Accurate Sequence Analysis of a Monoclonal Antibody by Top-Down and Middle-Down Orbitrap Mass Spectrometry Applying Multiple Ion Activation Techniques
Open accessAbstract
Targeted top-down (TD) and middle-down (MD) mass spectrometry (MS) offer reduced sample manipulation during protein analysis, limiting the risk of introducing artifactual modifications to better capture sequence information on the proteoforms present. This provides some advantages when characterizing biotherapeutic molecules such as monoclonal antibodies, particularly for the class of biosimilars. Here, we describe the results obtained analyzing a monoclonal IgG1, either in its ∼150 kDa intact form or after highly specific digestions yielding ∼25 and ∼50 kDa subunits, using an Orbitrap mass spectrometer on a liquid chromatography (LC) time scale with fragmentation from ion–photon, ion–ion, and ion–neutral interactions. Ultraviolet photodissociation (UVPD) used a new 213 nm solid-state laser. Alternatively, we applied high-capacity electron-transfer dissociation (ETD HD), alone or in combination with higher energy collisional dissociation (EThcD). Notably, we verify the degree of complementarity of these ion activation methods, with the combination of 213 nm UVPD and ETD HD producing a new record sequence coverage of ∼40% for TD MS experiments. The addition of EThcD for the >25 kDa products from MD strategies generated up to 90% of complete sequence information in six LC runs. Importantly, we determined an optimal signal-to-noise threshold for fragment ion deconvolution to suppress false positives yet maximize sequence coverage and implemented a systematic validation of this process using the new software TDValidator. This rigorous data analysis should elevate confidence for assignment of dense MS 2 spectra and represents a purposeful step toward the application of TD and MD MS for deep sequencing of monoclonal antibodies.
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?
Tribrid Orbitrap instruments offer a variety of ion activation methods.
“tribrid Orbitrap instruments offer a variety of ion activation methods,45”
From Proton Transfer Charge Reduction Enables High-Throughput Top-Down Analysis of Large Proteoforms (2019) · cites this paper as [45]
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
Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry
Syka, J. E. P., Coon, J. J., Schroeder, M. J., Shabanowitz, J., & Hunt, D. F. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0402700101 · Cited by 2,370 · see citing works
Electron Capture Dissociation of Multiply Charged Protein Cations. A Nonergodic Process
Zubarev, R. A., Kelleher, N. L., & McLafferty, F. W. (1998) · Journal of the American Chemical Society · doi:10.1021/ja973478k · Cited by 1,881 · see citing works
Self-citationProteoform: a single term describing protein complexity
The Consortium for Top Down Proteomics, Smith, L. M., & Kelleher, N. L. (2013) · Nature Methods · doi:10.1038/nmeth.2369 · Cited by 1,528 · see citing works
Self-citationProtein Analysis by Shotgun/Bottom-up Proteomics
Zhang, Y., Fonslow, B. R., Shan, B., Baek, M.-C., & Yates, J. R. (2013) · Chemical Reviews · doi:10.1021/cr3003533 · Cited by 1,491 · see citing works
The therapeutic monoclonal antibody market
Ecker, D. M., Jones, S. D., & Levine, H. L. (2014) · mAbs · doi:10.4161/19420862.2015.989042 · Cited by 1,292 · see citing works
Development trends for human monoclonal antibody therapeutics
Nelson, A. L., Dhimolea, E., & Reichert, J. M. (2010) · Nature Reviews Drug Discovery · doi:10.1038/nrd3229 · Cited by 1,027 · see citing works
Characterization of Therapeutic Antibodies and Related Products
Beck, A., Wagner‐Rousset, E., Ayoub, D., DORSSELAER, A. V., & Cianférani, S. (2012) · Analytical Chemistry · doi:10.1021/ac3032355 · Cited by 588 · see citing works
Progress in Top-Down Proteomics and the Analysis of Proteoforms
Toby, T. K., Fornelli, L., & Kelleher, N. L. (2016) · Annual Review of Analytical Chemistry · doi:10.1146/annurev-anchem-071015-041550 · Cited by 576 · see citing works
Self-citationIdeS, a novel streptococcal cysteine proteinase with unique specificity for immunoglobulin G
von Pawel‐Rammingen, U., Johansson, B. P., & Björck, L. (2002) · The EMBO Journal · doi:10.1093/emboj/21.7.1607 · Cited by 475 · see citing works
Senko, M. W., Beu, S. C., & McLaffertycor, F. W. (1995) · Journal of the American Society for Mass Spectrometry · doi:10.1016/1044-0305(95)00017-8 · Cited by 451 · see citing works
Complete Protein Characterization Using Top-Down Mass Spectrometry and Ultraviolet Photodissociation
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. (2013) · Journal of the American Chemical Society · doi:10.1021/ja4029654 · Cited by 371 · see citing works
Self-citationEstimation of the aqueous solubility I: Application to organic nonelectrolytes
Jain, N., & Yalkowsky, S. H. (2001) · Journal of Pharmaceutical Sciences · doi:10.1002/1520-6017(200102)90:2 · Cited by 368 · see citing works
Expression of Recombinant Antibodies
Frenzel, A., Hust, M., & Schirrmann, T. (2013) · Frontiers in Immunology · doi:10.3389/fimmu.2013.00217 · Cited by 353 · see citing works
ProSight Lite: Graphical software to analyze top‐down mass spectrometry data
Fellers, R. T., Greer, J. B., Early, B. P., Yu, X., LeDuc, R. D., Kelleher, N. L., & Thomas, P. M. (2015) · PROTEOMICS · doi:10.1002/pmic.201400313 · Cited by 247 · see citing works
Self-citationZolot, R. S., Basu, S., & Million, R. P. (2013) · Nature Reviews Drug Discovery · doi:10.1038/nrd3980 · Cited by 229 · see citing works
Zhurov, K. O., Fornelli, L., Wodrich, M. D., Laskay, Ü. A., & Tsybin, Y. O. (2013) · Chemical Society Reviews · doi:10.1039/c3cs35477f · Cited by 226 · see citing works
Self-citationFornelli, L., Ayoub, D., Aizikov, K., Beck, A., & Tsybin, Y. O. (2014) · Analytical Chemistry · doi:10.1021/ac4036857 · Cited by 178 · see citing works
Self-citationAnalysis 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
Self-citationInformed-Proteomics: open-source software package for top-down proteomics
Park, J., Piehowski, P., Wilkins, C. S., Zhou, M., Mendoza, J., Fujimoto, G. M., Gibbons, B. C., Shaw, J., Shen, Y., Shukla, A. K., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4388 · Cited by 153 · see citing works
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
Self-citationMao, 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
A protease for 'middle-down' proteomics
Wu, C., Tran, J. C., Zamdborg, L., Durbin, K. R., Li, M., Ahlf, D. R., Early, B. P., Thomas, P. M., Sweedler, J. V., & Kelleher, N. L. (2012) · Nature Methods · doi:10.1038/nmeth.2074 · Cited by 128 · see citing works
Self-citationCover Picture: Proteomics 7'15
Fellers, R. T., Greer, J. B., Early, B. P., Yu, X., LeDuc, R. D., Kelleher, N. L., & Thomas, P. M. (2015) · PROTEOMICS · doi:10.1002/pmic.201570050 · Cited by 122 · see citing works
Self-citationBrunner, A. M., Lössl, P., Liu, F., Huguet, R., Mullen, C., Yamashita, M., Zabrouskov, V., Makarov, A., Altelaar, M. A. F., & Heck, A. J. R. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b00162 · Cited by 121 · see citing works
Self-citationSjögren, J., Olsson, F., & Beck, A. (2016) · The Analyst · doi:10.1039/c6an00071a · Cited by 105 · see citing works
Stoll, D., Harmes, D., Danforth, J., Wagner, E., Guillarme, D., Fekete, S., & Beck, A. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b01578 · Cited by 103 · see citing works
Cleland, T. P., DeHart, C. J., Fellers, R. T., VanNispen, A. J., Greer, J. B., LeDuc, R. D., Parker, W. R., Thomas, P. M., Kelleher, N. L., & Brodbelt, J. S. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00043 · Cited by 96 · see citing works
Self-citationMullard, A. (2016) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2016.15 · Cited by 94 · see citing works
Enhanced Fourier transform for Orbitrap mass spectrometry
Lange, O., Damoc, E., Wieghaus, A., & Makarov, A. (2014) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2014.05.019 · Cited by 89 · see citing works
Activated Ion-Electron Transfer Dissociation Enables Comprehensive Top-Down Protein Fragmentation
Riley, N. M., Westphall, M. S., & Coon, J. J. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00249 · Cited by 79 · see citing works
Fornelli, L., Ayoub, D., Aizikov, K., Liu, X., Damoc, E., Pevzner, P. A., Makarov, A., Beck, A., & Tsybin, Y. O. (2017) · Journal of Proteomics · doi:10.1016/j.jprot.2017.02.013 · Cited by 70 · see citing works
Self-citationFront-End Electron Transfer Dissociation: A New Ionization Source
Earley, L., Anderson, L. C., Bai, D. L., Mullen, C., Syka, J. E. P., English, A. M., Dunyach, J., Stafford, G. C., Shabanowitz, J., Hunt, D. F., et al. (2013) · Analytical Chemistry · doi:10.1021/ac401783f · Cited by 67 · see citing works
Self-citationCotham, V. C., & Brodbelt, J. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.6b00302 · Cited by 63 · see citing works
Enhanced Dissociation of Intact Proteins with High Capacity Electron Transfer Dissociation
Riley, N. M., Mullen, C., Weisbrod, C. R., Sharma, S., Senko, M. W., Zabrouskov, V., Westphall, M. S., Syka, J. E. P., & Coon, J. J. (2015) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-015-1306-8 · Cited by 59 · see citing works
Self-citationAdvantages of Extended Bottom-Up Proteomics Using Sap9 for Analysis of Monoclonal Antibodies
Srzentić, K., Fornelli, L., Laskay, Ü. A., Monod, M., Beck, A., Ayoub, D., & Tsybin, Y. O. (2014) · Analytical Chemistry · doi:10.1021/ac502766n · Cited by 57 · see citing works
Self-citationHe, L., Anderson, L. C., Barnidge, D. R., Murray, D. L., Hendrickson, C. L., & Marshall, A. G. (2017) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-017-1602-6 · Cited by 56 · see citing works
Biosimilars: A Multidisciplinary Perspective
Khraishi, M. M., Stead, D., Lukáš, M., Scotté, F., & Schmid, H. (2016) · Clinical Therapeutics · doi:10.1016/j.clinthera.2016.02.023 · Cited by 54 · see citing works
Bioinformatics Analysis of Top-Down Mass Spectrometry Data with ProSight Lite
DeHart, C. J., Fellers, R. T., Fornelli, L., Kelleher, N. L., & Thomas, P. M. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-6783-4_18 · Cited by 43 · see citing works
Self-citationBrodie, N. I., Huguet, R., Zhang, T., Viner, R., Zabrouskov, V., Pan, J., Petrotchenko, E. V., & Borchers, C. H. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.7b03655 · Cited by 43 · see citing works
Self-citationExtended bottom-up proteomics with secreted aspartic protease Sap9
Laskay, Ü. A., Srzentić, K., Monod, M., & Tsybin, Y. O. (2014) · Journal of Proteomics · doi:10.1016/j.jprot.2014.07.035 · Cited by 30 · see citing works
Self-citationHigh resolution top-down experimental strategies on the Orbitrap platform
Scheffler, K., Viner, R., & Damoc, E. (2017) · Journal of Proteomics · doi:10.1016/j.jprot.2017.03.028 · Cited by 21 · see citing works
Emmanouilides, C. E., Karampola, M. I., & Beredima, M. (2015) · Journal of Oncology Pharmacy Practice · doi:10.1177/1078155215603232 · Cited by 20 · see citing works
He, L., Weisbrod, C. R., & Marshall, A. G. (2017) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2017.11.012 · Cited by 16 · see citing works
FDA approvals for the first 6 months of 2016
Mullard, A. (2016) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2016.161 · Cited by 7 · see citing works
Flagged first, then by citations
Research works printed but not linked: 4
- [14]von Pawel-Rammingen U; Johansson BP; Bjorck L EMBO J 2002, 21, 1607– 1615. 11927545 PMC125946
- [22]Zubarev RA; Kelleher NL; McLafferty FW J. Am. Chem. Soc 1998, 120, 3265– 3266.
- [35]Lange O; Damoc E; Wieghaus A; Makarov A Int. J. Mass Spectrom 2014, 369, 16– 22.
- [44]He L; Weisbrod CR; Marshall AG Int. J. Mass Spectrom 2018, 427, 107– 113.
Cited by
Sorted by citations
ROS-dependent S-palmitoylation activates cleaved and intact gasdermin D
Du, G., Healy, L. B., David, L., Walker, C., El‐Baba, T. J., Lutomski, C. A., Goh, B., Gu, B., Pi, X., Devant, P., et al. (2024) · Nature · doi:10.1038/s41586-024-07373-5 · Cited by 303 · see citing works
Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules
Brodbelt, J. S., Morrison, L. J., & Santos, I. C. (2019) · Chemical Reviews · doi:10.1021/acs.chemrev.9b00440 · Cited by 291 · see citing works
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
Self-citationIon Activation Methods for Peptides and Proteins
Macias, L. A., Santos, I. C., & Brodbelt, J. S. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.9b04859 · Cited by 107 · see citing works
Ro, S., Schachner, L. F., Koo, C. W., Purohit, R., Remis, J., Kenney, G. E., Liauw, B., Thomas, P. M., Patrie, S. M., Kelleher, N., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-10590-6 · Cited by 85 · see citing works
Self-citationProton Transfer Charge Reduction Enables High-Throughput Top-Down Analysis of Large Proteoforms
Huguet, R., Mullen, C., Srzentić, K., Greer, J. B., Fellers, R. T., Zabrouskov, V., Syka, J. E. P., Kelleher, N. L., & Fornelli, L. (2019) · Analytical Chemistry · doi:10.1021/acs.analchem.9b03925 · Cited by 94 · see citing works
Self-citationBeck, A., D’Atri, V., Ehkirch, A., Fekete, S., Hernandez‐Alba, O., Gahoual, R., Leize‐Wagner, E., François, Y., Guillarme, D., & Cianférani, S. (2019) · Expert Review of Proteomics · doi:10.1080/14789450.2019.1578215 · Cited by 90 · see citing works
Middle-down approach: a choice to sequence and characterize proteins/proteomes by mass spectrometry
Pandeswari, P. B., & Sabareesh, V. (2019) · RSC Advances · doi:10.1039/c8ra07200k · Cited by 86 · see citing works
Zhan, X., Li, B., Zhan, X., Schlüter, H., Jungblut, P., & Coorssen, J. (2019) · Proteomes · doi:10.3390/proteomes7040036 · Cited by 71 · see citing works
Mass Spectrometry Methods for Measuring Protein Stability
Vallejo, D. D., Ramírez, C. R., Parson, K. F., Han, Y., Gadkari, V. V., & Ruotolo, B. T. (2022) · Chemical Reviews · doi:10.1021/acs.chemrev.1c00857 · Cited by 82 · see citing works
Instrumentation at the leading edge of proteomics
Peters-Clarke, T. M., Coon, J., & Riley, N. (2024) · Analytical Chemistry · doi:10.1021/acs.analchem.3c04497 · Cited by 78 · see citing works
Shaw, J. B., Liu, W., Vasil′ev, Y. V., Bracken, C. C., Malhan, N., Guthals, A., Beckman, J. S., & Voinov, V. G. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.9b03129 · Cited by 77 · see citing works
Thorough Performance Evaluation of 213 nm Ultraviolet Photodissociation for Top-down Proteomics
Fornelli, L., Srzentić, K., Toby, T. K., Doubleday, P. F., Huguet, R., Mullen, C., Melani, R. D., Seckler, H. S., DeHart, C. J., Weisbrod, C. R., et al. (2019) · Molecular & Cellular Proteomics · doi:10.1074/mcp.tir119.001638 · Cited by 75 · see citing works
Self-citationJin, Y., Lin, Z., Xu, Q., Fu, C., Zhang, Z., Zhang, Q., Pritts, W. A., & Ge, Y. (2019) · mAbs · doi:10.1080/19420862.2018.1525253 · Cited by 68 · see citing works
van der Burgt, Y. E. M., Kilgour, D. P. A., Tsybin, Y. O., Srzentić, K., Fornelli, L., Beck, A., Wuhrer, M., & Nicolardi, S. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b04515 · Cited by 62 · see citing works
Self-citationDecoding the protein composition of whole nucleosomes with Nuc-MS
Schachner, L. F., Jooß, K., Morgan, M. A., Piunti, A., Meiners, M. J., Kafader, J. O., Lee, A. S., Iwanaszko, M., Cheek, M. A., Burg, J. M., et al. (2021) · Nature Methods · doi:10.1038/s41592-020-01052-9 · Cited by 66 · see citing works
Self-citationLiu, 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
Lodge, J. M., Schauer, K. L., Brademan, D. R., Riley, N. M., Shishkova, E., Westphall, M. S., & Coon, J. J. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.0c00705 · Cited by 49 · see citing works
Sanders, J. D., Mullen, C., Watts, E., Holden, D. D., Syka, J. E. P., Schwartz, J. C., & Brodbelt, J. S. (2019) · Analytical Chemistry · doi:10.1021/acs.analchem.9b04026 · Cited by 53 · see citing works
Self-citationShi, L., Xiao, G., Dillon, T. M., Ricci, M. S., & Bondarenko, P. V. (2020) · mAbs · doi:10.1080/19420862.2020.1739825 · Cited by 52 · see citing works
Hale, O. J., Hughes, J. W., Sisley, E. K., & Cooper, H. J. (2022) · Analytical Chemistry · doi:10.1021/acs.analchem.1c05353 · Cited by 48 · see citing works
Gomes, F. P., Diedrich, J. K., Saviola, A. J., Memili, E., Moura, A. A., & Yates, J. R. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.9b03856 · Cited by 46 · see citing works
Accurate Estimation of Context-Dependent False Discovery Rates in Top-Down Proteomics
LeDuc, R. D., Fellers, R. T., Early, B. P., Greer, J. B., Shams, D. P., Thomas, P. M., & Kelleher, N. L. (2019) · Molecular & Cellular Proteomics · doi:10.1074/mcp.ra118.000993 · Cited by 44 · see citing works
Self-citationProSight Native: Defining Protein Complex Composition from Native Top-Down Mass Spectrometry Data
Durbin, K. R., Robey, M. T., Voong, L. N., Fellers, R. T., Lutomski, C. A., El‐Baba, T. J., Robinson, C. V., & Kelleher, N. L. (2023) · Journal of Proteome Research · doi:10.1021/acs.jproteome.3c00171 · Cited by 47 · see citing works
Self-citationA 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
Kline, J. T., Mullen, C. H., Durbin, K. R., Oates, R. N., Huguet, R., Syka, J. E., & Fornelli, L. (2021) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.1c00062 · Cited by 39 · see citing works
Self-citationJooß, K., Schachner, L. F., Watson, R., Gillespie, Z. B., Howard, S. A., Cheek, M. A., Meiners, M. J., Sobh, A., Licht, J. D., Keogh, M., et al. (2021) · Analytical Chemistry · doi:10.1021/acs.analchem.0c04975 · Cited by 44 · see citing works
Self-citationStandard procedures for native CZE-MS of proteins and protein complexes up to 800 kDa
Jooss, K., McGee, J., Melani, R., & Kelleher, N. (2020) · bioRxiv · doi:10.1002/elps.202000317 · Cited by 32 · see citing works
Self-citationAdams, L. M., DeHart, C. J., Drown, B., Anderson, L. C., Bocik, W., Boja, E. S., Hiltke, T., Hendrickson, C. L., Rodriguez, H., Caldwell, M. A., et al. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.102768 · Cited by 38 · see citing works
Self-citationMiddle-Down Multi-Attribute Analysis of Antibody-Drug Conjugates with Electron Transfer Dissociation
Chen, B., Lin, Z., Zhu, Y., Jin, Y., Larson, E., Xu, Q., Fu, C., Zhang, Z., Zhang, Q., Pritts, W. A., et al. (2019) · Analytical Chemistry · doi:10.1021/acs.analchem.9b02194 · Cited by 38 · see citing works
Structural Characterization of Glycosaminoglycan Carbohydrates Using Ultraviolet Photodissociation
Klein, D. R., Leach, F. E., Amster, I. J., & Brodbelt, J. S. (2019) · Analytical Chemistry · doi:10.1021/acs.analchem.9b00521 · Cited by 38 · see citing works
Hernandez‐Alba, O., Houel, S., Hessmann, S., Erb, S., Rabuka, D., Huguet, R., Josephs, J. L., Beck, A., Drake, P. M., & Cianférani, S. (2019) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-019-02296-2 · Cited by 37 · see citing works
Self-citationMelani, R. D., Srzentić, K., Gerbasi, V. R., McGee, J. P., Huguet, R., Fornelli, L., & Kelleher, N. L. (2019) · mAbs · doi:10.1080/19420862.2019.1668226 · Cited by 35 · see citing works
Self-citationTop-down Mass Spectrometry Analysis of Human Serum Autoantibody Antigen-Binding Fragments
Wang, Z., Liu, X., Muther, J. J., James, J. A., Smith, K., & Wu, S. (2019) · Scientific Reports · doi:10.1038/s41598-018-38380-y · Cited by 34 · see citing works
Next-Generation Serology by Mass Spectrometry: Readout of the SARS-CoV-2 Antibody Repertoire
Melani, R. D., Soye, B. J. D., Kafader, J. O., Forte, E., Hollas, M. A. R., Blagojevic, V., Negrão, F., McGee, J. P., Drown, B., Lloyd-Jones, C., et al. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.1c00882 · Cited by 32 · see citing works
Self-citationTop-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
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
Xu, T., Zhang, F., Chen, D., Sun, L., Tomazela, D. M., & Fayadat‐Dilman, L. (2023) · mAbs · doi:10.1080/19420862.2023.2229102 · Cited by 29 · see citing works
Mass Spectrometry Strategies for O-Glycoproteomics
Helms, A., & Brodbelt, J. S. (2024) · Cells · doi:10.3390/cells13050394 · Cited by 28 · see citing works
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
Nagornov, K. O., Kozhinov, A. N., Gasilova, N., Menin, L., & Tsybin, Y. O. (2020) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.0c00190 · Cited by 29 · 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
Defining proteoform-specific interactions for drug targeting in a native cell signalling environment
Lutomski, C. A., Bennett, J. L., El‐Baba, T. J., Wu, D., Hinkle, J. D., Burnap, S. A., Liko, I., Mullen, C., Syka, J. E. P., Struwe, W. B., et al. (2025) · Nature Chemistry · doi:10.1038/s41557-024-01711-w · Cited by 29 · see citing works
Self-citationElevated N-Linked Glycosylation of IgG V Regions in Myasthenia Gravis Disease Subtypes
Mandel‐Brehm, C., Fichtner, M. L., Jiang, R., Winton, V. J., Vazquez, S. E., Pham, M. C., Hoehn, K. B., Kelleher, N. L., Nowak, R. J., Kleinstein, S. H., et al. (2021) · The Journal of Immunology · doi:10.4049/jimmunol.2100225 · Cited by 27 · see citing works
Self-citationTargeted Quantification of Proteoforms in Complex Samples by Proteoform Reaction Monitoring
Huang, C.-F., Kline, J. T., Negrão, F., Robey, M. T., Toby, T. K., Durbin, K. R., Fellers, R. T., Friedewald, J., Levitsky, J., Abecassis, M., et al. (2024) · Analytical Chemistry · doi:10.1021/acs.analchem.3c05578 · Cited by 23 · see citing works
Self-citationImpact of Internal Fragments on Top-Down Analysis of Intact Proteins by 193 nm UVPD
Dunham, S. D., Wei, B., Lantz, C., Loo, J. A., & Brodbelt, J. S. (2022) · Journal of Proteome Research · doi:10.1021/acs.jproteome.2c00583 · Cited by 24 · see citing works
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
Rommelfanger, S. R., Zhou, M., Shaghasi, H., Tzeng, S., Evans, B. S., Paša‐Tolić, L., Umen, J., & Pesavento, J. J. (2021) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.1c00029 · Cited by 23 · see citing works
Blevins, M. S., Kim, D., Crittenden, C. M., Hong, S., Yeh, H., Petty, J. T., & Brodbelt, J. S. (2019) · ACS Nano · doi:10.1021/acsnano.9b06470 · Cited by 24 · see citing works
Walker, J. N., Lam, R., & Brodbelt, J. S. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.2c05765 · Cited by 22 · 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
The Proteoform Landscape of Tau from the Human Brain
Xu, T., Su, T., Soye, B. J. D., Kandi, S., Huang, C., Wilkins, J. T., Castellani, R. J., Kafader, J. O., Patrie, S. M., Vassar, R. J., et al. (2025) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5c00139 · Cited by 20 · see citing works
Self-citationAnalytical tools for the characterization of deamidation in monoclonal antibodies
Spanov, B., Govorukhina, N. I., van de Merbel, N. C., & Bischoff, R. (2021) · Journal of Chromatography Open · doi:10.1016/j.jcoa.2021.100025 · Cited by 19 · see citing works
Kellie, J. F., Schneck, N. A., Causon, J., Baba, T., Mehl, J. T., & Pohl, K. I. (2022) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.2c00206 · Cited by 19 · see citing works
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
Mojumdar, A., Yoo, H.-J., Kim, D., Park, J., Park, S., Jeon, E., Choi, S., Choi, J. H., Park, M., Bang, G., et al. (2024) · Journal of Analytical Science & Technology · doi:10.1186/s40543-024-00437-1 · Cited by 19 · see citing works
Oates, R. N., Lieu, L. B., Kline, J. T., Mullen, C., Srzentić, K., Huguet, R., McAlister, G. C., Huang, J., Bergen, D., Melani, R. D., et al. (2024) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-024-05534-z · Cited by 18 · see citing works
Self-citationSchachner, L. F., Soye, B. D., Ro, S., Kenney, G. E., Ives, A. N., Su, T., Goo, Y., Jewett, M. C., Rosenzweig, A., & Kelleher, N. (2022) · ACS Chemical Biology · doi:10.1021/acschembio.2c00324 · Cited by 16 · see citing works
Self-citationLC-MS characterization of antibody-based therapeutics
Robotham, A. C., & Kelly, J. F. (2020) · Elsevier eBooks · doi:10.1016/b978-0-08-103019-6.00001-1 · Cited by 17 · see citing works
MS-TAFI: A Tool for the Analysis of Fragment Ions Generated from Intact Proteins.
Juetten, K. J., & Brodbelt, J. (2022) · Journal of Proteome Research · doi:10.1021/acs.jproteome.2c00594 · Cited by 14 · see citing works
A multiparameter optimization in middle‐down analysis of monoclonal antibodies by LC–MS/MS
Dhenin, J., Dupré, M., Druart, K., Krick, A., Mauriac, C., & Chamot‐Rooke, J. (2023) · Journal of Mass Spectrometry · doi:10.1002/jms.4909 · 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
Lieu, L. B., Nagy, C., Huang, J., Mullen, C., McAlister, G. C., Zabrouskov, V., Srzentić, K., Durbin, K. R., Melani, R. D., & Fornelli, L. (2024) · Analytical Chemistry · doi:10.1021/acs.analchem.4c03872 · Cited by 15 · see citing works
Self-citationUltraviolet Photodissociation of Protonated Peptides and Proteins Can Proceed with H/D Scrambling
Modzel, M., Wollenberg, D. T. W., Trelle, M. B., Larsen, M. R., & Jørgensen, T. J. D. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.0c02957 · Cited by 15 · see citing works
Schachner, L. F., Tran, D. P., Lee, A. S., McGee, J. P., Jooß, K., Durbin, K. R., Seckler, H. S., Adams, L. M., Cline, E. N., Melani, R. D., et al. (2021) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2021.116591 · Cited by 15 · see citing works
Self-citationWei, 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
Self-citationCheng, J., Wang, L., Rive, C. M., Holt, R. A., Morin, G. B., & Chen, D. D. Y. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00223 · Cited by 14 · see citing works
Griaud, F., Denefeld, B., Kao‐Scharf, C., Dayer, J., Lang, M., Chen, J., & Berg, M. (2019) · Analytical Chemistry · doi:10.1021/acs.analchem.8b05886 · Cited by 12 · see citing works
Révész, Á., Rokob, T. A., Fouque, D. J. D., Hüse, D., Háda, V., Turiák, L., Memboeuf, A., Vékey, K., & Drahos, L. (2019) · Analytical Chemistry · doi:10.1021/acs.analchem.9b03362 · Cited by 12 · see citing works
Precise Readout of MEK1 Proteoforms upon MAPK Pathway Modulation by Individual Ion Mass Spectrometry
Drown, B., Gupta, R., McGee, J. P., Hollas, M. A. R., Hergenrother, P. J., Kafader, J. O., & Kelleher, N. L. (2024) · Analytical Chemistry · doi:10.1021/acs.analchem.3c04758 · Cited by 11 · see citing works
Self-citationKline, J. T., Huang, J., Lieu, L. B., Srzentić, K., Bergen, D., Mullen, C., McAlister, G. C., Durbin, K. R., Melani, R. D., & Fornelli, L. (2024) · PROTEOMICS · doi:10.1002/pmic.202400223 · Cited by 11 · see citing works
Self-citationWeisbrod, C. R., Anderson, L. C., Greer, J. B., DeHart, C. J., & Hendrickson, C. L. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.0c01064 · Cited by 11 · see citing works
Schaffer, L. V., Anderson, L. C., Butcher, D. S., Shortreed, M. R., Miller, R., Pavelec, C. M., & Smith, L. M. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00403 · Cited by 11 · see citing works
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
Self-citationAnalysis of the topology of ubiquitin chains
Geis‐Asteggiante, L., Lee, A. E., & Fenselau, C. (2019) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2019.06.025 · Cited by 11 · see citing works
Fagerquist, C. K. (2020) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2020.116433 · Cited by 11 · see citing works
Zhao, J., Peng, W., Dong, X., & Mechref, Y. S. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00659 · Cited by 11 · see citing works
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
Self-citationDunham, 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
Cejkov, M., Greer, T., Johnson, R. O., Zheng, X., & Li, N. (2021) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.0c00458 · Cited by 9 · see citing works
Dunham, S. D., Sanders, J. D., Holden, D. D., & Brodbelt, J. S. (2022) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.1c00296 · Cited by 9 · see citing works
Watts, E., Bashyal, A., Dunham, S. D., Crittenden, C. M., & Brodbelt, J. S. (2024) · Antibodies · doi:10.3390/antib13020030 · Cited by 8 · see citing works
Hellinger, J., & Brodbelt, J. S. (2024) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.3c00405 · Cited by 8 · see citing works
Dong, H., Xu, Y., Ye, H., Huang, M., Hu, J., Xian, Y., Zeng, X., Bai, W., & Luo, D. (2021) · Food Analytical Methods · doi:10.1007/s12161-021-02168-0 · Cited by 8 · see citing works
DeHart, C. J., Fornelli, L., Anderson, L. C., Fellers, R. T., Lu, D., Hendrickson, C., Lahav, G., Gunawardena, J., & Kelleher, N. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/455527 · Cited by 6 · see citing works
Self-citationCysteine-Directed Isobaric Labeling Combined with GeLC-FAIMS-MS for Quantitative Top-Down Proteomics
Matzanke, T., Kaulich, P. T., Jeong, K., Takemori, A., Takemori, N., Kohlbacher, O., & Tholey, A. (2025) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00835 · Cited by 7 · see citing works
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
Samgina, T. Y., Vasileva, I. D., Zubarev, R. A., & Lebedev, А. T. (2024) · Analytical Chemistry · doi:10.1021/acs.analchem.4c02109 · Cited by 7 · see citing works
Pepi, L. E., Leach, F. E., Klein, D. R., Brodbelt, J. S., & Amster, I. J. (2021) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.1c00119 · Cited by 7 · see citing works
Degnan, D. J., Zemaitis, K. J., Lewis, L. A., McCue, L. A., Bramer, L., Fulcher, J. M., Veličković, D., Paša‐Tolić, L., & Zhou, M. (2023) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.3c00180 · Cited by 6 · see citing works
Kandi, S., Cline, E. N., Rivera, B. M., Viola, K. L., Zhu, J., Condello, C., LeDuc, R. D., Klein, W. L., Kelleher, N. L., & Patrie, S. M. (2023) · Journal of Proteome Research · doi:10.1021/acs.jproteome.3c00353 · Cited by 6 · see citing works
Self-citationNagornov, K. O., Kozhinov, A. N., Gasilova, N., Menin, L., & Tsybin, Y. O. (2022) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.1c00336 · Cited by 6 · see citing works
Advancing Intact Protein Quantitation with Updated Deconvolution Routines
Robey, M. T., Utley, D., Greer, J. B., Fellers, R. T., Kelleher, N. L., & Durbin, K. R. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.3c02345 · Cited by 7 · see citing works
Self-citationIsoForma: An R Package for Quantifying and Visualizing Positional Isomers in Top-Down LC-MS/MS Data
Degnan, D. J., Lewis, L. A., Bramer, L., McCue, L. A., Pesavento, J. J., Zhou, M., & Pena, A. B. (2024) · Journal of Proteome Research · doi:10.1021/acs.jproteome.3c00681 · Cited by 6 · see citing works
How to Deal With Internal Fragment Ions?
Grimaud, A., Babović, M., Holck, F. H., Jensen, O. N., & Schwämmle, V. (2024) · bioRxiv · doi:10.1016/j.mcpro.2024.100896 · Cited by 5 · see citing works
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
Vinh, J. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-814013-0.00017-x · Cited by 5 · see citing works
Characterization of Insulin Dimers by Top-Down Mass Spectrometry
Gammelgaard, S. K., Petersen, S. B., Haselmann, K. F., & Nielsen, P. K. (2020) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.0c00257 · Cited by 5 · see citing works
- Authors
- Fornelli, L., Srzentić, K., Huguet, R., Mullen, C., Sharma, S., Zabrouskov, V., Fellers, R. T., Durbin, K. R., Compton, P. D., & Kelleher, N. L.
- Affiliations
- Northwestern University (US)
- Thermo Fisher Scientific (United States) (US)
- Proteinaceous, Incorporated, Evanston, Illinois 60201, United States
- Corresponding author
- Kelleher, Neil L.
- ORCID
- Venue
- Analytical Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2018-06-12
- Volume
- 90
- Issue
- 14
- Pages
- 8421-8429
- ISSN
- 0003-2700 (ISSN-L)
- 1520-6882
- PMC
- PMC6071867
- OpenAlex
- W2808336234
- Cited by
- 150
- References
- 44
- Citations by year
- 2026: 12 · 2025: 21 · 2024: 24 · 2023: 15 · 2022: 15 · 2021: 22 · 2020: 17 · 2019: 21 · 2018: 3
- FWCI
- 6.80
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Analytical Chemistry (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of General Medical Sciences (GM067193)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Immunology and Microbiology › Immunology › Biosimilars and Bioanalytical Methods
- Keywords
- monoclonal antibodies, top-down mass spectrometry, middle-down mass spectrometry, biosimilars, protein sequence determination, ultraviolet photodissociation, electron transfer dissociation, higher-energy collisional dissociation, ion activation, biologic therapy
- MeSH terms
- Rituximab, Antineoplastic Agents, Immunological, Amino Acid Sequence, Antibodies, Monoclonal, Chromatography, Liquid, Immunoglobulin G, Ions, Mass Spectrometry, Sequence Analysis, Protein
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
