Publications

Send requests for reprints to mattbush@uw.edu.

Related resources: ORCID | Google Scholar | My Bibliography from NIH NCBI.

Preprints

  • A deep learning accelerated drug discovery platform for ultra-large virtual screens. Guangfeng Zhou, Domnita-Valeria Rusnac, Hahnbeom Park, Daniele Canzani, Hai Minh Nguyen, Lance Stewart, Matthew F. Bush, Phuong Tran Nguyen, Heike Wulff, Vladimir Yarov-Yarovoy, Ning Zheng, Frank DiMaio. bioRxiv , , DOI:10.1101/2024.03.28.587262. (Link)
  • Selecting Reducing Agents for Native Mass Spectrometry. Theresa A. Gozzo, Christopher J. Weir, May A. Constabel, Matthew F. Bush. ChemRxiv , , DOI: 10.26434/chemrxiv-2024-2nmh4. (Link)
  • HSPB5 disease-associated mutations have long-range effects on structure and dynamics through networks of quasi-ordered interactions. Christopher N. Woods, Lindsey D. Ulmer, Maria K. Janowska, Natalie L. Stone, Ellie I. James, Miklos Guttman, Matthew F. Bush, Rachel E. Klevit. bioRxiv , , DOI:10.1101/2022.05.30.493970. (Link)
  1. A deep learning accelerated drug discovery platform for ultra-large virtual screens. Guangfeng Zhou, Domnita-Valeria Rusnac, Hahnbeom Park, Daniele Canzani, Hai Minh Nguyen, Lance Stewart, Matthew F. Bush, Phuong Tran Nguyen, Heike Wulff, Vladimir Yarov-Yarovoy, Ning Zheng, Frank DiMaio. Nature Commun. 2024, 15, 7761. (Link)
    1. High-Performance Workflow for Identifying Site-Specific Crosslinks Originating from a Genetically Incorporated, Photoreactive Amino Acid. Lindsey D. Ulmer, Daniele Canzani, Christopher N. Woods, Natalie L. Stone, Maria K. Janowska, Rachel E. Klevit, Matthew F. Bush. J. Proteome Res. 2024, , in press. (Link)
    1. Metastability of Protein Solution Structures in the Absence of Solvent: Rugged Energy Landscapes and Glass-Like Behavior. Tyler C. Cropley, Fanny C. Liu, Mengqi Chai, Matthew F. Bush, Christian Bleiholder. J. Am. Chem. Soc. 2024, 146, 11115–11125. (Link)
    1. Drugs Form Ternary Complexes with Human Liver Fatty Acid Binding Protein (FABP1) and FABP1 Binding Alters Drug Metabolism. King Clyde B. Yabut, Alice Martynova, Abhinav Nath, Benjamin P. Zercher, Matthew F. Bush, Nina Isoherranen. Mol. Pharmcol. 2024, 105, 395-410. (Link)
    1. Quantitatively Differentiating Antibodies Using Charge-State Manipulation, Collisional Activation, and Ion Mobility – Mass Spectrometry. Theresa A. Gozzo, Matthew F. Bush. Anal. Chem. 2024, 96, 505–513. (Link)
    1. Elucidating the Impact of Bacterial Lipases, Human Serum Albumin, and FASII Inhibition on the Utilization of Exogenous Fatty Acids by Staphylococcus aureus. Emily L. Pruitt, Rutan Zhang, Dylan H. Ross, Nathaniel K. Ashford, Xi Chen, Francis Alonzo III, Matthew F. Bush, Brian J. Werth, Libin Xu. mSphere 2023, 8, e00368-23. (Link)
    1. Towards IMn with Electrostatic Drift Fields: Resetting the Potential of Trapped Ions Between Dimensions of Tandem Ion Mobility. Benjamin P. Zercher, Yuan Feng, Matthew F. Bush. Int. J. Mass Spectrom. 2024, 495, 117163. (Link)
      1. Sample pH Can Drift during Native Mass Spectrometry Experiments: Results from Ratiometric Fluorescence Imaging. Meagan M. Gadzuk-Shea, Evan E. Hubbard, Theresa A. Gozzo, Matthew F. Bush. J. Am. Soc. Mass Spectrom. 2023, 34, 1675–1684. (Link)
        1. Are the Gas-Phase Structures of Molecular Elephants Enduring or Ephemeral? Results from Time-Dependent, Tandem Ion Mobility. Benjamin P. Zercher, Seoyeon Hong, Addison E. Roush, Yuan Feng, Matthew F. Bush. Anal. Chem. 2023, 95, 9589–9597. (Link|PubMed)
          1. A Flexible, Modular Platform for Multidimensional Ion Mobility of Native-like Ions. Rachel M. Eaton, Benjamin Zercher, AnneClaire Wageman, Matthew F. Bush. J. Am. Soc. Mass Spectrom. 2023, 34, 1175–1185. (Link|PubMed)
            1. Effects of charge on protein ion structure: Lessons from cation-to-anion, proton-transfer reactions. Theresa A. Gozzo, Matthew F. Bush. Mass Spectrom. Reviews 2024, 43, 500-525. (Link)
            1. Enhancing the Depth of Analyses with Next-Generation Ion Mobility Experiments. Benjamin P. Zercher, Theresa A. Gozzo, AnneClaire Wageman, Matthew F. Bush. Annu. Rev. Anal. Chem. 2023, 16, 27–48. (Link | PubMed)
            1. Disordered Region Encodes α-crystallin Chaperone Activity Towards Lens Client γD-crystallin. Christopher N. Woods, Lindsey D. Ulmer, Miklos Guttman, Matthew F. Bush, Rachel E. Klevit. Proc. Natl. Acad. Sci. 2023, 120, e221376512. (Link|PubMed)
            1. High-Precision, Gas-Phase Hydrogen/Deuterium-Exchange Kinetics by Mass Spectrometry Enabled by Exchange Standards Sanjit S. Uppal, Abhigya Mookherjee, Rick Harkewicz, Sarah E. Beasley, Matthew F. Bush, Miklos Guttman. Anal. Chem. 2020, 92, 7725-7732. (Link|PubMed)
            1. FBXL5 Regulates IRP2 Stability in Iron Homeostasis via an Oxygen-Responsive [2Fe2S] Cluster. Hui Wang, Hui Shi, Malini Rajan, Elizabeth R. Canarie, Seoyeon Hong, Daniele Simoneschi, Michele Pagano, Matthew F. Bush, Stefan Stoll, Elizabeth A. Leibold, Ning Zheng. Mol. Cell 2020, 78,31-41. (Link)
            1. Degronomics: Mapping the Interacting Peptidome of a Ubiquitin Ligase Using an Integrative Mass Spectrometry Strategy. Daniele Canzani, Domnita̧ -Valeria Rusnac, Ning Zheng, Matthew F. Bush. Anal. Chem. 2019, 91, 12775-12783. (Link|PubMed)
            1. Collision-Induced Unfolding Is Sensitive to the Polarity of Proteins and Protein Complexes. Seoyeon Hong, Matthew F. Bush. J. Am. Soc. Mass Spectrom. 2019, 30, 2430–2437. (Link)
            1. Principles of Ion Selection, Alignment, and Focusing in Tandem Ion Mobility Implemented Using Structures for Lossless Ion Manipulations (SLIM). Rachel M. Eaton, Samuel J. Allen, Matthew F. Bush. J. Am. Soc. Mass Spectrom. 2019, 30, 1115-1125. (Link|PubMed)
            1. Determining Collision Cross‐Sections of Aromatic Compounds in Crude Oil by Using Aromatic Compound Mixture as Calibration Standard. Dongwan Lim; Kimberly L. Davidson; Seungwoo Son; Arif Ahmed; Matthew F. Bush; Sunghwan Kim. Bull. Korean Chem. Soc. 2019, 40, 122-127. (Link)
            1. Recommendations for Reporting Ion Mobility Mass Spectrometry Measurements. Gabelica, V.; Shvartsburg, A. A.; Afonso, C.; Barran, P.; Benesch, J. L.; Bleiholder, C.; Bowers, M. T.; Bilbao, A.; Bush, M. F.; Campbell, J. L.; Campuzano, I. D. G.; Causon, T. J.; Clowers, B. H.; Creaser, C.; De Pauw, E.; Far, J.; Fernandez-Lima, F.; Fjeldsted, J. C.; Giles, K.; Groessl, M.; Hogan, C. J.; Hann, S.; Kim, H. I.; Kurulugama, R. T.; May, J. C.; McLean, J. A.; Pagel, K.; Richardson, K.; Ridgeway, M. E.; Rosu, F.; Sobott, F.; Thalassinos, K.; Valentine, S. J.; Wyttenbach, T. Mass Spectrom. Rev. 2019, 38, 291-320. (Link)

            1. Recognition of Diglycine C-end Degron by CRL2KLHDC2 Ubiquitin Ligase. Domniţa-Valeria Rusnac, Hsiu-Chuan Lin, Daniele Canzani, Karena X. Tien, Thomas R. Hinds, Ashley F. Tsue, Matthew F. Bush, Hsueh-Chi S. Yen, Ning Zheng Mol. Cell 2018, 72, 813–822. (Link)

            1. Effects of Charge State on the Structures of Serum Albumin Ions in the Gas Phase: Insights from Cation-to-Anion Proton-Transfer Reactions, Ion Mobility, and Mass Spectrometry. Meagan M. Gadzuk-Shea, Matthew F. Bush. J. Phys. Chem. B 2018, 122, 9947–9955. (Link)

            1. Ion Mobility of Proteins in Nitrogen Gas: Effects of Charge State, Charge Distribution, and Structure. Daniele Canzani, Kenneth J. Laszlo, Matthew F. Bush. J. Phys. Chem. A 2018, 122, 5625−5634. (Link)

            1. Structural characterization of small molecular ions by ion mobility mass spectrometry in nitrogen drift gas: improving the accuracy of trajectory method calculations. Jong Wha Lee, Hyun Hee L. Lee, Kimberly L. Davidson, Matthew F. Bush, Hugh I. Kim. Analyst 2018, 143, 1786-1796. (Link)

            1. Collision Cross Sections and Ion Structures: Development of a General Calculation Method via High-quality Ion Mobility Measurements and Theoretical Modeling. Jong Wha Lee, Kimberly L. Davidson, Matthew F. Bush, Hugh I. Kim. Analyst 2017, 142, 4289–4298. (Link)

            1. Effects of Charge State, Charge Distribution, and Structure on the Ion Mobility of Protein Ions in Helium Gas: Results from Trajectory Method Calculations. Kenneth J. Laszlo, Matthew F. Bush. J. Phys. Chem. A 2017, 121, 7768–7777. (Link)

            1. Large-scale Structural Characterization of Drug and Drug-Like Compounds by High-Throughput Ion Mobility-Mass Spectrometry. Kelly M. Hines, Dylan Ross, Kimberly L. Davidson, Matthew F. Bush, Libin Xu. Anal. Chem. 2017, 89, 9023–9030. (Link)

            1. Interpreting the Collision Cross Sections of Native-Like Protein Ions: Insights from Cation-to-Anion Proton-Transfer Reactions. Kenneth J. Laszlo, Matthew F. Bush. Anal. Chem. 2017, 89, 7607–7614. (Link|PubMed)

            1. Structural Dynamics of Native-Like Ions in the Gas Phase: Results from Tandem Ion Mobility of Cytochrome c. Samuel J. Allen, Rachel M. Eaton, Matthew F. Bush. Anal. Chem. 2017, 89, 7527–7534. (Link)

            1. Effects of Solution Structure on the Folding of Lysozyme Ions in the Gas-Phase. Kenneth J. Laszlo, Eleanor B. Munger, Matthew F. Bush. J. Phys. Chem. B 2017, 121, 2759–2766. (Link|PubMed)

            1. Native-like and Denatured Cytochrome c Ions Yield Cation-to-Anion Proton-Transfer Products with Similar Collision Cross Sections. Kenneth J. Laszlo, John H. Buckner, Eleanor B. Munger, Matthew F. Bush. J. Am. Soc. Mass Spectrom. 2017, 28, 1382–1391. (Link|PubMed)

            1. Effects of Drift Gas Selection on the Ambient-Temperature, Ion Mobility Mass Spectrometry Analysis of Amino Acids. Kimberly L. Davidson and Matthew F. Bush. Anal. Chem. 2017, 89, 2017–2023. (Link)

            Droplets_TOC

            1. Nonspecific Aggregation in Native Electrokinetic Nanoelectrospray Ionization. Kimberly L. Davidson; Derek R. Oberreit; Christopher J. Hogan; Matthew F. Bush. Int. J. Mass Spectrom. 2017, 420, 35–42. (Link | Cover)
              • This research was selected for the cover of the special issue on “New developments and applications of mass spectrometry methods for studying non-covalent protein interactions”. (Cover)

            slim_toc

            1. Analysis of Native-Like Ions using Structures for Lossless Ion Manipulations. Samuel J. Allen, Rachel M. Eaton, and Matthew F. Bush. Anal. Chem. 2016, 88, 9118–9126. (Link)

            rf_cofinement_toc_2

            1. Radio-Frequency (RF) Confinement in Ion Mobility Spectrometry: Apparent Mobilities and Effective Temperatures. Samuel J. Allen, Matthew F. Bush. J. Am. Soc. Mass Spectrom. 2016, 27, 2054–2063. (Link)

            rational_peptide_TOC

            1. Toward a Rational Design of Highly Folded Peptide Cation Conformations. 3D Gas-Phase Ion Structures and Ion Mobility Characterization. Robert Pepin, Kenneth J. Laszlo, Aleš Marek, Bo Peng, Matthew F. Bush, Helène Lavanant, Carlos Afonso, František Tureček. J. Am. Soc. Mass Spectrom. 2016, 27, 1647–1660. (Link)

            Ubiquitin_CAPTR_TOC-01

            1. Folding of Protein Ions in the Gas Phase after Cation-to-Anion Proton-Transfer Reactions (CAPTR). Kenneth J. Laszlo, Eleanor B. Munger, and Matthew F. Bush. J. Am. Chem. Soc. 2016, 138, 9581–9588. (Link|PUBMED)

            thermal_breathing_TOC

            1. Does Thermal Breathing Affect Collision Cross Sections of Gas Phase Peptide Ions? An Ab Initio Molecular Dynamics Study. Robert Pepin, Alessio Petrone, Kenneth J. Laszlo, Matthew F. Bush, Xiaosong Li, and František Tureček. J. Phys. Chem. Lett. 2016, 7, 2765–2771. (Link|PubMed)

            toc_laser_activation

            1. Infrared Laser Activation of Soluble and Membrane Protein Assemblies in the Gas Phase. Victor A. Mikhailov, Idlir Liko, Todd H. Mize, Matthew F. Bush, Justin L.P. Benesch, Carol V. Robinson. Anal. Chem. 2016, 88, 7060–7067. (Link)

            GA

            1. Ion mobility mass spectrometry of peptide, protein, and protein complex ions using a radio-frequency confining drift cell. Samuel J. Allen, Kevin Giles, Tony Gilbert, Matthew F. Bush. Analyst 2016, 141, 884-891. (Link|PUBMED|PDF)
              • Selected for Hot original research articles in Analyst 2016. “This themed collection features the original research articles published in Analyst in 2016 marked as HOT, as recommended by referees.”
              • One of the top 25 most downloaded articles published in the Analyst in 2016. (Link)

            CAPTR_TOC_350

            1. Analysis of Native-Like Proteins and Protein Complexes Using Cation to Anion Proton Transfer Reactions (CAPTR). Kenneth J. Laszlo; Matthew F. Bush. J. Am. Soc. Mass Spectrom. 2015, 26, 2152-2161. (Link|PUBMED)
              • This article was highlighted in ASMS News and Views (Link)

            malic_acid_toc

            1. Collision cross section calibrants for negative ion mode traveling wave ion mobility-mass spectrometry. Jay G. Forsythe, Anton S. Petrov, Chelsea A. Walker, Samuel J. Allen, Jarrod S. Pellissier, Matthew F. Bush, Nicholas V. Hud, Facundo M. Fernández. Analyst 2015, 140, 6853-6861. (Link|PUBMED)

            photoleucine_toc

            1. Electron Transfer Reduction of the Diazirine Ring in Gas-Phase Peptide Ions. On the Peculiar Loss of [NH4O] from Photoleucine. Aleš Marek, Christopher J. Shaffer, Robert Pepin, Kristina Slováková, Kenneth J. Laszlo, Matthew F. Bush, František Tureček. J. Am. Soc. Mass. Spectrom. 2015, 26, 415-431. (Link|PUBMED)

            glggk

            1. Comprehensive Analysis of Gly-Leu-Gly-Gly-Lys Peptide Dication Structures and Cation-Radical Dissociations Following Electron Transfer: From Electron Attachment to Backbone Cleavage, Ion-Molecule Complexes, and Fragment Separation Robert Pepin, Kenneth J. Laszlo, Bo Peng, Aleš Marek, Matthew F. Bush, František Tureček. J. Phys. Chem. A 2014, 118, 308–324. (Link|PUBMED)

            toc_polarity_120-01

            1. Effects of Polarity on the Structures and Charge States of Native-like Proteins and Protein Complexes in the Gas Phase Samuel J. Allen, Alicia M. Schwartz, Matthew F. Bush. Anal. Chem. 2013, 85, 12055–12061. (Link|PUBMED)

            dn1e

            1. Hexamers of the Type II Secretion ATPase GspE from Vibrio cholerae with Increased ATPase Activity Connie Lu, Stewart Turley, Samuel T. Marionni, Young-Jun Park, Kelly K. Lee, Marcella Patrick, Ripal Shah, Maria Sandkvist, Matthew F. Bush, Wim G.J. Hol. Structure 2013, 21, 1707–1717. (Link|PUBMED)

            phosphopeptide

            1. Gas-Phase Structures of Phosphopeptide Ions: A Difficult Case František Tureček, Christopher L. Moss, Ioannis Pikalov, Robert Pepin, Kerim Gulyuz, Nicolas C. Polfer, Matthew F. Bush, Jeffery Brown, Jonathan Williams, Keith Richardson. Int. J. Mass Spectrom. 2013, 354–355, 249–256 . (Link)

            hydrazine_loos

            1. Electron Transfer Dissociation of Photolabeled Peptides. Backbone Cleavages Compete with Diazirine Ring Rearrangements Aleš Marek, Robert Pepin, Bo Peng, Kenneth J. Laszlo, Matthew F. Bush, František Tureček. J. Am. Soc. Mass Spectrom. 2013, 24, 1641–1653. (Link|PUBMED)

            cry2

            1. SCFFBXL3 ubiquitin ligase targets cryptochromes at their cofactor pocket Weiman Xing, Luca Busino, Thomas R. Hinds, Samuel T. Marionni, Nabiha H. Saifee, Matthew F. Bush, Michele Pagano, Ning Zheng. Nature 2013, 496, 64–68. (Link|PUBMED)

            Ion Mobility of Peptide Ions

            1. Ion mobility mass spectrometry of peptide ions: effects of drift gas and calibration strategies Matthew F. Bush, Iain D. G. Campuzano, Carol V. Robinson. Anal. Chem. 2012, 84, 7124–7130. (Link|PUBMED)

            1. Dissecting Heterogeneous Molecular Chaperone Complexes Using a Mass Spectrum Deconvolution Approach Florian Stengel, Andrew J. Baldwin, Matthew F. Bush, Gillian R. Hilton, Hadi Lioe, Eman Basha, Nomalie Jaya, Elizabeth Vierling, Justin L.P. Benesch. Chem. Biol. 2012, 19, 599–607. (Link|PUBMED)

            1. Traveling-wave ion mobility mass spectrometry of protein complexes: accurate calibrated collision cross-sections of human insulin oligomers Rune Salbo, Matthew F. Bush, Helle Naver, Iain Campuzano, Carol V. Robinson, Ingrid Pettersson, Thomas J. D. Jørgensen, Kim F. Haselmann. Rapid Commun. Mass Spectrom. 2012, 26, 1181–1193. (Link|PUBMED)

            Click for article.

            1. Assigning Structures to Gas-Phase Peptide Cations and Cation-Radicals. An Infrared Multiphoton Dissociation, Ion Mobility, Electron Transfer, and Computational Study of a Histidine Peptide Ion Christopher L. Moss, Julia Chamot-Rooke, Edith Nicol, Jeffery Brown, Iain Campuzano, Keith Richardson, Jonathan P. Williams, Matthew F. Bush, Benjamin Bythell, Bela Paizs, Frantisek Turecek. J. Phys. Chem B 2012, 116, 3445–3456. (Link|PUBMED)

            Click for article.

            1. Charge-State Dependent Compaction and Dissociation of Protein Complexes – Insights from Ion Mobility and Molecular Dynamics Zoe Hall, Argyris Politis, Matthew F. Bush, Lorna J. Smith, and Carol V. Robinson. J. Am. Chem. Soc. 2012, 134, 3429–3438. (Link|PUBMED)

            1. Structural Characterization of Drug-like Compounds by Ion Mobility Mass Spectrometry: Comparison of Theoretical and Experimentally Derived Nitrogen Collision Cross-sections Iain Campuzano, Matthew F. Bush, Carol V. Robinson, Claire Beaumont, Keith Richardson, Hyungjun Kim, Hugh I. Kim. Anal. Chem. 2012, 84, 1026-1033. (Link|PUBMED)

            Unfolding Landscapes & Noncovalent Adducts

            1. Gas-Phase Protein Assemblies: Unfolding Landscapes and Preserving Native-Like Structures Using Noncovalent Adducts Joanna Freeke, Matthew F. Bush, Carol V. Robinson, Brandon T. Ruotolo. Chem. Phys. Lett. 2012, 524, 1-9. (Link)

            1. Collision Cross Sections of Proteins and their Complexes: a Calibration Framework and Database for Gas-Phase Structural Biology Matthew F. Bush, Zoe Hall, Kevin Giles, John Hoyes, Carol V. Robinson, Brandon T. Ruotolo. Anal. Chem. 2010, 82, 9557-9565. (Link|PUBMED)

            1. Defining the mechanism of polymerization in the serpinopathies Ugo I. Ekeowa, Joanna Freeke, Elena Miranda, Bibek Gooptu, Matthew F. Bush, Juan Pérez, Jeff Teckman, Carol V. Robinson, David A. Lomas. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 17146–17151. (Link|PUBMED)

            Earlier Publications