of protein complexes with single amino acid resolution.

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Direct Determination of Antibody Chain Pairing by Top-down and Middle-down Mass Spectrometry Using Electron Capture Dissociation and Ultraviolet Photodissociation

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Shaw, J. B. [Corresponding Author] et al. Anal. Chem. 2020, 92, 766-773.

In this study, we developed methodology for determining antibody chain pairing from a single top-down or middle-down mass spectrum.

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 Sequencing Grade Tandem Mass Spectrometry for Top–Down Proteomics Using Hybrid Electron Capture Dissociation Methods in a Benchtop Orbitrap Mass Spectrometer

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Shaw, J. B. [Corresponding Author] et al. Anal. Chem. 2018, 90, 10819-10827.

In this work, we developed and implemented a new ExD device for fast and more extensive characterization of intact proteins. These gains extended to antibody sequence characterization.

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21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometer Greatly Expands Mass Spectrometry Toolbox

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Shaw, J. B. et al. J. Am. Soc. Mass Spectrom. 2016, 27, 1929-1937.

In this work, we designed and built a new spectrometer for a 21T Tesla FTICR MS.

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Complete Protein Characterization Using Top-Down Mass Spectrometry and Ultraviolet Photodissociation

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Shaw, J. B. et al. J. Am. Chem. Soc. 2013, 135, 12646-12651.

In this work, we implemented 193 nm ultraviolet photodissociation (UVPD) in an Orbitrap mass spectrometer for top-down protein characterization. We demonstrated unprecedent capabilities for intact protein characterization.

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Extending the Isotopically Resolved Mass Range of Orbitrap Mass Spectrometers

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Shaw, J. B. and Brodbelt, J. S. Anal. Chem. 2013, 85, 8313-8318.

In this study, we demonstrated simple modifications to Orbitrap mass spectrometers can significantly improve detection of large proteins, such as monoclonal antibodies.

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Complete List of Publications

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Most recent listed first

  • Jared B. Shaw, Sophie R. Harvey, Chen Du, Zhixin Xu, Regina M. Edgington, Eduardo Olmedillas, Erica Ollmann Saphire, and Vicki H. Wysocki ACS Central Science Article ASAP DOI: 10.1021/acscentsci.4c00461

  • Lantz, C.; Schrader, R.; Meeuwsen, J.; Shaw, J.; Goldberg, N. T.; Tichy, S.; Beckman, J.; Russell, D. H. Digital Quadrupole Isolation and Electron Capture Dissociation on an Extended Mass Range Q-TOF Provides Sequence and Structure Information on Proteins and Protein Complexes. J. Am. Soc. Mass Spectrom. 2023, 34 (8), 1753–1760. https://doi.org/10.1021/jasms.3c00184. 

  • Shaw, J. B. [Corresponding Author]; Cooper-Shepherd, D. A.; Hewitt, D.; Wildgoose, J. L.; Beckman, J. S.; Langridge, J. I.; Voinov, V. G. Enhanced Top-Down Protein Characterization with Electron Capture Dissociation and Cyclic Ion Mobility Spectrometry. Anal. Chem. 2022, 94 (9), 3888–3896. https://doi.org/10.1021/acs.analchem.1c04870.

  • Zhou, M.; Lee, J. Y.; Park, G. W.; Malhan, N.; Liu, T.; Shaw, J. B. [Corresponding Author] Evaluating the Performance of 193 Nm Ultraviolet Photodissociation for Tandem Mass Tag Labeled Peptides. Analytica 2021, 2 (4), 140–155. https://doi.org/10.3390/analytica2040014.

  • Shaw, J. B. Direct Determination of Antibody Chain Pairing. US Patent 11,152,198, 2021, October 19, 2021.

  • Novikova, I. V.; Zhou, M.; Du, C.; Parra, M.; Kim, D. N.; VanAernum, Z. L.; Shaw, J. B.; Hellmann, H.; Wysocki, V. H.; Evans, J. E. Tunable Heteroassembly of a Plant Pseudoenzyme–Enzyme Complex. ACS Chem. Biol. 2021, 16 (11), 2315–2325. https://doi.org/10.1021/acschembio.1c00475.

  • Gilchuk, P. et al. Proteo-Genomic Analysis Identifies Two Major Sites of Vulnerability on Ebolavirus Glycoprotein for Neutralizing Antibodies in Convalescent Human Plasma. Front. Immunol. 2021, 12, 706757. https://doi.org/10.3389/fimmu.2021.706757.

  • Beckman, J. S.; Voinov, V. G.; Hare, M.; Sturgeon, D.; Vasil’ev, Y.; Oppenheimer, D.; Shaw, J. B.; Wu, S.; Glaskin, R.; Klein, C.; Schwarzer, C.; Stafford, G. Improved Protein and PTM Characterization with a Practical Electron-Based Fragmentation on Q-TOF Instruments. J. Am. Soc. Mass Spectrom. 2021, 32 (8), 2081–2091. https://doi.org/10.1021/jasms.0c00482.

  • Zhou, M.; Liu, W.; Shaw, J. B. [Corresponding Author] Charge Movement and Structural Changes in the Gas-Phase Unfolding of Multimeric Protein Complexes Captured by Native Top-Down Mass Spectrometry. Anal. Chem. 2020, 92 (2), 1788–1795. https://doi.org/10.1021/acs.analchem.9b03469.

  • Velivelli, S. L. S.; Czymmek, K. J.; Li, H.; Shaw, J. B.; Buchko, G. W.; Shah, D. M. Antifungal Symbiotic Peptide NCR044 Exhibits Unique Structure and Multifaceted Mechanisms of Action That Confer Plant Protection. Proc. Natl. Acad. Sci. U.S.A. 2020, 117 (27), 16043–16054. https://doi.org/10.1073/pnas.2003526117.

  • Srzentić, K. et al. Interlaboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2020, 31 (9), 1783–1802. https://doi.org/10.1021/jasms.0c00036.

  • Shaw, J. B. [Corresponding Author]; Liu, W.; Vasil′ev, Y. V.; Bracken, C. C.; Malhan, N.; Guthals, A.; Beckman, J. S.; Voinov, V. G. Direct Determination of Antibody Chain Pairing by Top-down and Middle-down Mass Spectrometry Using Electron Capture Dissociation and Ultraviolet Photodissociation. Anal. Chem. 2020, 92 (1), 766–773. https://doi.org/10.1021/acs.analchem.9b03129.

  • Samarah, L. Z.; Khattar, R.; Tran, T. H.; Stopka, S. A.; Brantner, C. A.; Parlanti, P.; Veličković, D.; Shaw, J. B.; Agtuca, B. J.; Stacey, G.; Paša-Tolić, L.; Tolić, N.; Anderton, C. R.; Vertes, A. Single-Cell Metabolic Profiling: Metabolite Formulas from Isotopic Fine Structures in Heterogeneous Plant Cell Populations. Anal. Chem. 2020, 92 (10), 7289–7298. https://doi.org/10.1021/acs.analchem.0c00936.

  • Nagy, G.; Attah, I. K.; Conant, C. R.; Liu, W.; Garimella, S. V. B.; Gunawardena, H. P.; Shaw, J. B.; Smith, R. D.; Ibrahim, Y. M. Rapid and Simultaneous Characterization of Drug Conjugation in Heavy and Light Chains of a Monoclonal Antibody Revealed by High-Resolution Ion Mobility Separations in SLIM. Anal. Chem. 2020, 92 (7), 5004–5012. https://doi.org/10.1021/acs.analchem.9b05209.

  • Stopka, S. A.; Samarah, L. Z.; Shaw, J. B.; Liyu, A. V.; Veličković, D.; Agtuca, B. J.; Kukolj, C.; Koppenaal, D. W.; Stacey, G.; Paša-Tolić, L.; Anderton, C. R.; Vertes, A. Ambient Metabolic Profiling and Imaging of Biological Samples with Ultrahigh Molecular Resolution Using Laser Ablation Electrospray Ionization 21 Tesla FTICR Mass Spectrometry. Anal. Chem. 2019, 91 (8), 5028–5035. https://doi.org/10.1021/acs.analchem.8b05084.

  • Novikova, I.; Zhou, M.; Shaw, J.; Hellmann, H.; Evans, J. E. Dual Native MS and Cryo-EM Approach to Resolve Heteromeric Protein Assemblies and Subunit Stoichiometry. Microsc Microanal 2019, 25 (S2), 1214–1215. https://doi.org/10.1017/S1431927619006809.

  • Boiteau, R. M.; Fansler, S. J.; Farris, Y.; Shaw, J. B.; Koppenaal, D. W.; Pasa-Tolic, L.; Jansson, J. K. Siderophore Profiling of Co-Habitating Soil Bacteria by Ultra-High Resolution Mass Spectrometry. Metallomics 2019, 11 (1), 166–175. https://doi.org/10.1039/C8MT00252E.

  • Shaw, J. B. [Corresponding Author]; Malhan, N.; Vasil’ev, Y. V.; Lopez, N. I.; Makarov, A.; Beckman, J. S.; Voinov, V. G. Sequencing Grade Tandem Mass Spectrometry for Top–Down Proteomics Using Hybrid Electron Capture Dissociation Methods in a Benchtop Orbitrap Mass Spectrometer. Anal. Chem. 2018, 90 (18), 10819–10827. https://doi.org/10.1021/acs.analchem.8b01901.

  • Shaw, J. B.; Gorshkov, M. V.; Wu, Q.; Paša-Tolić, L. High Speed Intact Protein Characterization Using 4X Frequency Multiplication, Ion Trap Harmonization, and 21 Tesla FTICR-MS. Anal. Chem. 2018, 90 (9), 5557–5562. https://doi.org/10.1021/acs.analchem.7b04606.

  • LeDuc, R. D. et al. ProForma: A Standard Proteoform Notation. J. Proteome Res. 2018, 17 (3), 1321–1325. https://doi.org/10.1021/acs.jproteome.7b00851.

  • Gargano, A. F. G.; Shaw, J. B.; Zhou, M.; Wilkins, C. S.; Fillmore, T. L.; Moore, R. J.; Somsen, G. W.; Paša-Tolić, L. Increasing the Separation Capacity of Intact Histone Proteoforms Chromatography Coupling Online Weak Cation Exchange-HILIC to Reversed Phase LC UVPD-HRMS. J. Proteome Res. 2018, 17 (11), 3731–3800. https://doi.org/10.1021/acs.jproteome.8b00458.

  • Callister, S. J.; Fillmore, T. L.; Nicora, C. D.; Shaw, J. B.; Purvine, S. O.; Orton, D. J.; White, R. A.; Moore, R. J.; Burnet, M. C.; Nakayasu, E. S.; Payne, S. H.; Jansson, J. K.; Paša-Tolić, L. Addressing the Challenge of Soil Metaproteome Complexity by Improving Metaproteome Depth of Coverage through Two-Dimensional Liquid Chromatography. Soil Biol. Biochem. 2018, 125, 290–299. https://doi.org/10.1016/j.soilbio.2018.07.018.

  • Boiteau, R. M.; Shaw, J. B.; Pasa-Tolic, L.; Koppenaal, D. W.; Jansson, J. K. Micronutrient Metal Speciation Is Controlled by Competitive Organic Chelation in Grassland Soils. Soil Biol. Biochem. 2018, 120, 283–291. https://doi.org/10.1016/j.soilbio.2018.02.018.

  • Walker, L. R.; Tfaily, M. M.; Shaw, J. B.; Hess, N. J.; Paša-Tolić, L.; Koppenaal, D. W. Unambiguous Identification and Discovery of Bacterial Siderophores by Direct Injection 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Metallomics 2017, 9 (1), 82–92. https://doi.org/10.1039/c6mt00201c.

  • Staley, C. et al. Diurnal Cycling of Rhizosphere Bacterial Communities Is Associated with Shifts in Carbon Metabolism. Microbiome 2017, 5 (1). https://doi.org/10.1186/s40168-017-0287-1.

  • Qiu, J.; Yu, K.; Fei, X.; Liu, Y.; Nakayasu, E. S.; Piehowski, P. D.; Shaw, J. B.; Puvar, K.; Das, C.; Liu, X.; Luo, Z.-Q. A Unique Deubiquitinase That Deconjugates Phosphoribosyl-Linked Protein Ubiquitination. Cell Res. 2017, 27, 865–881. https://doi.org/10.1038/cr.2017.66.

  • Park, J. et al. Informed-Proteomics: Open-Source Software Package for Top-down Proteomics. Nat. Methods 2017, 14 (9), 909–914. https://doi.org/10.1038/nmeth.4388.

  • Blair, S. L.; MacMillan, A. C.; Drozd, G. T.; Goldstein, A. H.; Chu, R. K.; Paša-Tolić, L.; Shaw, J. B.; Tolić, N.; Lin, P.; Laskin, J.; Laskin, A.; Nizkorodov, S. A. Molecular Characterization of Organosulfur Compounds in Biodiesel and Diesel Fuel Secondary Organic Aerosol. Environ. Sci. Technol. 2017, 51 (1), 119–127. https://doi.org/10.1021/acs.est.6b03304.

  • Shaw, J. B.; Robinson, E. W.; Paša-Tolić, L. Vacuum Ultraviolet Photodissociation and FT-ICR Mass Spectrometry: Revisited. Anal. Chem. 2016, 88 (6), 3019–3023. https://doi.org/10.1021/acs.analchem.6b00148.

  • Shaw, J. B.; Lin, T.-Y.; Leach, F. E.; Tolmachev, A. V.; Tolić, N.; Robinson, E. W.; Koppenaal, D. W.; Paša-Tolić, L. 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometer Greatly Expands Mass Spectrometry Toolbox. J. Am. Soc. Mass Spectrom. 2016, 27, 1929–1937. https://doi.org/10.1007/s13361-016-1507-9.

  • Cotham, V. C.; Shaw, J. B.; Brodbelt, J. S. High-Throughput Bioconjugation for Enhanced 193 Nm Photodissociation via Droplet Phase Initiated Ion/Ion Chemistry Using a Front-End Dual Spray Reactor. Anal. Chem. 2015, 87 (18), 9396–9402. https://doi.org/10.1021/acs.analchem.5b02242.

  • Dang, X. et al. The First Pilot Project of the Consortium for Top-down Proteomics: A Status Report. PROTEOMICS 2014, 14 (10), 1130–1140. https://doi.org/10.1002/pmic.201300438.

  • Cannon, J. R.; Cammarata, M. B.; Robotham, S. A.; Cotham, V. C.; Shaw, J. B.; Fellers, R. T.; Early, B. P.; Thomas, P. M.; Kelleher, N. L.; Brodbelt, J. S. Ultraviolet Photodissociation for Characterization of Whole Proteins on a Chromatographic Time Scale. Anal. Chem. 2014, 86 (4), 2185–2192. https://doi.org/10.1021/ac403859a.

  • Xu, Z.; Shaw, J. B.; Brodbelt, J. S. Comparison of MS/MS Methods for Characterization of DNA/Cisplatin Adducts. J. Am. Soc. Mass Spectrom. 2013, 24 (2), 265–273.

  • Shaw, J. B.; Li, W.; Holden, D. D.; Zhang, Y.; Griep-Raming, J.; Fellers, R. T.; Early, B. P.; Thomas, P. M.; Kelleher, N. L.; Brodbelt, J. S. Complete Protein Characterization Using Top-Down Mass Spectrometry and Ultraviolet Photodissociation. J. Am. Chem. Soc. 2013, 135 (34), 12646–12651. https://doi.org/10.1021/ja4029654.

  • Shaw, J. B.; Kaplan, D. A.; Brodbelt, J. S. Activated Ion Negative Electron Transfer Dissociation of Multiply Charged Peptide Anions. Anal. Chem. 2013, 85 (9), 4721–4728. https://doi.org/10.1021/ac4005315.

  • Shaw, J. B.; Brodbelt, J. S. Extending the Isotopically Resolved Mass Range of Orbitrap Mass Spectrometers. Anal. Chem. 2013, 85 (17), 8313–8318. https://doi.org/10.1021/ac401634b.

  • Madsen, J. A.; Xu, H.; Robinson, M. R.; Horton, A. P.; Shaw, J. B.; Giles, D. K.; Kaoud, T. S.; Dalby, K. N.; Trent, M. S.; Brodbelt, J. S. High-Throughput Database Search and Large-Scale Negative Polarity LC-MS/MS with Ultraviolet Photodissociation for Complex Proteomic Samples. Mol. Cell. Proteomics 2013, 10.1074/mcp.O113.028258. https://doi.org/10.1074/mcp.O113.028258.

  • Madsen, J. A.; Ko, B. J.; Xu, H.; Iwashkiw, J. A.; Robotham, S. A.; Shaw, J. B.; Feldman, M. F.; Brodbelt, J. S. Concurrent Automated Sequencing of the Glycan and Peptide Portions of O-Linked Glycopeptide Anions by Ultraviolet Photodissociation Mass Spectrometry. Anal. Chem. 2013, 85 (19), 9253–9261. https://doi.org/10.1021/ac4021177.

  • Shaw, J. B.; Madsen, J. A.; Xu, H.; Brodbelt, J. S. Systematic Comparison of Ultraviolet Photodissociation and Electron Transfer Dissociation for Peptide Anion Characterization. J. Am. Soc. Mass Spectrom. 2012, 23 (10), 1707–1715.

  • Shaw, J. B.; Ledvina, A. R.; Zhang, X.; Julian, R. R.; Brodbelt, J. S. Tyrosine Deprotonation Yields Abundant and Selective Backbone Cleavage in Peptide Anions upon Negative Electron Transfer Dissociation and Ultraviolet Photodissociation. J. Am. Chem. Soc. 2012, 134 (38), 15624–15627.

  • Han, S.-W.; Lee, S.-W.; Bahar, O.; Schwessinger, B.; Robinson, M. R.; Shaw, J. B.; Madsen, J. A.; Brodbelt, J. S.; Ronald, P. C. Tyrosine Sulfation in a Gram-Negative Bacterium. Nat. Commun. 2012, 3, 1153. https://doi.org/10.1038/ncomms2157.

  • Vasicek, L. A.; Ledvina, A. R.; Shaw, J. B.; Griep-Raming, J.; Westphall, M. S.; Coon, J. J.; Brodbelt, J. S. Implementing Photodissociation in an Orbitrap Mass Spectrometer. J. Am. Soc. Mass Spectrom. 2011, 22 (6), 1105–1108. https://doi.org/10.1007/s13361-011-0119-7.

  • Shaw, J. B.; Brodbelt, J. S. Analysis of Protein Digests by Transmission-Mode Desorption Electrospray Ionization Mass Spectrometry with Ultraviolet Photodissociation. Int. J. Mass Spectrom. 2011, 308 (2), 203–208. https://doi.org/10.1016/j.ijms.2011.08.030.

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