Computational Strategies and Challenges for Using Native Ion Mobility Mass Spectrometry in Biophysics and Structural Biology
Open accessPublished version of a preprint
Abstract
Native mass spectrometry (MS) allows the interrogation of structural aspects of macromolecules in the gas phase, under the premise of having initially maintained their solution-phase noncovalent interactions intact. In the more than 25 years since the first reports, the utility of native MS has become well established in the structural biology community. The experimental and technological advances during this time have been rapid, resulting in dramatic increases in sensitivity, mass range, resolution, and complexity of possible experiments. As experimental methods have improved, there have been accompanying developments in computational approaches for analyzing and exploiting the profusion of MS data in a structural and biophysical context. In this perspective, we consider the computational strategies currently being employed by the community, aspects of best practice, and the challenges that remain to be addressed. Our perspective is based on discussions within the European Cooperation in Science and Technology Action on Native Mass Spectrometry and Related Methods for Structural Biology (EU COST Action BM1403), which involved participants from across Europe and North America. It is intended not as an in-depth review but instead to provide an accessible introduction to and overview of the topic-to inform newcomers to the field and stimulate discussions in the community about addressing existing challenges. Our complementary perspective (http://dx.doi.org/10.1021/acs.analchem.9b05792) focuses on software tools available to help researchers tackle some of the challenges enumerated here.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Spectral interpretation of native MS has largely relied on manual analysis, although deconvolution software such as UniDec and iFAMS has been developed in recent years.
“Spectral interpretation of native MS has largely relied on manual analysis, although deconvolution software such as UniDec and iFAMS has been developed in recent years.60,114”
From Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry (2020) · cites this paper as [60]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Lanucara, F., Holman, S. W., Gray, C. J., & Eyers, C. E. (2014) · Nature Chemistry · doi:10.1038/nchem.1889 · Cited by 901 · see citing works
Bush, M. F., Hall, Z., Giles, K., Hoyes, J. B., Robinson, C. V., & Ruotolo, B. T. (2010) · Analytical Chemistry · doi:10.1021/ac1022953 · Cited by 798 · see citing works
Recommendations for reporting ion mobility Mass Spectrometry measurements
Gabelica, V., Shvartsburg, A. A., Afonso, C., Barran, P., Benesch, J. L. P., Bleiholder, C., Bowers, M. T., Bilbao, A., Bush, M. F., Campbell, J. L., et al. (2019) · Mass Spectrometry Reviews · doi:10.1002/mas.21585 · Cited by 493 · see citing works
Self-citationFundamentals of ion mobility spectrometry
Gabelica, V., & Marklund, E. (2017) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2017.10.022 · Cited by 447 · see citing works
Self-citationBreuker, K., & McLafferty, F. W. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0807005105 · Cited by 422 · see citing works
Protein Complexes in the Gas Phase: Technology for Structural Genomics and Proteomics
Benesch, J. L. P., Ruotolo, B. T., Simmons, D. A., & Robinson, C. V. (2007) · Chemical Reviews · doi:10.1021/cr068289b · Cited by 408 · see citing works
Self-citationFundamentals of ion mobility spectrometry
Gabelica, V., & Marklund, E. G. (2018) · Archive ouverte UNIGE (University of Geneva) · Cited by 375 · see citing works
Self-citationCollision Cross Sections for Structural Proteomics
Marklund, E. G., Degiacomi, M. T., Robinson, C. V., Baldwin, A. J., & Benesch, J. L. P. (2015) · Structure · doi:10.1016/j.str.2015.02.010 · Cited by 270 · see citing works
Self-citationHall, Z., Politis, A., Bush, M. F., Smith, L. J., & Robinson, C. V. (2012) · Journal of the American Chemical Society · doi:10.1021/ja2096859 · Cited by 267 · see citing works
Self-citationMass spectrometry: come of age for structural and dynamical biology
Benesch, J. L. P., & Ruotolo, B. T. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.08.002 · Cited by 264 · see citing works
Self-citationQuaternary dynamics and plasticity underlie small heat shock protein chaperone function
Stengel, F., Baldwin, A. J., Painter, A. J., Jaya, N., Basha, E., Kay, L. E., Vierling, E., Robinson, C. V., & Benesch, J. L. P. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0910126107 · Cited by 242 · see citing works
Self-citationProtomers of Benzocaine: Solvent and Permittivity Dependence
Warnke, S., Seo, J., Boschmans, J., Sobott, F., Scrivens, J. H., Bleiholder, C., Bowers, M. T., Gewinner, S., Schöllkopf, W., Pagel, K., et al. (2015) · Journal of the American Chemical Society · doi:10.1021/jacs.5b01338 · Cited by 224 · see citing works
Self-citationThe diverse and expanding role of mass spectrometry in structural and molecular biology
Lössl, P., van de Waterbeemd, M., & Heck, A. J. (2016) · The EMBO Journal · doi:10.15252/embj.201694818 · Cited by 222 · see citing works
Bleiholder, C., Wyttenbach, T., & Bowers, M. T. (2011) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2011.06.014 · Cited by 215 · see citing works
Integrating diverse data for structure determination of macromolecular assemblies
Alber, F., Förster, F., Korkin, D., Topf, M., & Sali, A. (2008) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.77.060407.135530 · Cited by 206 · see citing works
Mass Spectrometry of Protein Complexes: From Origins to Applications
Mehmood, S., Allison, T. M., & Robinson, C. V. (2015) · Annual Review of Physical Chemistry · doi:10.1146/annurev-physchem-040214-121732 · Cited by 200 · see citing works
Self-citationIon Mobility Analysis of Molecular Dynamics
Wyttenbach, T., Pierson, N. A., Clemmer, D. E., & Bowers, M. T. (2013) · Annual Review of Physical Chemistry · doi:10.1146/annurev-physchem-040513-103644 · Cited by 188 · see citing works
Mass Measurements of Increased Accuracy Resolve Heterogeneous Populations of Intact Ribosomes
McKay, A. R., Ruotolo, B. T., Ilag, L. L., & Robinson, C. V. (2006) · Journal of the American Chemical Society · doi:10.1021/ja061468q · Cited by 177 · see citing works
AVERAGE CROSS-SECTIONAL AREAS OF MOLECULES BY GASEOUS DIFFUSION METHODS
Mack, E. (1925) · Journal of the American Chemical Society · doi:10.1021/ja01687a007 · Cited by 171 · see citing works
A mass spectrometry–based hybrid method for structural modeling of protein complexes
Politis, A., Stengel, F., Hall, Z., Hernández, H., Leitner, A., Walzthoeni, T., Robinson, C. V., & Aebersold, R. H. (2014) · Nature Methods · doi:10.1038/nmeth.2841 · Cited by 153 · see citing works
Self-citationHigh-Resolution Ion Cyclotron Mobility Spectrometry
Merenbloom, S. I., Glaskin, R. S., Henson, Z. B., & Clemmer, D. E. (2009) · Analytical Chemistry · doi:10.1021/ac801880a · Cited by 149 · see citing works
Benchmark Comparison for a Multi-Processing Ion Mobility Calculator in the Free Molecular Regime
Shrivastav, V., Nahin, M., Hogan, C. J., & Larriba‐Andaluz, C. (2017) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-017-1661-8 · Cited by 146 · see citing works
Zhong, Y., Hyung, S., & Ruotolo, B. T. (2011) · The Analyst · doi:10.1039/c0an00987c · Cited by 143 · see citing works
The mobile proton hypothesis in fragmentation of protonated peptides: A perspective
Boyd, R. K., & Somogyi, Á. (2010) · Journal of the American Society for Mass Spectrometry · doi:10.1016/j.jasms.2010.04.017 · Cited by 141 · see citing works
Hilton, G. R., & Benesch, J. L. P. (2012) · Journal of The Royal Society Interface · doi:10.1098/rsif.2011.0823 · Cited by 140 · see citing works
Self-citationPolitis, A., Park, A. Y., Hyung, S., Barsky, D., Ruotolo, B. T., & Robinson, C. V. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012080 · Cited by 137 · see citing works
Self-citationProjected Area of Convex Bodies
VOUK, V. (1948) · Nature · doi:10.1038/162330a0 · Cited by 136 · see citing works
Mass Spectrometry Methods for Studying Structure and Dynamics of Biological Macromolecules
Konermann, L., Vahidi, S., & Sowole, M. A. (2013) · Analytical Chemistry · doi:10.1021/ac4039306 · Cited by 136 · see citing works
Ben‐Nissan, G., & Sharon, M. (2017) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2017.10.026 · Cited by 124 · see citing works
Self-citationHall, Z., Politis, A., & Robinson, C. V. (2012) · Structure · doi:10.1016/j.str.2012.07.001 · Cited by 111 · see citing works
Self-citationThe Polydispersity of αB-Crystallin Is Rationalized by an Interconverting Polyhedral Architecture
Baldwin, A. J., Lioe, H., Hilton, G. R., Baker, L. A., Rubinstein, J. L., Kay, L. E., & Benesch, J. L. P. (2011) · Structure · doi:10.1016/j.str.2011.09.015 · Cited by 106 · see citing works
Self-citationCompaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry
Porrini, M., Rosu, F., Rabin, C., Darré, L., Gómez, H., Orozco, M., & Gabelica, V. (2017) · ACS Central Science · doi:10.1021/acscentsci.7b00084 · Cited by 105 · see citing works
Self-citationPacholarz, K. J., Porrini, M., Garlish, R. A., Burnley, R. J., Taylor, R. J., Henry, A. J., & Barran, P. E. (2014) · Angewandte Chemie International Edition · doi:10.1002/anie.201402863 · Cited by 104 · see citing works
Self-citationUncertainty in integrative structural modeling
Schneidman‐Duhovny, D., Pellarin, R., & Šali, A. (2014) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2014.08.001 · Cited by 102 · see citing works
Intrinsically Disordered p53 and Its Complexes Populate Compact Conformations in the Gas Phase
Pagel, K., Natan, E., Hall, Z., Fersht, A. R., & Robinson, C. V. (2012) · Angewandte Chemie International Edition · doi:10.1002/anie.201203047 · Cited by 94 · see citing works
Gas Phase Stability of Protein Ions in a Cyclic Ion Mobility Spectrometry Traveling Wave Device
Eldrid, C., Ujma, J., Kalfas, S., Tomczyk, N., Giles, K., Morris, M., & Thalassinos, K. (2019) · Analytical Chemistry · doi:10.1021/acs.analchem.8b05641 · Cited by 93 · see citing works
Self-citationMass spectrometry-enabled structural biology of membrane proteins
Calabrese, A. N., & Radford, S. E. (2018) · Methods · doi:10.1016/j.ymeth.2018.02.020 · Cited by 91 · see citing works
Proteins, Lipids, and Water in the Gas Phase
van der Spoel, D., Marklund, E. G., Larsson, D. S. D., & Caleman, C. (2010) · Macromolecular Bioscience · doi:10.1002/mabi.201000291 · Cited by 89 · see citing works
Self-citationIntegrating mass spectrometry with MD simulations reveals the role of lipids in Na+/H+ antiporters
Landreh, M., Marklund, E. G., Uzdavinys, P., Degiacomi, M. T., Coincon, M., Gault, J., Gupta, K., Liko, I., Benesch, J. L. P., Drew, D., et al. (2017) · Nature Communications · doi:10.1038/ncomms13993 · Cited by 84 · see citing works
Self-citationSalt Bridge Rearrangement (SaBRe) Explains the Dissociation Behavior of Noncovalent Complexes
Loo, R. R. O., & Loo, J. A. (2016) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-016-1375-3 · Cited by 82 · see citing works
Rolland, A. D., & Prell, J. S. (2019) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2019.04.023 · Cited by 80 · see citing works
On the Zwitterionic Nature of Gas-Phase Peptides and Protein Ions
Marchese, R., Grandori, R., Carloni, P., & Raugei, S. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000775 · Cited by 77 · see citing works
Self-citationBakhtiari, M., & Konermann, L. (2019) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.8b12173 · Cited by 74 · see citing works
Unique insights to intrinsically disordered proteins provided by ion mobility mass spectrometry
Stuchfield, D., & Barran, P. (2018) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2018.01.007 · Cited by 72 · see citing works
Self-citationMarchand, A., Livet, S., Rosu, F., & Gabelica, V. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.7b01736 · Cited by 71 · see citing works
Self-citationMeyer, T., Gabelica, V., Grubmüller, H., & Orozco, M. (2012) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.1130 · Cited by 67 · see citing works
Self-citationCharacterizing the Conformationome: Toward a Structural Understanding of the Proteome
Clemmer, D. E., Russell, D. H., & Williams, E. R. (2017) · Accounts of Chemical Research · doi:10.1021/acs.accounts.6b00548 · Cited by 66 · see citing works
On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys
Karaca, E., & Bonvin, A. M. J. J. (2013) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444913007063 · Cited by 58 · see citing works
Konermann, L., Metwally, H., McAllister, R. G., & Popa, V. (2018) · Methods · doi:10.1016/j.ymeth.2018.04.010 · Cited by 58 · see citing works
Triple-Stage Mass Spectrometry Unravels the Heterogeneity of an Endogenous Protein Complex
Ben-Nissan, G., Belov, M. E., Morgenstern, D., Levin, Y., Dym, O., Arkind, G., Lipson, C., Makarov, A. A., & Sharon, M. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.7b00518 · Cited by 54 · see citing works
Self-citationAn Atomistic View to the Gas Phase Proteome
Meyer, T., de la Cruz, X., & Orozco, M. (2009) · Structure · doi:10.1016/j.str.2008.11.006 · Cited by 52 · see citing works
D’Urzo, A., Konijnenberg, A., Rossetti, G., Habchi, J., Li, J., Carloni, P., Sobott, F., Longhi, S., & Grandori, R. (2014) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-014-1048-z · Cited by 52 · see citing works
Self-citationWang, G., de Jong, R. N., van den Bremer, E. T. J., Parren, P. W. H. I., & Heck, A. J. R. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.6b05129 · Cited by 52 · see citing works
A Computational Model for Protein Ionization by Electrospray Based on Gas-Phase Basicity
Marchese, R., Grandori, R., Carloni, P., & Raugei, S. (2012) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-012-0449-0 · Cited by 51 · see citing works
Self-citationTowards the analysis of high molecular weight proteins and protein complexes using TIMS-MS
Benigni, P., Marin, R., Molano-Arévalo, J. C., Garabedian, A., Wolff, J. J., Ridgeway, M. E., Park, M. A., & Fernandez-Lima, F. A. (2016) · International Journal for Ion Mobility Spectrometry · doi:10.1007/s12127-016-0201-8 · Cited by 50 · see citing works
It takes a dimer to tango: Oligomeric small heat shock proteins dissociate to capture substrate
Santhanagopalan, I., Degiacomi, M. T., Cooper-Shepherd, D. A., Hochberg, G. K. A., Benesch, J. L. P., & Vierling, E. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.ra118.005421 · Cited by 50 · see citing works
Self-citationXia, H., & Attygalle, A. B. (2017) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-017-1806-9 · Cited by 48 · see citing works
Standard Proteoforms and Their Complexes for Native Mass Spectrometry
Schachner, L. F., Ives, A. N., McGee, J. P., Melani, R. D., Kafader, J. O., Compton, P. D., Patrie, S. M., & Kelleher, N. L. (2019) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-019-02191-w · Cited by 48 · see citing works
Proton Dynamics in Protein Mass Spectrometry
Li, J., Lyu, W., Rossetti, G., Konijnenberg, A., Natalello, A., Ippoliti, E., Orozco, M., Sobott, F., Grandori, R., & Carloni, P. (2017) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.7b00127 · Cited by 47 · see citing works
Self-citationHansen, K., Lau, A. M. C., Giles, K., McDonnell, J. M., Struwe, W. B., Sutton, B. J., & Politis, A. (2018) · Angewandte Chemie International Edition · doi:10.1002/anie.201812018 · Cited by 47 · see citing works
Self-citationMass spectrometry beyond the native state
Chandler, S. A., & Benesch, J. L. P. (2017) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2017.11.019 · Cited by 45 · see citing works
Self-citationMarklund, E. G., & Benesch, J. L. P. (2019) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2018.12.011 · Cited by 45 · see citing works
Self-citationBonner, J., Lyon, Y. A., Nellessen, C. M., & Julian, R. R. (2017) · Journal of the American Chemical Society · doi:10.1021/jacs.7b02428 · Cited by 43 · see citing works
Theoretical investigations of the dissociation of charged protein complexes in the gas phase
Wanasundara, S. N., & Thachuk, M. (2007) · Journal of the American Society for Mass Spectrometry · doi:10.1016/j.jasms.2007.09.022 · Cited by 41 · see citing works
Konermann, L. (2017) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.7b05703 · Cited by 40 · see citing works
Native Mass Spectrometry: Towards High-Throughput Structural Proteomics
Kondrat, F. D. L., Struwe, W. B., & Benesch, J. L. P. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-2230-7_18 · Cited by 39 · see citing works
Self-citationEschweiler, J. D., Frank, A. T., & Ruotolo, B. T. (2017) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-017-1757-1 · Cited by 38 · see citing works
A Hydrodynamic Comparison of Solution and Gas Phase Proteins and Their Complexes
Hewitt, D., Marklund, E. G., Scott, D. J., Robinson, C. V., & Borysik, A. J. (2014) · The Journal of Physical Chemistry B · doi:10.1021/jp501950d · Cited by 36 · see citing works
Self-citationKune, C., Far, J., & Pauw, E. D. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.6b03215 · Cited by 34 · see citing works
Analysis of Native-Like Ions Using Structures for Lossless Ion Manipulations
Allen, S., Eaton, R. M., & Bush, M. F. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.6b02089 · Cited by 30 · see citing works
Conformational States of Macromolecular Assemblies Explored by Integrative Structure Calculation
Thalassinos, K., Pandurangan, A. P., Xu, M., Alber, F., & Topf, M. (2013) · Structure · doi:10.1016/j.str.2013.08.006 · Cited by 29 · see citing works
Self-citationCalvo, F., Chirot, F., Albrieux, F., Lemoine, J., Tsybin, Y. O., Pernot, P., & Dugourd, P. (2012) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-012-0391-1 · Cited by 26 · see citing works
Sivalingam, G. N., Cryar, A., Williams, M. A., Gooptu, B., & Thalassinos, K. (2018) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2018.01.008 · Cited by 23 · see citing works
Self-citationProbing the Dissociation of Protein Complexes by Means of Gas-Phase H/D Exchange Mass Spectrometry
Mistarz, U. H., Chandler, S. A., Brown, J. M., Benesch, J. L. P., & Rand, K. D. (2018) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-018-2064-1 · Cited by 23 · see citing works
Self-citationChirot, F., Calvo, F., Albrieux, F., Lemoine, J., Tsybin, Y. O., & Dugourd, P. (2011) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-011-0281-y · Cited by 21 · see citing works
Young, M. N., & Bleiholder, C. (2017) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-017-1605-3 · Cited by 21 · see citing works
Cooper-Shepherd, D. A., Marty, M. T., Giles, K., Baldwin, A. J., & Benesch, J. L. P. (2014) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2014.09.007 · Cited by 19 · see citing works
Self-citationEM∩IM: software for relating ion mobility mass spectrometry and electron microscopy data
Degiacomi, M. T., & Benesch, J. L. P. (2015) · The Analyst · doi:10.1039/c5an01636c · Cited by 18 · see citing works
Self-citationCanzani, D., Laszlo, K. J., & Bush, M. F. (2018) · The Journal of Physical Chemistry A · doi:10.1021/acs.jpca.8b04474 · Cited by 17 · see citing works
Kulesza, A. J., Marklund, E. G., MacAleese, L., Chirot, F., & Dugourd, P. (2018) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.8b03825 · Cited by 17 · see citing works
Self-citationOn the Effect of Sphere-Overlap on Super Coarse-Grained Models of Protein Assemblies
Degiacomi, M. T. (2018) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-018-1974-2 · Cited by 13 · see citing works
Self-citationMcAlary, L., Harrison, J. A., Aquilina, J. A., Fitzgerald, S. P., Kelso, C., Benesch, J. L. P., & Yerbury, J. J. (2019) · Analytical Chemistry · doi:10.1021/acs.analchem.9b01699 · Cited by 13 · see citing works
Self-citationTamò, G. E., Maesani, A., Träger, S., Degiacomi, M. T., Floreano, D., & Peraro, M. D. (2017) · Scientific Reports · doi:10.1038/s41598-017-00266-w · Cited by 10 · see citing works
Self-citationMolecular self-occlusion as a means for accelerating collision cross-section calculations
Marklund, E. G. (2015) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2015.06.006 · Cited by 9 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Christofi, E., & Barran, P. E. (2023) · Chemical Reviews · doi:10.1021/acs.chemrev.2c00600 · Cited by 239 · see citing works
Self-citationZhou, M., Lantz, C., Brown, K. A., Ge, Y., Paša-Tolić, L., Loo, J. A., & Lermyte, F. (2020) · Chemical Science · doi:10.1039/d0sc04392c · Cited by 146 · see citing works
Approaches to Heterogeneity in Native Mass Spectrometry
Rolland, A. D., & Prell, J. S. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.1c00696 · Cited by 71 · see citing works
Characterizing Endogenous Protein Complexes with Biological Mass Spectrometry
Rogawski, R., & Sharon, M. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.1c00217 · Cited by 58 · see citing works
Self-citationAziz, D. M., Hassan, S. A., Amin, A. A. M., Abdullah, M. N., Qurbani, K., & Aziz, S. B. (2023) · RSC Advances · doi:10.1039/d3ra06469g · Cited by 58 · see citing works
Comby‐Zerbino, C., Dagany, X., Chirot, F., Dugourd, P., & Antoine, R. (2021) · Materials Advances · doi:10.1039/d1ma00261a · Cited by 52 · see citing works
Folding dynamics of polymorphic G‐quadruplex structures
Grün, J. T., & Schwalbe, H. (2021) · Biopolymers · doi:10.1002/bip.23477 · Cited by 52 · see citing works
Turzo, S. B. A., Seffernick, J. T., Rolland, A. D., Donor, M. T., Heinze, S., Prell, J. S., Wysocki, V. H., & Lindert, S. (2022) · Nature Communications · doi:10.1038/s41467-022-32075-9 · Cited by 47 · see citing works
Top-down mass spectrometry of native proteoforms and their complexes: a community study
Habeck, T., Brown, K. A., Soye, B. J. D., Lantz, C., Zhou, M., Alam, N., Hossain, M. A., Jung, W., Keener, J. E., Volný, M., et al. (2024) · Nature Methods · doi:10.1038/s41592-024-02279-6 · Cited by 49 · see citing works
Computational tools and algorithms for ion mobility spectrometry‐mass spectrometry
Ross, D. H., Bhotika, H., Zheng, X., Smith, R. D., Burnum-Johnson, K., & Pena, A. B. (2024) · PROTEOMICS · doi:10.1002/pmic.202200436 · Cited by 24 · see citing works
Konermann, L., Aliyari, E., & Lee, J. (2021) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.1c00944 · Cited by 23 · see citing works
Collision Cross Sections for Native Proteomics: Challenges and Opportunities
Ruotolo, B. T. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.1c00686 · Cited by 20 · see citing works
Lee, K. W., Salome, A. Z., Westphall, M. S., Grant, T., & Coon, J. J. (2023) · Journal of Proteome Research · doi:10.1021/acs.jproteome.2c00595 · Cited by 18 · see citing works
Yasmeen, R., Ahmed, S., Bhat, A. R., Bajju, G. D., & Sheikh, H. N. (2024) · Inorganica Chimica Acta · doi:10.1016/j.ica.2024.122155 · Cited by 16 · see citing works
Compaction of RNA Hairpins and Their Kissing Complexes in Native Electrospray Mass Spectrometry
Abi‐Ghanem, J., Rabin, C., Porrini, M., Rosu, F., & Gabelica, V. (2020) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.0c00060 · Cited by 15 · see citing works
Self-citationNative mass spectrometry for the investigation of protein structural (dis)order
Santambrogio, C., Ponzini, E., & Grandori, R. (2022) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2022.140828 · Cited by 13 · see citing works
Self-citationPimlott, D. J. D., & Konermann, L. (2021) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2021.116678 · Cited by 12 · see citing works
Persson, L. J. P., Sahin, C., Landreh, M., & Marklund, E. G. (2024) · Analytical Chemistry · doi:10.1021/acs.analchem.4c03272 · Cited by 10 · see citing works
Self-citationLin, Y.-F., Jones, B. J., Ridgeway, M. E., Panczyk, E. M., Somogyi, Á., Kaplan, D. A., Marathe, I. A., Yun, S., Kirby, K. A., Sarafianos, S. G., et al. (2025) · Analytical Chemistry · doi:10.1021/acs.analchem.4c03557 · Cited by 10 · see citing works
Palomino‐Hernández, O., Santambrogio, C., Rossetti, G., Fernández, C. O., Grandori, R., & Carloni, P. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.1c10954 · Cited by 10 · see citing works
Self-citationBrodmerkel, M. N., Thiede, L., Santis, E. D., Uetrecht, C., Caleman, C., & Marklund, E. G. (2024) · Physical Chemistry Chemical Physics · doi:10.1039/d3cp06344e · Cited by 9 · see citing works
Self-citationRibaudo, G., Ongaro, A., Oselladore, E., Memo, M., & Gianoncelli, A. (2021) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.1c00962 · Cited by 10 · see citing works
Aliyari, E., & Konermann, L. (2021) · Analytical Chemistry · doi:10.1021/acs.analchem.1c02836 · Cited by 9 · see citing works
Fenton-Chemistry-Based Oxidative Modification of Proteins Reflects Their Conformation
Nehls, T., Heymann, T., Meyners, C., Hausch, F., & Lermyte, F. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22189927 · Cited by 9 · see citing works
Computational methods for advanced mass spectrometry – a review
Alaribe, C. S., Titilayo, B. E., Ikpatt, U. N., Oladipupo, A. R., Alabi, F. A., & Ikwugbado, R. I. (2025) · Physical Sciences Reviews · doi:10.1515/psr-2024-0006 · Cited by 8 · see citing works
Wilson, K. M., Burkus-Matesevac, A., Maddox, S. W., & Chouinard, C. D. (2021) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.0c00372 · Cited by 6 · see citing works
Propagating Error through Traveling-Wave Ion Mobility Calibration
Edwards, A. N., Tran, H. M., & Gallagher, E. S. (2021) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.1c00144 · Cited by 6 · see citing works
Turzo, S. B. A., Seffernick, J. T., Rolland, A. D., Donor, M. T., Heinze, S., Prell, J. S., Wysocki, V. H., & Lindert, S. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.27.445812 · Cited by 6 · see citing works
Makey, D. M., Langridge, D., Richardson, K., Schroeder, R., Ujma, J., Giles, K., & Ruotolo, B. T. (2026) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.6c00022 · Cited by 5 · see citing works
Valadbeigi, Y., & Causon, T. J. (2024) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.4c00207 · Cited by 4 · see citing works
Jin, Y., Ganguly, P., Wessel, L., Zhu, Z., Rijs, A. M., Shea, J., Buratto, S. K., & Bowers, M. T. (2026) · Journal of the American Chemical Society · doi:10.1021/jacs.6c01293 · Cited by 3 · see citing works
Tomlinson, L. J., Batchelor, M. R., Sarsby, J., Byrne, D. P., Brownridge, P., Bayliss, R. W., Eyers, P. A., & Eyers, C. E. (2022) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.1c00271 · Cited by 3 · see citing works
Evaluation for Ion Heating of H2A-H2B Dimer in Ion Mobility Spectrometry–Mass Spectrometry
Saikusa, K., Asakawa, D., Fuchigami, S., & Akashi, S. (2023) · Mass Spectrometry · doi:10.5702/massspectrometry.a0131 · Cited by 2 · see citing works
Adapting a trapped ion mobility spectrometry-Q-TOF mass spectrometer for native mass spectrometryPreprint
Lin, Y.-F., Jones, B., Ridgeway, M. E., Panczyk, E. M., Somogyi, Á., Kaplan, D. A., Marathe, I. A., Yun, S., Laganowsky, A. D., Park, M. A., et al. (2024) · ChemRxiv · doi:10.26434/chemrxiv-2024-xmjml-v2 · Cited by 2 · see citing works
Deconvolution of High-Dimensional Ion Mobility Data Using Reversible-Jump Markov Chain Monte Carlo
Riedel, J., Safferthal, M., Szekeres, G. P., & Pagel, K. (2026) · Analytical Chemistry · doi:10.1021/acs.analchem.5c06427 · Cited by 1 · see citing works
anon, R., Ahmed, S., Bhat, A. R., Bajju, G. D., & Sheikh, H. N. (2024) · SSRN Electronic Journal · doi:10.2139/ssrn.4781062 · Cited by 1 · see citing works
- Authors
- Allison, T. M., Barran, P., Cianférani, S., Degiacomi, M. T., Gabelica, V., Grandori, R., Marklund, E. G., Menneteau, T., Migas, L. G., Politis, A., Sharon, M., Sobott, F., Thalassinos, K., & Benesch, J. L. P.
- Affiliations
- University of Canterbury (NZ)
- University of Manchester (GB)
- Centre National de la Recherche Scientifique (FR)
- Durham University (GB)
- University of Milano-Bicocca (IT)
- Uppsala University (SE)
- Institute of Structural and Molecular Biology (GB)
- King's College London (GB)
- Weizmann Institute of Science (IL)
- University of Leeds (GB)
- University of Oxford (GB)
- Corresponding author
- Benesch, Justin L. P.
- ORCID
- Venue
- Analytical Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2020-07-15
- Volume
- 92
- Issue
- 16
- Pages
- 10872-10880
- ISSN
- 0003-2700 (ISSN-L)
- 1520-6882
- OpenAlex
- W3042745199
- Cited by
- 38
- References
- 84
- Citations by year
- 2026: 3 · 2025: 2 · 2024: 8 · 2023: 5 · 2022: 4 · 2021: 14 · 2020: 2
- FWCI
- 0.74
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Analytical Chemistry (publishedVersion)
- ChemRxiv (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Research Explorer (The University of Manchester) (publishedVersion, other-oa)
- White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (acceptedVersion)
- Durham Research Online (Durham University) (acceptedVersion)
- HAL (submittedVersion, other-oa)
- Durham Research Online (Durham University) (submittedVersion, cc-by)
- BOA (University of Milano-Bicocca) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Royal College of Surgeons in Ireland (submittedVersion, cc-by-nc-nd)
- Research Portal (King's College London) (submittedVersion)
- Funders
- European Cooperation in Science and Technology (BM1403)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- native ion mobility-mass spectrometry, non-covalent interactions, structural biology, biophysics, software tools
- MeSH terms
- Biophysics, Proteins, Mass Spectrometry, Computational Biology
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
