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

The promise and challenge of high-throughput sequencing of the antibody repertoire

Georgiou, G., Ippolito, G. C., Beausang, J., Busse, C. E., Wardemann, H., & Quake, S. R. (2014) · Nature Biotechnology · doi:10.1038/nbt.2782 · Cited by 652 · see citing works

Electron Capture Dissociation of Gaseous Multiply-Charged Proteins Is Favored at Disulfide Bonds and Other Sites of High Hydrogen Atom Affinity

Zubarev, R. A., Kruger, N. A., Fridriksson, E. K., Lewis, M. A., Horn, D. M., Carpenter, B. K., & McLafferty, F. W. (1999) · Journal of the American Chemical Society · doi:10.1021/ja981948k · Cited by 557 · see citing works

Disulfide bond structures of IgG molecules

Liu, H., & May, K. M. L. (2012) · mAbs · doi:10.4161/mabs.4.1.18347 · Cited by 487 · see citing works

Automated de novo sequencing of proteins by tandem high-resolution mass spectrometry

Horn, D. M., Zubarev, R. A., & McLafferty, F. W. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.19.10313 · Cited by 243 · see citing works

Isolation of potent neutralizing antibodies from a survivor of the 2014 Ebola virus outbreak

Bornholdt, Z. A., Turner, H. L., Murin, C. D., Li, W., Sok, D., Souders, C. A., Piper, A. E., Goff, A. J., Shamblin, J. D., Wollen-Roberts, S. E., et al. (2016) · Science · doi:10.1126/science.aad5788 · Cited by 214 · see citing works

A proteomics approach for the identification and cloning of monoclonal antibodies from serum

Cheung, W. C., Beausoleil, S. A., Zhang, X., Sato, S., Schieferl, S. M., Wieler, J. S., Beaudet, J. G., Ramenani, R. K., Popova, L., Comb, M. J., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2167 · Cited by 183 · see citing works

Analysis of Intact Monoclonal Antibody IgG1 by Electron Transfer Dissociation Orbitrap FTMS

Fornelli, L., Damoc, E., Thomas, P. M., Kelleher, N. L., Aizikov, K., Denisov, E. V., Makarov, A., & Tsybin, Y. O. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m112.019620 · Cited by 161 · see citing works

Accurate Sequence Analysis of a Monoclonal Antibody by Top-Down and Middle-Down Orbitrap Mass Spectrometry Applying Multiple Ion Activation Techniques

Fornelli, L., Srzentić, K., Huguet, R., Mullen, C., Sharma, S., Zabrouskov, V., Fellers, R. T., Durbin, K. R., Compton, P. D., & Kelleher, N. L. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b00984 · Cited by 150 · see citing works

Proteomics-Grade de Novo Sequencing Approach

Savitski, M. M., Nielsen, M. L., Kjeldsen, F., & Zubarev, R. A. (2005) · Journal of Proteome Research · doi:10.1021/pr050288x · Cited by 148 · see citing works

Structural Analysis of Intact Monoclonal Antibodies by Electron Transfer Dissociation Mass Spectrometry

Tsybin, Y. O., Fornelli, L., Stoermer, C., Lubeck, M., Parra, J., Nallet, S., Wurm, F. M., & Hartmer, R. (2011) · Analytical Chemistry · doi:10.1021/ac201293m · Cited by 138 · see citing works

Top-Down Structural Analysis of an Intact Monoclonal Antibody by Electron Capture Dissociation-Fourier Transform Ion Cyclotron Resonance-Mass Spectrometry

Mao, Y., Valeja, S. G., Rouse, J. C., Hendrickson, C. L., & Marshall, A. G. (2013) · Analytical Chemistry · doi:10.1021/ac303525n · Cited by 129 · see citing works

Expanding the structural analysis capabilities on an Orbitrap-based mass spectrometer for large macromolecular complexes

Fort, K. L., van de Waterbeemd, M., Boll, D., Reinhardt-Szyba, M., Belov, M. E., Sasaki, E., Zschoche, R., Hilvert, D., Makarov, A. A., & Heck, A. J. R. (2018) · The Analyst · doi:10.1039/c7an01629h · Cited by 122 · see citing works

Facile Disulfide Bond Cleavage in Gaseous Peptide and Protein Cations by Ultraviolet Photodissociation at 157 nm

Fung, Y. M. E., Kjeldsen, F., Silivra, O. A., Chan, T. ‐. D., & Zubarev, R. A. (2005) · Angewandte Chemie International Edition · doi:10.1002/anie.200501533 · Cited by 120 · see citing works

When monoclonal antibodies are not monospecific: hybridomas frequently express additional functional variable regions

Bradbury, A. R. M., Trinklein, N. D., Thie, H., Wilkinson, I. C., Tandon, A. K., Anderson, S., Bladen, C. L., Jones, B., Aldred, S. F., Bestagno, M., et al. (2018) · mAbs · doi:10.1080/19420862.2018.1445456 · Cited by 115 · see citing works

Direct Elucidation of Disulfide Bond Partners Using Ultraviolet Photodissociation Mass Spectrometry

Agarwal, A., Diedrich, J. K., & Julian, R. R. (2011) · Analytical Chemistry · doi:10.1021/ac201650v · Cited by 110 · see citing works

SO2−· electron transfer ion/ion reactions with disulfide linked polypeptide ions

Chrisman, P. A., Pitteri, S. J., Hogan, J. M., & McLuckey, S. A. (2005) · Journal of the American Society for Mass Spectrometry · doi:10.1016/j.jasms.2005.02.010 · Cited by 107 · see citing works

Screening for Disulfide Bonds in Proteins by MALDI In-Source Decay and LIFT-TOF/TOF-MS

Schnaible, V., Wefing, S., Resemann, A., Suckau, D., Bücker, A., Wolf-Kümmeth, S., & Hoffmann, D. E. (2002) · Analytical Chemistry · doi:10.1021/ac025807j · Cited by 100 · see citing works

Characterization of disulfide bond position in proteins and sequence analysis of cystine-bridged peptides by tandem mass spectrometry

Bean, M. F., & Carr, S. A. (1992) · Analytical Biochemistry · doi:10.1016/0003-2697(92)90331-z · Cited by 89 · see citing works

Human Monoclonal Antibodies Derived From Memory B Cells Following Live Attenuated Dengue Virus Vaccination or Natural Infection Exhibit Similar Characteristics

Smith, S. A., de Alwis, R., Kose, N., Durbin, A. P., Whitehead, S. S., de Silva, A. M., & Crowe, J. E. (2013) · The Journal of Infectious Diseases · doi:10.1093/infdis/jit119 · Cited by 87 · see citing works

Facilitating Protein Disulfide Mapping by a Combination of Pepsin Digestion, Electron Transfer Higher Energy Dissociation (EThcD), and a Dedicated Search Algorithm SlinkS

Liu, F., van Breukelen, B., & Heck, A. J. R. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o114.039057 · Cited by 86 · see citing works

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

Shaw, J., Malhan, N., Vasil’ev, Y. V., Lopez, N. I., Makarov, A., Beckman, J. S., & Voinov, V. G. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b01901 · Cited by 79 · see citing works

Exploring ECD on a Benchtop Q Exactive Orbitrap Mass Spectrometer

Fort, K. L., Cramer, C. N., Voinov, V. G., Vasil’ev, Y. V., Lopez, N. I., Beckman, J. S., & Heck, A. J. R. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00622 · Cited by 77 · see citing works

De Novo Protein Sequencing by Combining Top-Down and Bottom-Up Tandem Mass Spectra

Liu, X., Dekker, L. J. M., Wu, S., VanDuijn, M. M., Luider, T. M., Tolić, N., Kou, Q., Dvorkin, M. V., Alexandrova, S., Vyatkina, K., et al. (2014) · Journal of Proteome Research · doi:10.1021/pr401300m · Cited by 72 · see citing works

Sequencing-Grade De novo Analysis of MS/MS Triplets (CID/HCD/ETD) From Overlapping Peptides

Guthals, A., Clauser, K. R., Frank, A. M., & Bandeira, N. (2013) · Journal of Proteome Research · doi:10.1021/pr400173d · Cited by 72 · see citing works

Electron transfer dissociation of multiply protonated and fixed charge disulfide linked polypeptides

Gunawardena, H. P., Gorenstein, L., Erickson, D. E., Xia, Y., & McLuckey, S. A. (2007) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2007.01.017 · Cited by 69 · see citing works

De Novo MS/MS Sequencing of Native Human Antibodies

Guthals, A., Gan, Y., Murray‐Nerger, L. A., Chen, Y., Stinson, J., Nakamura, G. R., Lill, J. R., Sandoval, W. N., & Bandeira, N. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00608 · Cited by 60 · see citing works

Proteomics-directed cloning of circulating antiviral human monoclonal antibodies

Sato, S., Beausoleil, S. A., Popova, L., Beaudet, J. G., Ramenani, R. K., Zhang, X., Wieler, J. S., Schieferl, S. M., Cheung, W. C., & Polakiewicz, R. D. (2012) · Nature Biotechnology · doi:10.1038/nbt.2406 · Cited by 58 · see citing works

Preferential cleavage of SS and CS bonds in electron detachment dissociation and infrared multiphoton dissociation of disulfide-linked peptide anions

Kalli, A., & Håkansson, K. (2007) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2007.01.001 · Cited by 57 · see citing works

Multiplexed Middle-Down Mass Spectrometry as a Method for Revealing Light and Heavy Chain Connectivity in a Monoclonal Antibody

Srzentić, K., Nagornov, K. O., Fornelli, L., Lobas, A. A., Ayoub, D., Kozhinov, A. N., Gasilova, N., Menin, L., Beck, A., Gorshkov, M. V., et al. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b02398 · Cited by 55 · see citing works

Structural Analysis of an Intact Monoclonal Antibody by Online Electrochemical Reduction of Disulfide Bonds and Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

Nicolardi, S., Deelder, A. M., Palmblad, M., & van der Burgt, Y. E. M. (2014) · Analytical Chemistry · doi:10.1021/ac500383c · Cited by 49 · see citing works

Does Electron Capture Dissociation Cleave Protein Disulfide Bonds?

Ganisl, B., & Breuker, K. (2012) · ChemistryOpen · doi:10.1002/open.201200038 · Cited by 48 · see citing works

Enhancing protein disulfide bond cleavage by UV excitation and electron capture dissociation for top-down mass spectrometry

Wongkongkathep, P., Li, H., Zhang, X., Loo, R. R. O., Julian, R. R., & Loo, J. A. (2015) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2015.07.008 · Cited by 47 · see citing works

De Novo Sequencing of Peptides from Top-Down Tandem Mass Spectra

Vyatkina, K., Wu, S., Dekker, L. J. M., VanDuijn, M. M., Liu, X., Tolić, N., Dvorkin, M. V., Alexandrova, S., Luider, T. M., Paša‐Tolić, L., et al. (2015) · Journal of Proteome Research · doi:10.1021/pr501244v · Cited by 43 · see citing works

Bond-selective photodissociation of aliphatic disulfides

Bookwalter, C., Zoller, D. L., Ross, P. L., & Johnston, M. V. (1995) · Journal of the American Society for Mass Spectrometry · doi:10.1016/1044-0305(95)00483-t · Cited by 42 · see citing works

Characterization of Disulfide Linkages in Proteins by 193 nm Ultraviolet Photodissociation (UVPD) Mass Spectrometry

Quick, M. M., Crittenden, C. M., Rosenberg, J. A., & Brodbelt, J. S. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b01556 · Cited by 41 · see citing works

Shotgun Protein Sequencing with Meta-contig Assembly

Guthals, A., Clauser, K. R., & Bandeira, N. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.015768 · Cited by 29 · see citing works

De Novo Sequencing of Top-Down Tandem Mass Spectra: A Next Step towards Retrieving a Complete Protein Sequence

Vyatkina, K. (2017) · Proteomes · doi:10.3390/proteomes5010006 · Cited by 26 · see citing works

Simplified identification of disulfide, trisulfide, and thioether pairs with 213 nm UVPD

Bonner, J., Talbert, L. E., Akkawi, N., & Julian, R. R. (2018) · The Analyst · doi:10.1039/c8an01582a · Cited by 24 · see citing works

Facile Disulfide Bond Cleavage in Gaseous Peptide and Protein Cations by Ultraviolet Photodissociation at 157 nm

Fung, Y. M. E., Kjeldsen, F., Silivra, O. A., Chan, T. ‐. D., & Zubarev, R. A. (2005) · Angewandte Chemie · doi:10.1002/ange.200501533 · Cited by 21 · see citing works

Top-down analysis of protein samples by de novo sequencing techniques

Vyatkina, K., Wu, S., Dekker, L. J. M., VanDuijn, M. M., Liu, X., Tolić, N., Luider, T. M., Paša‐Tolić, L., & Pevzner, P. A. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw307 · Cited by 20 · see citing works

Comprehensive de Novo Peptide Sequencing from MS/MS Pairs Generated through Complementary Collision Induced Dissociation and 351 nm Ultraviolet Photodissociation

Horton, A. P., Robotham, S. A., Cannon, J. R., Holden, D. D., Marcotte, E. M., & Brodbelt, J. S. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.7b00130 · Cited by 18 · see citing works

Top-down proteomics: challenges, innovations, and applications in basic and clinical research

Brown, K. A., Melby, J. A., Roberts, D. S., & Ge, Y. (2020) · Expert Review of Proteomics · doi:10.1080/14789450.2020.1855982 · Cited by 152 · see citing works

Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry

Zhou, 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

Interlaboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass Spectrometry

Srzentič, K., Fornelli, L., Tsybin, Y. O., Loo, J., Seckler, H. S., Agar, J. N., Anderson, L. C., Bai, D.-N. L., Beck, A., Brodbelt, J., et al. (2020) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.0c00036 · Cited by 98 · see citing works

Human Plasma IgG1 Repertoires are Simple, Unique, and Dynamic

Bondt, A., Hoek, M., Tamara, S., de Graaf, S. C., Peng, W., Schulte, D., van Rijswijck, D. M. H., den Boer, M. A., Greisch, J., Varkila, M. R. J., et al. (2020) · Cell Systems · doi:10.1016/j.cels.2021.08.008 · Cited by 87 · 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

Native top‐down mass spectrometry for higher‐order structural characterization of proteins and complexes

Liu, R., Xia, S., & Li, H. (2022) · Mass Spectrometry Reviews · doi:10.1002/mas.21793 · Cited by 59 · see citing works

Deciphering combinatorial post-translational modifications by top-down mass spectrometry

Brodbelt, J. (2022) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2022.102180 · Cited by 50 · see citing works

Progress and challenges in mass spectrometry-based analysis of antibody repertoires

Snapkov, I., Chernigovskaya, M., Sinitcyn, P. G., Quý, K. L., Nyman, T. A., & Greiff, V. (2021) · Trends in biotechnology · doi:10.1016/j.tibtech.2021.08.006 · Cited by 50 · see citing works

Improved Protein and PTM Characterization with a Practical Electron-Based Fragmentation on Q-TOF Instruments

Beckman, J. S., Voinov, V. G., Hare, M. C., Sturgeon, D., Vasil’ev, Y. V., Oppenheimer, D., Shaw, J., Wu, S., Glaskin, R. S., Klein, C., et al. (2021) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.0c00482 · Cited by 49 · see citing works

A perspective toward mass spectrometry-based de novo sequencing of endogenous antibodies

de Graaf, S. C., Hoek, M., Tamara, S., & Heck, A. J. R. (2022) · mAbs · doi:10.1080/19420862.2022.2079449 · Cited by 43 · see citing works

Top-“Double-Down” Mass Spectrometry of Histone H4 Proteoforms: Tandem Ultraviolet-Photon and Mobility/Mass-Selected Electron Capture Dissociations

Fouque, K. J. D., Miller, S. A., Pham, K., Bhanu, N. V., Cintron-Diaz, Y. L., Leyva, D., Kaplan, D. A., Voinov, V. G., Ridgeway, M. E., Park, M. A., et al. (2022) · Analytical Chemistry · doi:10.1021/acs.analchem.2c03147 · Cited by 40 · see citing works

Proteoform Differentiation using Tandem Trapped Ion Mobility, Electron Capture Dissociation, and ToF Mass Spectrometry

Fouque, K. J. D., Kaplan, D. A., Voinov, V. G., Holck, F. H., Jensen, O. N., & Fernandez-Lima, F. A. (2021) · Analytical Chemistry · doi:10.1021/acs.analchem.1c01735 · Cited by 34 · see citing works

Extending Native Top-Down Electron Capture Dissociation to MDa Immunoglobulin Complexes Provides Useful Sequence Tags Covering Their Critical Variable Complementarity-Determining Regions

Greisch, J., den Boer, M. A., Lai, S., Gallagher, K. J., Bondt, A., Commandeur, J., & Heck, A. J. R. (2021) · Analytical Chemistry · doi:10.1021/acs.analchem.1c03740 · Cited by 32 · see citing works

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

Shaw, J., Cooper-Shepherd, D., Hewitt, D., Wildgoose, J., Beckman, J., Langridge, J., & Voinov, V. G. (2022) · Analytical Chemistry · doi:10.1021/acs.analchem.1c04870 · Cited by 29 · see citing works

Top-Down and Middle-Down Mass Spectrometry of Antibodies

Khristenko, N. A., Nagornov, K. O., Garcia, C., Gasilova, N., Gant, M. S., Druart, K., Kozhinov, A. N., Menin, L., Chamot‐Rooke, J., & Tsybin, Y. O. (2025) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2025.100989 · Cited by 31 · see citing works

Added Value of Internal Fragments for Top-Down Mass Spectrometry of Intact Monoclonal Antibodies and Antibody–Drug Conjugates

Wei, B., Lantz, C., Liu, W., Viner, R., Loo, R. R. O., Campuzano, I. D. G., & Loo, J. A. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.3c01426 · Cited by 30 · see citing works

Comprehensive Middle-Down Mass Spectrometry Characterization of an Antibody–Drug Conjugate by Combined Ion Activation Methods

Watts, E., Williams, J. D., Miesbauer, L. J., Bruncko, M., & Brodbelt, J. S. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.0c01232 · Cited by 28 · see citing works

Selectivity over coverage in de novo sequencing of IgGs

den Boer, M. A., Greisch, J., Tamara, S., Bondt, A., & Heck, A. J. R. (2020) · Chemical Science · doi:10.1039/d0sc03438j · Cited by 28 · see citing works

Inference of B cell clonal families using heavy/light chain pairing information

Ralph, D., & Matsen, F. A., IV (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010723 · Cited by 27 · see citing works

Generating Informative Sequence Tags from Antigen-Binding Regions of Heavily Glycosylated IgA1 Antibodies by Native Top-Down Electron Capture Dissociation

Greisch, J., den Boer, M. A., Beurskens, F. J. M., Schuurman, J., Tamara, S., Bondt, A., & Heck, A. J. R. (2021) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.0c00461 · Cited by 25 · see citing works

A Direct MS-Based Approach to Profile Human Milk Secretory Immunoglobulin A (IgA1) Reveals Donor-Specific Clonal Repertoires With High Longitudinal Stability

Bondt, A., Dingess, K. A., Hoek, M., van Rijswijck, D. M. H., & Heck, A. J. R. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.789748 · Cited by 24 · see citing works

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

Shaw, J., Harvey, S. R., Du, C., Xu, Z., Edgington, R. M., Olmedillas, E., Saphire, E. O., & Wysocki, V. H. (2024) · ACS Central Science · doi:10.1021/acscentsci.4c00461 · Cited by 27 · see citing works

To 200,000 m / z and Beyond: Native Electron Capture Charge Reduction Mass Spectrometry Deconvolves Heterogeneous Signals in Large Biopharmaceutical Analytes

Huray, K. I. P. L., Wörner, T. P., Moreira, T., Dembek, M., Reinhardt-Szyba, M., Devine, P. W. A., Bond, N. J., Fort, K. L., Makarov, A., & Sobott, F. (2024) · ACS Central Science · doi:10.1021/acscentsci.4c00462 · Cited by 23 · see citing works

Shedding light on both ends: An update on analytical approaches for N- and C-terminomics.

Koudelka, T., Winkels, K., Kaleja, P., & Tholey, A. (2021) · Biochimica et biophysica acta. Molecular cell research · doi:10.1016/j.bbamcr.2021.119137 · Cited by 20 · see citing works

Top-down mass spectrometry and assigning internal fragments for determining disulfide bond positions in proteins

Wei, B., Zenaidee, M. A., Lantz, C., Williams, B. J., Totten, S. M., Loo, R. R. O., & Loo, J. A. (2022) · The Analyst · doi:10.1039/d2an01517j · Cited by 21 · see citing works

Into the Dark Serum Proteome: Personalized Features of IgG1 and IgA1 Repertoires in Severe COVID-19 Patients

Bondt, A., Hoek, M., Dingess, K. A., Tamara, S., de Graaf, S. C., Peng, W., den Boer, M. A., Damen, M. J. A., Zwart, C., Barendregt, A., et al. (2023) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2023.100690 · Cited by 21 · see citing works

Mapping a Conformational Epitope of Hemagglutinin A Using Native Mass Spectrometry and Ultraviolet Photodissociation

Mehaffey, M. R., Lee, J., Jung, J., Lanzillotti, M. B., Escobar, E. E., Morgenstern, K. R., Georgiou, G., & Brodbelt, J. S. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.0c02237 · Cited by 21 · see citing works

Highly Robust de Novo Full-Length Protein Sequencing

Mai, Z., Zhou, Z., He, Q., & Zhang, G. (2022) · Analytical Chemistry · doi:10.1021/acs.analchem.1c03718 · Cited by 19 · see citing works

Recent advances in structural mass spectrometry methods in the context of biosimilarity assessment: from sequence heterogeneities to higher order structures

Castel, J.-G., Delaux, S., Hernandez‐Alba, O., & Cianférani, S. (2023) · Journal of Pharmaceutical and Biomedical Analysis · doi:10.1016/j.jpba.2023.115696 · Cited by 19 · see citing works

Improved characterization of trastuzumab deruxtecan with PTCR and internal fragments implemented in middle-down MS workflows

Beaumal, C., Deslignière, E., Diemer, H., Carapito, C., Cianférani, S., & Hernandez‐Alba, O. (2023) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-023-05059-x · Cited by 18 · see citing works

De novo glycan sequencing by electronic excitation dissociation MS 2 -guided MS 3 analysis on an Omnitrap-Orbitrap hybrid instrument

Wei, J., Papanastasiou, D. K., Kosmopoulou, M., Smyrnakis, A., Hong, P., Tursumamat, N., Klein, J., Xia, C., Tang, Y., Zaia, J., et al. (2023) · Chemical Science · doi:10.1039/d3sc00870c · Cited by 18 · see citing works

Enhancing Biomolecule Analysis and 2DMS Experiments by Implementation of (Activated Ion) 193 nm UVPD on a FT-ICR Mass Spectrometer

Theisen, A., Wootton, C. A., Haris, A., Morgan, T. E., Lam, Y. P. Y., Barrow, M. P., & O’Connor, P. B. (2022) · Analytical Chemistry · doi:10.1021/acs.analchem.2c02354 · Cited by 16 · see citing works

Effective discrimination of gas-phase peptide conformers using TIMS-ECD-ToF MS/MS

Fouque, K. J. D., Wellmann, M., Leyva, D., Santos-Fernandez, M., Cintron-Diaz, Y. L., Gomez-Hernandez, M. E., Kaplan, D. A., Voinov, V. G., & Fernandez-Lima, F. A. (2021) · Analytical Methods · doi:10.1039/d1ay01461g · Cited by 16 · see citing works

Innovations and trends in antibody repertoire analysis

Townsend, D. R., Towers, D. M., Lavinder, J. J., & Ippolito, G. C. (2024) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2024.103082 · Cited by 15 · see citing works

Internal Fragments Enhance Middle-Down Mass Spectrometry Structural Characterization of Monoclonal Antibodies and Antibody-Drug Conjugates

Wei, B., Lantz, C., Loo, R. R. O., Campuzano, I. D. G., & Loo, J. A. (2024) · Analytical Chemistry · doi:10.1021/acs.analchem.3c04526 · Cited by 12 · see citing works

Characterization of a Monoclonal Antibody by Native and Denaturing Top-Down Mass Spectrometry

Oates, R. N., Lieu, L. B., Srzentić, K., Damoc, E., & Fornelli, L. (2024) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.4c00224 · Cited by 14 · see citing works

Characterization of Variable Region Genes and Discovery of Key Recognition Sites in the Complementarity Determining Regions of the Anti-Thiacloprid Monoclonal Antibody

Liu, P., Guo, Y., Jiao, S., Chang, Y., Liu, Y., Zou, R., Liu, Y., Chen, M., Guo, Y., & Zhu, G. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21186857 · Cited by 12 · see citing works

Beyond bulk single-chain sequencing: Getting at the whole receptor

Curtis, N. C., & Lee, J. (2020) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2020.10.008 · Cited by 12 · see citing works

CE-MS/MS and CE-timsTOF to separate and characterize intramolecular disulfide bridges of monoclonal antibody subunits and their application for the assessment of subunit reduction protocols

Schairer, J., Römer, J., Lang, D., & Neusüß, C. (2024) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-024-05161-8 · Cited by 11 · see citing works

Hydrophilic Interaction Chromatography Coupled to Ultraviolet Photodissociation Affords Identification, Localization, and Relative Quantitation of Glycans on Intact Glycoproteins

James, V. K., van der Zon, A. A. M., Escobar, E. E., Dunham, S. D., Gargano, A., & Brodbelt, J. S. (2024) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00600 · Cited by 11 · see citing works

Mass spectrometry characterization of antibodies at the intact and subunit levels: from targeted to large-scale analysis

Kline, J. T., Melani, R., & Fornelli, L. (2023) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2023.117117 · Cited by 9 · see citing works

Investigation of Product Ions Generated by 193 nm Ultraviolet Photodissociation of Peptides and Proteins Containing Disulfide Bonds

Macias, L. A., & Brodbelt, J. S. (2022) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.2c00124 · Cited by 10 · see citing works

Leveraging Complementary Ion Activation Methods with Proton Transfer Charge Reduction Reactions for Comprehensive Characterization of Monoclonal Antibody Heavy Chain Subunits

Dunham, S. D., Juetten, K. J., Hellinger, J., Gadallah, M. I., Dioli, O. E., & Brodbelt, J. S. (2025) · Analytical Chemistry · doi:10.1021/acs.analchem.5c01075 · Cited by 9 · see citing works

Revealing the Fates of Proteins in the Gas Phase

Webb, I. K. (2024) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2024.117312 · Cited by 8 · see citing works

Conformational Characterization of Peptides and Proteins by 193 nm Ultraviolet Photodissociation in the Collision Cell of a Trapped Ion Mobility Spectrometry-Time-of-Flight Mass Spectrometer

Butalewicz, J. P., Escobar, E. E., Wootton, C. A., Theisen, A., Park, M. A., Seeley, E. H., & Brodbelt, J. S. (2024) · Analytical Chemistry · doi:10.1021/acs.analchem.4c02686 · Cited by 8 · see citing works

Progress in Top-Down LC-MS Analysis of Antibodies: Review

You, J., & Park, H.-M. (2023) · Biotechnology and Bioprocess Engineering · doi:10.1007/s12257-023-0011-x · Cited by 7 · see citing works

Monitoring mAb proteoforms in mouse plasma using an automated immunocapture combined with top‐down and middle‐down mass spectrometry

Dhenin, J., Lafont, V., Dupré, M., Krick, A., Mauriac, C., & Chamot‐Rooke, J. (2023) · PROTEOMICS · doi:10.1002/pmic.202300069 · Cited by 7 · see citing works

Emerging native Orbitrap mass spectrometry for probing higher-order structures of proteins: Recent progress and applications

Li, L., Zhang, Y., Lv, Y., Qu, F., & Ma, Q. (2023) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2023.117424 · Cited by 6 · see citing works

Integrated Top-Down and Bottom-Up Mass Spectrometry for Characterization of Diselenide Bridging Patterns of Synthetic Selenoproteins

Watts, E., Thyer, R. T., Ellington, A. D., & Brodbelt, J. S. (2022) · Analytical Chemistry · doi:10.1021/acs.analchem.2c01433 · Cited by 5 · see citing works

Panda-UV Unlocks Deeper Protein Characterization with Internal Fragments in Ultraviolet Photodissociation Mass Spectrometry

Zhu, Y., Liu, Z., Liu, J., Zhao, H., Feng, R., Shu, K., Wang, F., & Chang, C. (2024) · Analytical Chemistry · doi:10.1021/acs.analchem.4c00253 · Cited by 5 · see citing works

Sequencing the monoclonal antibody variable regions using multiple charge integration middle-down strategy and ultraviolet photodissociation

Liu, Z., Liu, Z., Zhao, H., Xiao, C., Yang, X., & Wang, F. (2024) · Analytica Chimica Acta · doi:10.1016/j.aca.2024.343450 · Cited by 5 · see citing works

No patient is the same; lessons learned from antibody repertoire profiling in hospitalized severe COVID-19 patientsPreprint

Bondt, A., Hoek, M., Dingess, K. A., Tamara, S., de Graaf, S. C., Peng, W., den Boer, M. A., Damen, M. J. A., Zwart, C., Barendregt, A., et al. (2022) · medRxiv · doi:10.1101/2022.12.23.22283896 · Cited by 4 · see citing works

On the Utility of Infrared Photoactivation for Native Top-Down and Complex-Down Orbitrap Mass Spectrometry of Soluble Proteoform Complexes

Nagy, C., Lieu, L. B., Mullen, C., McAlister, G., Melani, R. D., Hinkle, J. D., & Fornelli, L. (2026) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.5c00385 · Cited by 3 · see citing works

The Rise of Trapped Ion Mobility Spectrometry: Principles, Applications, and Recent Developments

Panczyk, E. M., Martelli, C., Ridgeway, M. E., Ekelöf, M., Hornburg, D., Jones, B. J., Wootton, C. A., Lewis, M. R., Pengelley, S., Greisch, J., et al. (2026) · Mass Spectrometry Reviews · doi:10.1002/mas.70034 · Cited by 3 · see citing works

Development of Top-Down Mass Spectrometry Strategies in the Chromatographic Time Scale (LC-TD-MS) for the Extended Characterization of an Anti-EGFR Single-Domain Antibody-Drug Conjugate in Both Reduced and Nonreduced Forms

Benazza, R., Letissier, L., Papadakos, G. A., Thom, J., Diemer, H., Cotton, G., Cianférani, S., & Hernandez‐Alba, O. (2025) · Analytical Chemistry · doi:10.1021/acs.analchem.4c03323 · Cited by 3 · see citing works

Ion Activation Methods for Top-Down Proteomics.

Walker, J. N., & Brodbelt, J. (2026) · Mass spectrometry reviews (Print) · doi:10.1002/mas.70023 · Cited by 1 · see citing works

A Prototype timsOmni Platform Enables Confident Annotation of the Key Hypervariable CDR3 Regions of IgG Immunoglobulins Using Low- and High-Energy Electron-Based Fragmentation

Ollivier, S., Schuster, D., van Rijswijck, D. M. H., Stroganova, I., Smyrnakis, A., Fiala, J., Kosmopoulou, M., Suckau, D., Pengelley, S., Raether, O., et al. (2026) · Analytical Chemistry · doi:10.1021/acs.analchem.5c07288 · Cited by 2 · see citing works

Automating Middle-Down Mass Spectrometry Analysis for Extensive Antibody Characterization

Carfagno, A. K., Lieu, L. B., Kline, J. T., Fornelli, L., & Durbin, K. R. (2026) · Analytical Chemistry · doi:10.1021/acs.analchem.5c06408 · Cited by 2 · see citing works

From Congestion to Clarity: On the Complementarity of Resolving Power and Spectral Simplification for Intact Protein Characterization

Lieu, L. B., Huang, J., Kline, J. T., Bergen, D., McAlister, G. C., Durbin, K. R., Mullen, C., Melani, R. D., & Fornelli, L. (2026) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.6c00016 · Cited by 3 · see citing works

Applications of native mass spectrometry and ultraviolet photodissociation in protein structure and interaction analysis

Jieying, X. U. E., Liu, Z.-Y., & Wang, F. (2024) · Chinese Journal of Chromatography · doi:10.3724/sp.j.1123.2024.01021 · Cited by 2 · see citing works

Revealing Formylation Sites in Intact Amphibian Disulfide Peptides: A Top-Down Study Using ExD

Samgina, T. Y., Mazur, D. M., Vasil’ev, Y. V., Hare, M. C., & Lebedev, А. T. (2025) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.4c00456 · Cited by 2 · see citing works

ExD vs EThcD: What’s Better for the Direct Sequencing of Endogenous Amphibian Disulfide Peptides

Mazur, D. M., Samgina, T. Y., Vasil’ev, Y. V., Hare, M. C., Li, Y., & Lebedev, А. T. (2025) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.5c00155 · Cited by 2 · see citing works

Native Top-Down Mass Spectrometry Combined with High-Resolution Charge Variant Analysis of Trastuzumab Originator and Biosimilars

Beaumal, C., Srzentić, K., Carillo, S., & Bones, J. (2026) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.5c00438 · Cited by 1 · see citing works

De novo sequencing and native mass spectrometry revealed hetero-association of dirigent protein homologs and potential interacting proteins in Forsythia × intermedia

Zhou, M., Laureanti, J. A., Bell, C. J., Kwon, M. J., Meng, Q., Novikova, I. V., Thomas, D., Nicora, C., Sontag, R. L., Bedgar, D. L., et al. (2021) · The Analyst · doi:10.1039/d1an01476e · Cited by 1 · see citing works

Antibody proteomics

Kazieva, L. S., Farafonova, T. E., & Zgoda, V. G. (2023) · Biomeditsinskaya Khimiya · doi:10.18097/pbmc20236901005 · Cited by 1 · see citing works

Mimicking LysC Proteolysis by ‘Arginine Modification-cum-Trypsin Digestion’: Comparison of Bottom-up & Middle-down Proteomic Approaches by ESI Q-TOF MS

Pandeswari, P. B., Chary, R. N., Kamalanathan, A. S., Prabhakar, S., & Sabareesh, V. (2021) · Protein and Peptide Letters · doi:10.2174/0929866528666210929163307 · Cited by 1 · see citing works

Fundamentals and Applications of Charge Transfer Dissociation Mass Spectrometry

Sasiene, Z. J. (2021) · doi:10.33915/etd.8063 · Cited by 1 · see citing works

Development of fine-tuned top-down mass spectrometry strategies in the chromatographic time scale (LC-TD-MS) for the complete characterization of an anti EGFR single domain antibody-drug conjugate (sdADC)Preprint

Benazza, R., Papadakos, G., Thom, J., Diemer, H., Cotton, G., Cianférani, S., & Hernandez‐Alba, O. (2024) · ChemRxiv · doi:10.26434/chemrxiv-2024-wnx5w · Cited by 1 · see citing works

A prototype timsOmni platform enables confident annotation of key hypervariable regions of IgG immunoglobulins using low- and high-energy electron-based fragmentationPreprint

Ollivier, S., Schuster, D., van Rijswijck, D. M. H., Stroganova, I., Smyrnakis, A., Fiala, J., Kosmopoulou, M., Suckau, D., Pengelley, S., Raether, O., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.10.29.685408 · Cited by 1 · see citing works

Introductory Chapter: Proteoforms

Zhan, X. (2020) · Proteoforms - Concept and Applications in Medical Sciences · doi:10.5772/intechopen.91403 · Cited by 1 · see citing works

Advanced structural elucidation of new antibody formats by mass spectrometry

Graf, T., Leiß, M., Haberger, M., & Bulau, P. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-822318-5.00005-3

Probing highly polymorphic proteins by mass spectrometry

Hoek, M. (2022) · doi:10.33540/1535

Analysis for disulfide bonds in polypeptide sequences based on ultraviolet photodissociation combined with linear ion trap mass spectrometry

He-Yi, X., Zhang, D., Li, Y., Huang, Z., Xin-Hua, D., Xiang, F., Rui-feng, X., Fang-Jun, W., Yang, G., & Jiang, Y. (2023) · Chinese Journal of Analytical Chemistry · doi:10.1016/j.cjac.2023.100285

De novo antibody sequencing based on mass spectrometry

Peng, W. (2024) · doi:10.33540/2133

Impact of Supercharging on Top-Down Characterization of Monoclonal Antibodies by Collision Induced DissociationPreprint

Amunugama, L., & Shaw, J. (2025) · SSRN Electronic Journal · doi:10.2139/ssrn.5772691

The Road to the Full Sequencing of Natural Frogs’ Peptides Relying Solely on Mass Spectrometry

Samgina, T. Y., & Lebedev, А. T. (2025) · Mass Spectrometry · doi:10.5702/massspectrometry.a0182

Impact of supercharging on top-down characterization of monoclonal antibodies by collision induced dissociation

Amunugama, L., & Shaw, J. (2026) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2026.117578

Direct determination of antibody chain pairing

Shaw, J. (2023) · OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)

Multiplexed Middle-Down Mass Spectrometry as a Method for Revealing Light and Heavy Chain Connectivity in a Monoclonal Antibody

Srzentić, K., Nagornov, K. O., Fornelli, L., Lobas, A. A., Ayoub, D., Kozhinov, A. N., Gasilova, N., Menin, L., Beck, A., Gorshkov, M. V., et al. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b02398 · Cited by 55 · see citing works

Electron Activated Dissociation Technique for Middle-Down Mass Spectrometric Analysis of Disulphide Bonds and Free Thiols: Application in Characterising Monoclonal Antibody Biotherapeutic FragmentsPreprint

Akinloye, A., Donnellan, L., Young, C., Mittal, P., Condina, M. R., & Hoffmann, P. (2026) · ChemRxiv · doi:10.26434/chemrxiv.15005972/v1

Structural Analysis of Monoclonal Antibodies with Top-down and Middle-down Electron Transfer Dissociation Mass Spectrometry: The First Decade

Fornelli, L., Ayoub, D., Srzentić, K., Nagornov, K. O., Kozhinov, A. N., Gasilova, N., Menin, L., Beck, A., & Tsybin, Y. O. (2022) · CHIMIA International Journal for Chemistry · doi:10.2533/chimia.2022.114 · Cited by 10 · see citing works

Characterization and Comparison of Disulfide Linkages and Scrambling Patterns in Therapeutic Monoclonal Antibodies: Using LC-MS with Electron Transfer Dissociation

Wang, Y., Lu, Q., Wu, S., Karger, B. L., & Hancock, W. S. (2011) · Analytical Chemistry · doi:10.1021/ac200128d · Cited by 109 · see citing works