Unabridged Analysis of Human Histone H3 by Differential Top-Down Mass Spectrometry Reveals Hypermethylated Proteoforms from MMSET/NSD2 Overexpression

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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

Accelerating the Field of Epigenetic Histone Modification Through Mass Spectrometry–Based Approaches

Lu, C., Coradin, M., Porter, E. G. P., & Garcia, B. A. (2020) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r120.002257 · Cited by 70 · see citing works

Global profiling of phosphorylation-dependent changes in cysteine reactivity

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Top-Down Characterization of Heavily Modified Histones Using 193 nm Ultraviolet Photodissociation Mass Spectrometry

Greer, S. M., & Brodbelt, J. S. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00801 · Cited by 58 · see citing works

Increasing the Separation Capacity of Intact Histone Proteoforms Chromatography Coupling Online Weak Cation Exchange-HILIC to Reversed Phase LC UVPD-HRMS

Gargano, A. F. G., Shaw, J. B., Zhou, M., Wilkins, C. S., Fillmore, T. L., Moore, R. J., Somsen, G. W., & Paša-Tolić, L. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00458 · Cited by 53 · see citing works

Label-free, direct localization and relative quantitation of the RNA nucleobase methylations m6A, m5C, m3U, and m5U by top-down mass spectrometry

Glasner, H., Riml, C., Micura, R., & Breuker, K. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx470 · Cited by 52 · see citing works

Mass spectrometry‐based characterization of histones in clinical samples: applications, progress, and challenges

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Front-End Electron Transfer Dissociation Coupled to a 21 Tesla FT-ICR Mass Spectrometer for Intact Protein Sequence Analysis

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Gel-based proteomics in disease research: Is it still valuable?

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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

A Targeted, Differential Top-Down Proteomic Methodology for Comparison of ApoA-I Proteoforms in Individuals with High and Low HDL Efflux Capacity

Seckler, H. D. S., Fornelli, L., Mutharasan, R., Thaxton, C., Fellers, R. T., Daviglus, M., Sniderman, A., Rader, D. J., Kelleher, N., Lloyd-Jones, D., et al. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00100 · Cited by 39 · see citing works

Extensive Characterization of Heavily Modified Histone Tails by 193 nm Ultraviolet Photodissociation Mass Spectrometry via a Middle–Down Strategy

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Deciphering the Interplay among Multisite Phosphorylation, Interaction Dynamics, and Conformational Transitions in a Tripartite Protein System

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The Contribution of Mass Spectrometry-Based Proteomics to Understanding Epigenetics

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Estimating the Distribution of Protein Post-Translational Modification States by Mass Spectrometry

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Improving data quality and preserving HCD-generated reporter ions with EThcD for isobaric tag-based quantitative proteomics and proteome-wide PTM studies

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Characterizing crosstalk in epigenetic signaling to understand disease physiology

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Top-down mass spectrometry of histone modifications in sorghum reveals potential epigenetic markers for drought acclimation

Zhou, M., Malhan, N., Ahkami, A. H., Engbrecht, K., Myers, G., Dahlberg, J., Hollingsworth, J., Sievert, J. A., Hutmacher, R., Madera, M., et al. (2020) · Methods · doi:10.1016/j.ymeth.2019.10.007 · Cited by 23 · see citing works

Combining SDS‐PAGE to capillary zone electrophoresis‐tandem mass spectrometry for high‐resolution top‐down proteomics analysis of intact histone proteoforms

Fang, F., Gao, G., Wang, Q., Wang, Q., & Sun, L. (2024) · PROTEOMICS · doi:10.1002/pmic.202300650 · Cited by 22 · see citing works

Enhanced Characterization of Histones Using 193 nm Ultraviolet Photodissociation and Proton Transfer Charge Reduction

Walker, J. N., Lam, R., & Brodbelt, J. S. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.2c05765 · Cited by 22 · see citing works

Top-down/Bottom-up Mass Spectrometry Workflow Using Dissolvable Polyacrylamide Gels

Takemori, N., Takemori, A., Wongkongkathep, P., Nshanian, M., Loo, R. R. O., Lermyte, F., & Loo, J. A. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.7b00357 · Cited by 22 · 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

Capillary zone electrophoresis‐high field asymmetric ion mobility spectrometry‐tandem mass spectrometry for top‐down characterization of histone proteoforms

Wang, Q., Fang, F., Wang, Q., & Sun, L. (2023) · PROTEOMICS · doi:10.1002/pmic.202200389 · Cited by 20 · see citing works

Bullet points to evaluate the performance of the middle-down proteomics workflow for histone modification analysis

Coradin, M., Mendoza, M. R., Sidoli, S., Alpert, A. J., Lu, C., & Garcia, B. A. (2020) · Methods · doi:10.1016/j.ymeth.2020.01.013 · Cited by 20 · see citing works

Quantitative Top–Down Proteomics Reveals Significant Differences in Histone Proteoforms Between Metastatic and Nonmetastatic Colorectal Cancer Cells

Fang, F., Fries, B. D., Wang, Z., Liu, X., Hummon, A. B., & Sun, L. (2025) · PROTEOMICS · doi:10.1002/pmic.202400336 · Cited by 19 · see citing works

Simultaneous Proteoform Analysis of Histones H3 and H4 with a Simplified Middle-Down Proteomics Method

Schräder, C. U., Ziemianowicz, D. S., Merx, K., & Schriemer, D. C. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.7b03948 · Cited by 18 · see citing works

Ultrahigh Resolution Ion Isolation by Stored Waveform Inverse Fourier Transform 21 T Fourier Transform Ion Cyclotron Resonance Mass Spectrometry.

Smith, D. F., Blakney, G. T., Beu, S., Anderson, L. C., Weisbrod, C. R., & Hendrickson, C. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.9b04954 · Cited by 15 · see citing works

Middle-Down Mass Spectrometry Reveals Activity-Modifying Phosphorylation Barcode in a Class C G Protein-Coupled Receptor

Ives, A. N., Dunn, H. A., Afsari, H. S., Seckler, H. S., Foroutan, M., Chavez, E., Melani, R. D., Fellers, R. T., LeDuc, R. D., Thomas, P. M., et al. (2022) · Journal of the American Chemical Society · doi:10.1021/jacs.2c10697 · Cited by 15 · see citing works

Evolution of Mass Spectrometers for High m/z Biological Ion Formation, Transmission, Analysis and Detection: A Personal Perspective

Campuzano, I. D. G., & Loo, J. A. (2025) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.4c00348 · Cited by 20 · see citing works

Proteomics ofPseudomonas aeruginosa: the increasing role of post-translational modifications

Gaviard, C., Jouenne, T., & Hardouin, J. (2018) · Expert Review of Proteomics · doi:10.1080/14789450.2018.1516550 · Cited by 17 · see citing works

A large scale mass spectrometry-based histone screening for assessing epigenetic developmental toxicity

Verhelst, S., Puyvelde, B. V., Willems, S., Daled, S., Cornelis, S., Corveleyn, L., Willems, E., Deforce, D. L. D., Clerck, L. D., & Dhaenens, M. (2022) · Scientific Reports · doi:10.1038/s41598-022-05268-x · Cited by 16 · see citing works

Narrowband Modulation Two-Dimensional Mass Spectrometry and Label-Free Relative Quantification of Histone Peptides

Halper, M., Delsuc, M., Breuker, K., & van Agthoven, M. A. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.0c02843 · Cited by 16 · see citing works

Investigating pathological epigenetic aberrations by epi-proteomics

Robusti, G., Vai, A., Bonaldi, T., & Noberini, R. (2022) · Clinical Epigenetics · doi:10.1186/s13148-022-01371-y · Cited by 14 · see citing works

Ultraviolet Photodissociation of ESI- and MALDI-Generated Protein Ions on a Q-Exactive Mass Spectrometer

Dilillo, M., de Graaf, E. L., Yadav, A., Belov, M. E., & McDonnell, L. A. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00896 · Cited by 13 · 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

Increased Single-Spectrum Top-Down Protein Sequence Coverage in Trapping Mass Spectrometers with Chimeric Ion Loading

Weisbrod, 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

Chromatographic efficiency and selectivity in top-down proteomics of histones

Zhou, Y., Zhang, X., Fornelli, L., Compton, P. D., Kelleher, N. L., & Wirth, M. J. (2016) · Journal of Chromatography B · doi:10.1016/j.jchromb.2016.12.027 · Cited by 10 · see citing works

Genetic, epigenetic, and molecular determinants of multiple myeloma and precursor plasma cell disorders: a pathophysiological overview

Sutanto, H., Sandra, D. Y., Safira, A., Adytia, G. J., Waitupu, A., & Romadhon, P. Z. (2025) · Medical Oncology · doi:10.1007/s12032-025-02807-0 · Cited by 11 · see citing works

Quantifying Positional Isomers (QPI) by Top-Down Mass Spectrometry

Brunner, A. M., Lössl, P., Geurink, P., Ovaa, H., Albanese, P., Altelaar, A. M. M., Heck, A., & Scheltema, R. A. (2021) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2021.100070 · Cited by 9 · see citing works

Proteomic approaches for cancer epigenetics research

Marchione, D. M., Garcia, B. A., & Wojcik, J. B. (2018) · Expert Review of Proteomics · doi:10.1080/14789450.2019.1550363 · Cited by 7 · see citing works

Targeted detection and quantitation of histone modifications from 1,000 cells

Abshiru, N. A., Sikora, J. W., Camarillo, J. M., Morris, J. A., Compton, P. D., Lee, T. H., Neelamraju, Y., Haddox, S., Sheridan, C. K., Carroll, M. P., et al. (2020) · PLoS ONE · doi:10.1371/journal.pone.0240829 · Cited by 7 · see citing works

PrSM-Level Side-by-Side Comparison of Online LC-MS Methods with Intact Histone H3 and H4 Proteoforms

Lui, K.-W., & Ngai, S. M. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.1c00308 · Cited by 5 · see citing works

Profiling Dopamine-Induced Oxidized Proteoforms of β-synuclein by Top-Down Mass Spectrometry

Luise, A., Cecco, E. D., Ponzini, E., Sollazzo, M., Mauri, P., Sobott, F., Legname, G., Grandori, R., & Santambrogio, C. (2021) · Antioxidants · doi:10.3390/antiox10060893 · Cited by 4 · see citing works

The Role of Proteomics in Cancer Research

Panis, C., Corrêa, S., Binato, R., & Abdelhay, E. S. F. W. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-811785-9.00003-x · Cited by 4 · see citing works

Unravelling Post-translational Modification (PTM) Complexity: Advances in Quantitative Histone Proteoform Mass Spectrometry

Poncha, K. F., Paparella, A. T., & Young, N. L. (2025) · Mass spectrometry reviews (Print) · doi:10.1002/mas.21941 · Cited by 6 · see citing works

Small Molecule Inhibitors of the Human Histone Lysine Methyltransferase NSD2 / WHSC1 / MMSET Identified from a Quantitative High-Throughput Screen with Nucleosome SubstratePreprint

Coussens, N. P., Kales, S. C., Henderson, M. J., Lee, O. W., Horiuchi, K. Y., Wang, Y., Chen, Q., Kuznetsova, E., Wu, J., Cheff, D. M., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/208439 · 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

Direct Readout of Multivalent Chromatin Reader-Nucleosome Interactions by Nucleosome Mass Spectrometry

Lee, A. S., Fisher, N. P., Marunde, M., Su, P., Khan, L. F., Ezell, R. J., Gillespie, Z. B., Graham, B., Taylor, H. F., Onuoha, U. C., et al. (2026) · ACS Central Science · doi:10.1021/acscentsci.5c00736

Sequential Ion-Ion Reactions for Enhanced Gas-Phase Sequencing of Large Intact Proteins in a Tribrid Orbitrap Mass SpectrometerPreprint

Kline, J. T., Mullen, C., Durbin, K. R., Oates, R. N., Huguet, R., Syka, J. E. P., & Fornelli, L. (2021) · ChemRxiv · doi:10.26434/chemrxiv.14036810 · Cited by 2 · see citing works

Evaluating C4 and Diphenyl Nanocapillary Columns for Top‐Down Analysis of Endogenous Histone Proteoforms and Larger Proteins

Pathak, K., & Gomes, F. P. (2026) · Journal of Mass Spectrometry · doi:10.1002/jms.70021 · Cited by 2 · see citing works

Histone protein profiling in rice reveals a correlation between canonical and noncanonical function and evolution

Sengupta, A., Narula, K., Sharma, A., Chakraborty, N., & Chakraborty, S. (2024) · Journal of Proteins and Proteomics · doi:10.1007/s42485-024-00129-9 · Cited by 1 · see citing works

Large Scale Toxicoepigenetics on Histones: A Mass Spectrometry-based Screening Assay Applied to Developmental ToxicityPreprint

Verhelst, S., Puyvelde, B. V., Willems, S., Daled, S., Cornelis, S., Corveleyn, L., Willems, E., Deforce, D. L. D., Clerck, L. D., & Dhaenens, M. (2021) · Research Square · doi:10.21203/rs.3.rs-620816/v1 · Cited by 1 · see citing works

Will Liquid Biopsy Deliver the Expected Breakthrough in Clinical Oncology? Contribution of Mass Spectrometry-Based ProteomicsPreprint

Traldi, P., Agostini, M., & Hamdan, M. H. (2024) · Preprints.org · doi:10.20944/preprints202403.1312.v1

Mass Spectrometry and Chemical Biology in Epigenetics Drug Discovery

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Faculty Opinions recommendation of High-Throughput Analysis of Intact Human Proteins Using UVPD and HCD on an Orbitrap Mass Spectrometer.

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EXOSC4 is recruited by histone H3 co-modified with K9me3 and acetylations to surveil non-coding transcriptionPreprint

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La spectrométrie de masse haute résolution : application à la FT-ICR bidimensionnelle et à la protéomique dans les domaines de l’archéologie et la paléontologie

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Combining SDS-PAGE with Capillary Zone Electrophoresis–Tandem Mass Spectrometry for Top-Down Proteomics Analysis of Intact Histone Proteoforms

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Abstract IA26: Aberrant histone methylation in multiple myeloma.

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Histone Methyltransferase MMSET/NSD2 Alters EZH2 Binding and Reprograms the Myeloma Epigenome through Global and Focal Changes in H3K36 and H3K27 Methylation

Popovic, R., Martínez-García, E., Γιαννοπούλου, Ε., Zhang, Q., Zhang, Q., Ezponda, T., Shah, M. Y., Zheng, Y., Will, C., Small, E. C., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004566 · Cited by 240 · see citing works

Histone Methyltransferase MMSET/NSD2 Alters EZH2 Binding and Reprograms the Myeloma Epigenome through Global and Focal Changes in H3K36 and H3K27

Popovic, R., Martínez-García, E., Giannopoulou, E. G., Zhang, Q., Zhang, Q., Ezponda, T., Shah, M. Y., Zheng, Y., Will, C. M., Small, E. C., et al. (2016)

MMSET dysregulates gene expression in myeloma through global and focal changes in H3K36 and H3K27 methylation

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Genome-wide nucleosome mapping in multiple myeloma

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