PEPPI-MS: Polyacrylamide-Gel-Based Prefractionation for Analysis of Intact Proteoforms and Protein Complexes by Mass Spectrometry
Open accessAbstract
Prefractionation of complex mixtures of proteins derived from biological samples is indispensable for proteome analysis via top-down mass spectrometry (MS). Polyacrylamide gel electrophoresis (PAGE), which enables high-resolution protein separation based on molecular size, is a widely used technique in biochemical experiments and has the potential to be useful in sample fractionation for top-down MS analysis. However, the lack of a means to efficiently recover the separated proteins in-gel has always been a barrier to its use in sample prefractionation. In this study, we present a novel experimental workflow, called Passively Eluting Proteins from Polyacrylamide gels as Intact species for MS (“PEPPI-MS”), which allows top-down MS of PAGE-separated proteins. The optimization of Coomassie brilliant blue staining followed by the passive extraction step in the PEPPI-MS workflow enabled the efficient recovery of proteins, separated on commercial precast gels, from a wide range of molecular weight regions in under 10 min. Two-dimensional separation combining offline PEPPI-MS with online reversed-phase liquid chromatographic separation resulted in identification of over 1000 proteoforms recovered from the target region of the gel (≤50 kDa). Given the widespread availability and relatively low cost of traditional sodium dodecyl sulfate (SDS)-PAGE equipment, the PEPPI-MS workflow will be a powerful prefractionation strategy for top-down proteomics.
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Using PEPPI, good protein recovery and high-resolution separation were achieved for top-down proteomics of proteins <50 kDa.
“Using PEPPI, good protein recovery, and high-resolution separation was achieved for top-down proteomics of protein <50 kDa.”
From Top-down proteomics: challenges, innovations, and applications in basic and clinical research (2020) · cites this paper as [85]
PEPPI-MS was introduced as an alternative gel-based separation technique.
“More recently, PEPPI (passively eluting protein from polyacrylamide gel as intact species)-MS was introduced as an alternative gel-based separation technique [85].”
From Top-down proteomics: challenges, innovations, and applications in basic and clinical research (2020) · cites this paper as [85]
Progress in native purification methods (GeLFrEE separation, native gel electrophoresis, ion exchange chromatography, hydrophobic interaction chromatography, and online buffer exchange) has made these methods more applicable for complex mixtures and for characterisation of endogenous ligands.
“In recent years, important progress in native purification methods such as native gel-eluted liquid fraction entrapment electrophoresis (GeLFrEE) separation,36 native gel electrophoresis,37 ion exchange chromatography (IEX),38 hydrophobic interaction chromatography (HIC),39,40 and online buffer exchange, has made these methods more applicable for complex mixtures and for characterisation of endo”
From Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry (2020) · cites this paper as [37]
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Cites
Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4
LAEMMLI, U. K. (1970) · Nature · doi:10.1038/227680a0 · Cited by 249,961 · see citing works
ggplot2: Elegant Graphics for Data Analysis
Wickham, H. (2009) · doi:10.1007/978-0-387-98141-3 · Cited by 14,447 · see citing works
In-gel digestion for mass spectrometric characterization of proteins and proteomes
Shevchenko, A., Tomas, H., Havli, J., Olsen, J. V., & Mann, M. (2006) · Nature Protocols · doi:10.1038/nprot.2006.468 · Cited by 4,867 · see citing works
Wessel, D., & Flügge, U. (1984) · Analytical Biochemistry · doi:10.1016/0003-2697(84)90782-6 · Cited by 3,997 · see citing works
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
Afgan, E., Baker, D., Batut, B., van den Beek, M., Bouvier, D., Čech, M., Chilton, J., Clements, D., Coraor, N., Grüning, B. A., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky379 · Cited by 3,662 · see citing works
UpSetR: an R package for the visualization of intersecting sets and their properties
Conway, J. R., Lex, A., & Gehlenborg, N. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx364 · Cited by 3,586 · see citing works
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
Blue native electrophoresis for isolation of membrane protein complexes in enzymatically active form
Schägger, H., & von JAGOW, G. (1991) · Analytical Biochemistry · doi:10.1016/0003-2697(91)90094-a · Cited by 2,237 · see citing works
The Orbitrap: a new mass spectrometer
Hu, Q., Noll, R. J., Li, H., Makarov, A., Hardman, M., & Cooks, R. G. (2005) · Journal of Mass Spectrometry · doi:10.1002/jms.856 · Cited by 1,338 · see citing works
Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology
Gygi, S. P., Corthals, G. L., Zhang, Y., Rochon, Y. P., & Aebersold, R. H. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.160270797 · Cited by 1,311 · see citing works
Schägger, H., Cramer, W. A., & Vonjagow, G. (1994) · Analytical Biochemistry · doi:10.1006/abio.1994.1112 · Cited by 1,242 · see citing works
Rosenfeld, J., Capdevielle, J., Guillemot, J. C., & Ferrara, P. (1992) · Analytical Biochemistry · doi:10.1016/0003-2697(92)90061-b · Cited by 1,239 · see citing works
Hellman, U., Wernstedt, C., Góñez, L. J., & Heldin, C. (1995) · Analytical Biochemistry · doi:10.1006/abio.1995.1070 · Cited by 753 · see citing works
Mapping intact protein isoforms in discovery mode using top-down proteomics
Tran, J. C., Zamdborg, L., Ahlf, D. R., Lee, J. E., Catherman, A. D., Durbin, K. R., Tipton, J. D., Vellaichamy, A., Kellie, J. F., Li, M., et al. (2011) · Nature · doi:10.1038/nature10575 · Cited by 665 · 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
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
Hendrickson, C. L., Quinn, J. P., Kaiser, N. K., Smith, D. F., Blakney, G. T., Chen, T., Marshall, A. G., Weisbrod, C. R., & Beu, S. C. (2015) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-015-1182-2 · Cited by 278 · see citing works
Wickham, H. (2009) · Springer eBooks · doi:10.1007/978-0-387-98141-3_1 · Cited by 258 · see citing works
Georgiou, C. D., Grintzalis, K., Zervoudakis, G., & Papapostolou, I. (2008) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-008-1996-x · Cited by 248 · see citing works
On the Scalability and Requirements of Whole Protein Mass Spectrometry
Compton, P. D., Zamdborg, L., Thomas, P. M., & Kelleher, N. L. (2011) · Analytical Chemistry · doi:10.1021/ac2010795 · Cited by 243 · see citing works
Senko, M. W., Remes, P. M., Canterbury, J. D., Mathur, R., Song, Q., Eliuk, S. M., Mullen, C., Earley, L., Hardman, M., Blethrow, J. D., et al. (2013) · Analytical Chemistry · doi:10.1021/ac403115c · Cited by 238 · see citing works
Top-Down Proteomics: Ready for Prime Time?
Chen, B., Brown, K. A., Lin, Z., & Ge, Y. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.7b04747 · Cited by 210 · see citing works
Identification and Quantification of Proteoforms by Mass Spectrometry
Schaffer, L. V., Millikin, R. J., Miller, R. M., Anderson, L. C., Fellers, R. T., Ge, Y., Kelleher, N. L., LeDuc, R. D., Liu, X., Payne, S. H., et al. (2019) · PROTEOMICS · doi:10.1002/pmic.201800361 · Cited by 209 · see citing works
Self-citationTran, J. C., & Doucette, A. A. (2008) · Analytical Chemistry · doi:10.1021/ac702197w · Cited by 206 · see citing works
Cohen, S. L., & Chait, B. T. (1997) · Analytical Biochemistry · doi:10.1006/abio.1997.2072 · Cited by 191 · see citing works
Features and applications of blue‐native and clear‐native electrophoresis
Wittig, I., & Schägger, H. (2008) · PROTEOMICS · doi:10.1002/pmic.200800017 · Cited by 184 · see citing works
Surfactant effects on protein structure examined by electrospray ionization mass spectrometry
Loo, R. R. O., Dales, N., & Andrews, P. C. (1994) · Protein Science · doi:10.1002/pro.5560031109 · Cited by 184 · see citing works
Self-citationFractionation of Thylakoid Membranes with the Nonionic Detergent Octyl-β-d-glucopyranoside
Camm, E. L., & Green, B. R. (1980) · PLANT PHYSIOLOGY · doi:10.1104/pp.66.3.428 · Cited by 171 · see citing works
Dual-Pressure Linear Ion Trap Mass Spectrometer Improving the Analysis of Complex Protein Mixtures
Second, T. P., Blethrow, J. D., Schwartz, J. C., Merrihew, G. E., MacCoss, M. J., Swaney, D. L., Russell, J. D., Coon, J. J., & Zabrouskov, V. (2009) · Analytical Chemistry · doi:10.1021/ac901278y · Cited by 160 · see citing works
Cai, W., Tucholski, T., Chen, B., Alpert, A. J., McIlwain, S., Kohmoto, T., Jin, S., & Ge, Y. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.7b00380 · Cited by 135 · see citing works
Multiplexed size separation of intact proteins in solution phase for mass spectrometry.
Tran, J. C., & Doucette, A. (2009) · Analytical Chemistry · doi:10.1021/ac900729r · Cited by 123 · see citing works
Anderson, L. C., DeHart, C. J., Kaiser, N. K., Fellers, R. T., Smith, D. F., Greer, J. B., LeDuc, R. D., Blakney, G. T., Thomas, P. M., Kelleher, N. L., et al. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00696 · Cited by 94 · see citing works
Self-citationStaining of Proteins in Gels with Coomassie G-250 without Organic Solvent and Acetic Acid
Lawrence, A.-M., & Besir, H. (2009) · Journal of Visualized Experiments · doi:10.3791/1350 · Cited by 91 · see citing works
Evaluation of the Compact High-Field Orbitrap for Top-Down Proteomics of Human Cells
Ahlf, D. R., Compton, P. D., Tran, J. C., Early, B. P., Thomas, P. M., & Kelleher, N. L. (2012) · Journal of Proteome Research · doi:10.1021/pr3004216 · Cited by 89 · see citing works
A comprehensive pipeline for translational top-down proteomics from a single blood draw
Toby, T. K., Fornelli, L., Srzentić, K., DeHart, C. J., Levitsky, J., Friedewald, J., & Kelleher, N. L. (2019) · Nature Protocols · doi:10.1038/s41596-018-0085-7 · Cited by 86 · 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
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
Borchers, C. H., Peter, J. F., Hall, M. C., Kunkel, T. A., & Tomer, K. B. (2000) · Analytical Chemistry · doi:10.1021/ac990937m · Cited by 73 · see citing works
Front-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-citationPedersen, S. N., & Francesconi, K. A. (2000) · Rapid Communications in Mass Spectrometry · doi:10.1002/(sici)1097-0231(20000430)14:8 · Cited by 64 · see citing works
Seelert, H., & Krause, F. (2008) · Electrophoresis · doi:10.1002/elps.200800061 · Cited by 62 · 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
Wang, Z., Ma, H., Smith, K., & Wu, S. (2017) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2017.09.001 · Cited by 57 · see citing works
Galvani, M., Hamdan, M. H., & Righetti, P. G. (2000) · Rapid Communications in Mass Spectrometry · doi:10.1002/1097-0231(20001030)14:20 · Cited by 49 · see citing works
FT-ICR MS optimization for the analysis of intact proteins
Tolmachev, A. V., Robinson, E. W., Wu, S., Paša‐Tolić, L., & Smith, R. D. (2008) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2008.10.010 · Cited by 48 · see citing works
Controlled Ion Ejection from an External Trap for Extended m/z Range in FT-ICR Mass Spectrometry
Kaiser, N. K., Savory, J., & Hendrickson, C. L. (2014) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-014-0871-6 · Cited by 46 · see citing works
A Method for the Quantitative Recovery of Proteins from Polyacrylamide Gels
Scheer, J. M., & Ryan, C. A. (2001) · Analytical Biochemistry · doi:10.1006/abio.2001.5384 · Cited by 42 · see citing works
A Method for Label-Free, Differential Top-Down Proteomics
Ntai, I., Toby, T. K., LeDuc, R. D., & Kelleher, N. L. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-3524-6_8 · Cited by 41 · see citing works
Anderson, L. C., English, A. M., Wang, W.-H., Bai, D. L., Shabanowitz, J., & Hunt, D. F. (2015) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2014.06.023 · Cited by 37 · see citing works
Self-citationGalvani, M., Bordini, E., Piubelli, C., & Hamdan, M. H. (2000) · Rapid Communications in Mass Spectrometry · doi:10.1002/(sici)1097-0231(20000115)14:1 · Cited by 37 · see citing works
rawDiag: An R Package Supporting Rational LC–MS Method Optimization for Bottom-up Proteomics
Trachsel, C., Panse, C., Kockmann, T., Wolski, W., Grossmann, J., & Schlapbach, R. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00173 · Cited by 34 · see citing works
Jørgensen, C. S., Jagd, M., Sørensen, B. K., McGuire, J., Barkholt, V., Højrup, P., & Houen, G. (2004) · Analytical Biochemistry · doi:10.1016/j.ab.2004.03.012 · Cited by 30 · see citing works
Jin, Y., & Manabe, T. (2005) · Electrophoresis · doi:10.1002/elps.200410187 · Cited by 30 · see citing works
Zhang, J., Roth, M. J., Chang, A. N., Plymire, D. A., Corbett, J. R., Greenberg, B. M., & Patrie, S. M. (2013) · Analytical Chemistry · doi:10.1021/ac402394w · 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
Self-citationTakemori, N., Komori, N., Thompson, J. N., Yamamoto, M., & Matsumoto, H. (2007) · PROTEOMICS · doi:10.1002/pmic.200700343 · Cited by 21 · see citing works
Self-citationArmirotti, A., Benatti, U., & Damonte, G. (2009) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.3925 · Cited by 20 · see citing works
Electroelution of Proteins from Polyacrylamide Gels
Jenö, P., & Horst, M. (1996) · Springer protocols handbooks/Springer protocols · doi:10.1007/978-1-60327-259-9_32 · Cited by 14 · see citing works
Vanfleteren, J. R. (1989) · Analytical Biochemistry · doi:10.1016/0003-2697(89)90657-x · Cited by 6 · see citing works
ACCURATE DETERMINATION OF MOLECULAR MASS FOR PROTEINS ISOLATED FROM POLYACRYLAMIDE GELS
Asquith, T. N., Takigiku, R., Purdon, M. P., Gauggel, D. L., Keough, T. W., & Lacey, M. P. (1993) · Elsevier eBooks · doi:10.1016/b978-0-12-058757-5.50016-0 · Cited by 3 · see citing works
Greber (1999) · doi:10.1002/(sici)1522-2683(19990101)20:4/5
Self-citation
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Sorted by citations
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Melby, J. A., Roberts, D. S., Larson, E. J., Brown, K. A., Bayne, E. F., Jin, S., & Ge, Y. (2021) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.1c00099 · Cited by 191 · 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
Roberts, D. S., Loo, J. A., Tsybin, Y. O., Liu, X., Wu, S., Chamot-Rooke, J., Agar, J. N., Paša-Tolić, L., Smith, L. M., & Ge, Y. (2024) · Nature Reviews Methods Primers · doi:10.1038/s43586-024-00318-2 · Cited by 154 · 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
Self-citationProteomes Are of Proteoforms: Embracing the Complexity
Carbonara, K., Andonovski, M., & Coorssen, J. R. (2021) · Proteomes · doi:10.3390/proteomes9030038 · Cited by 115 · see citing works
Sample preparation and fractionation techniques for intact proteins for mass spectrometric analysis.
Thomas, S. L., Thacker, J. B., Schug, K. A., & Maráková, K. (2020) · Journal of Separation Science · doi:10.1002/jssc.202000936 · Cited by 51 · see citing works
Recent advances in top‐down proteome sample processing ahead of MS analysis
Nickerson, J. L., Baghalabadi, V., Rajendran, S. R. C. K., Jakubec, P. J., Said, H., McMillen, T. S., Dang, Z., & Doucette, A. A. (2021) · Mass Spectrometry Reviews · doi:10.1002/mas.21706 · Cited by 54 · see citing works
Xu, T., Wang, Q., Wang, Q., & Sun, L. (2024) · Analytical Methods · doi:10.1039/d4ay00651h · Cited by 53 · see citing works
Cassidy, L., Helbig, A. O., Kaulich, P. T., Weidenbach, K., Schmitz, R. A., & Tholey, A. (2020) · Journal of Proteomics · doi:10.1016/j.jprot.2020.103988 · Cited by 52 · see citing works
Kaulich, P. T., Jeong, K., Kohlbacher, O., & Tholey, A. (2024) · Nature Methods · doi:10.1038/s41592-024-02481-6 · Cited by 38 · see citing works
Takemori, A., Kaulich, P. T., Cassidy, L., Takemori, N., & Tholey, A. (2022) · Analytical Chemistry · doi:10.1021/acs.analchem.2c02777 · Cited by 33 · see citing works
Self-citationIdentification of Splice Variants and Isoforms in Transcriptomics and Proteomics
Su, T., Hollas, M. A. R., Fellers, R. T., & Kelleher, N. L. (2023) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-020722-044021 · Cited by 37 · see citing works
Kline, J. T., Belford, M., Boeser, C. L., Huguet, R., Fellers, R. T., Greer, J. B., Greer, S. M., Horn, D., Durbin, K. R., Dunyach, J.-J., et al. (2023) · Journal of Proteome Research · doi:10.1021/acs.jproteome.3c00488 · Cited by 27 · see citing works
Quantitative Top-Down Proteomics by Isobaric Labeling with Thiol-Directed Tandem Mass Tags.
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One-step double network hydrogels of photocurable monomers and bacterial cellulose fibers
Roig-Sánchez, S., Kam, D., Malandain, N., Keneth, E. S., Shoseyov, O., Magdassi, S., Laromaine, A., & Roig, A. (2022) · Carbohydrate Polymers · doi:10.1016/j.carbpol.2022.119778 · Cited by 29 · see citing works
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Guo, Y., Cupp-Sutton, K. A., Zhao, Z.-T., Anjum, S., & Wu, S. (2023) · Analytical Science Advances · doi:10.1002/ansa.202300016 · Cited by 25 · see citing works
Targeted 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
Functional Diversity and Evolution of the Drosophila Sperm Proteome
Garlovsky, M. D., Sandler, J., & Karr, T. L. (2022) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2022.100281 · Cited by 26 · see citing works
Takemori, A., Ishizaki, J., Nakashima, K., Shibata, T., Kato, H., Kodera, Y., Suzuki, T., Hasegawa, H., & Takemori, N. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00749 · Cited by 23 · see citing works
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Habeck, T., & Lermyte, F. (2022) · Essays in Biochemistry · doi:10.1042/ebc20220098 · Cited by 22 · see citing works
Mensah, E. O., Надточий, Л., Adadi, P., & Agyei, D. (2024) · Food Bioscience · doi:10.1016/j.fbio.2024.103975 · Cited by 23 · see citing works
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Forte, E., Sanders, J. M., Pla, I., Kanchustambham, V. L., Hollas, M. A. R., Huang, C.-F., Sanchez, A., Peterson, K. N., Melani, R. D., Huang, A., et al. (2024) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2024.100876 · Cited by 22 · see citing works
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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
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Kline, J. T., Belford, M. W., Huang, J., Greer, J. B., Bergen, D., Fellers, R. T., Greer, S. M., Horn, D. M., Zabrouskov, V., Huguet, R., et al. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.3c01534 · Cited by 16 · see citing works
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Kaulich, P. T., Cassidy, L., & Tholey, A. (2023) · PROTEOMICS · doi:10.1002/pmic.202200542 · Cited by 14 · see citing works
Immunoproteomics: A Review of Techniques, Applications, and Advancements
Gomase, V. S., Dhamane, S. P., & Kakade, P. G. (2024) · Protein and Peptide Letters · doi:10.2174/0109298665333029240926092919 · Cited by 14 · see citing works
GeLC‐FAIMS‐MS workflow for in‐depth middle‐down proteomics
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Self-citationTranslating Senotherapeutic Interventions into the Clinic with Emerging Proteomic Technologies
Dey, A. K., Banarjee, R., Boroumand, M., Rutherford, D. V., Strassheim, Q., Nyunt, T., Olinger, B., & Basisty, N. (2023) · Biology · doi:10.3390/biology12101301 · Cited by 12 · see citing works
TopPICR: A Companion R Package for Top-Down Proteomics Data Analysis
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Gel-Based Sample Fractionation with SP3-Purification for Top-Down Proteomics
Takemori, A., Sugiyama, N., Kline, J. T., Fornelli, L., & Takemori, N. (2025) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00941 · Cited by 12 · see citing works
Self-citationMiles, H. N., Delafield, D. G., & Li, L. (2021) · RSC Chemical Biology · doi:10.1039/d1cb00039j · Cited by 12 · see citing works
Pujari, S. S., Wu, M., Thomforde, J., Wang, Z. A., Chao, C., Olson, N. M., Erber, L. N., Pomerantz, W. C. K., Cole, P. A., & Tretyakova, N. Y. (2021) · Angewandte Chemie International Edition · doi:10.1002/anie.202109418 · Cited by 12 · see citing works
Kaulich, P. T., Winkels, K., Kaulich, T. B., Treitz, C., Cassidy, L., & Tholey, A. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.1c00766 · Cited by 12 · see citing works
Omics in the detection and identification of biosynthetic pathways related to mycotoxin synthesis
González‐López, N. M., Huertas‐Ortiz, K. A., Leguizamón, J. E., Arias-Cortés, M. M., Tere-Peña, C. P., García‐Castañeda, J. E., & Monroy, Z. J. R. (2021) · Analytical Methods · doi:10.1039/d1ay01017d · Cited by 11 · see citing works
Proteomics-based host-specific biomarkers for tuberculosis: The future of TB diagnosis
Pandey, D., & Ghosh, D. (2024) · Journal of Proteomics · doi:10.1016/j.jprot.2024.105245 · Cited by 10 · see citing works
Zou, Y.-Q., Huang, C.-F., Sturrock, G. R., Kelleher, N. L., & Fitzgerald, M. C. (2024) · Analytical Chemistry · doi:10.1021/acs.analchem.4c04469 · Cited by 7 · see citing works
Yun, G., Park, J., Duong, V., Mok, J.-H., Jeon, J., Nam, O., Lee, J., Jin, E., & Lee, H. (2020) · Molecules · doi:10.3390/molecules25133028 · Cited by 9 · see citing works
Zhao, Z., Guo, Y., Cupp‐Sutton, K. A., Wang, Z., Liu, X., & Wu, S. (2025) · Analytical Chemistry · doi:10.1021/acs.analchem.5c02334 · Cited by 8 · see citing works
Cline, E. N., Alvarez, C., Duan, J., & Patrie, S. M. (2021) · Analytical Chemistry · doi:10.1021/acs.analchem.1c00396 · Cited by 8 · see citing works
Cysteine-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
Self-citationSample preparation and cleanup methods for clinical top-down proteomics
Kamal, A., Carfagno, A., Nagy, C., & Fornelli, L. (2025) · Espert Review of Proteomics · doi:10.1080/14789450.2025.2539913 · Cited by 6 · see citing works
Sample preparation for structural mass spectrometry via polyacrylamide gel electrophoresis
Takemori, A., & Takemori, N. (2022) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2022.08.051 · Cited by 7 · see citing works
Self-citationIn-depth structural proteomics integrating mass spectrometry and polyacrylamide gel electrophoresis
Takemori, N., & Takemori, A. (2023) · Frontiers in Analytical Science · doi:10.3389/frans.2022.1107183 · Cited by 4 · see citing works
Self-citationEpigenetic repression of antiviral genes by SARS-CoV-2 NSP1
Anastasakis, D. G., Benhalevy, D., Çuburu, N., Altan‐Bonnet, N., & Hafner, M. (2024) · PLoS ONE · doi:10.1371/journal.pone.0297262 · Cited by 6 · see citing works
Properties, Origin, and Consistency of Truncated Proteoforms Across Top-Down Proteomic Studies
Kaulich, P. T., Fulcher, J., & Tholey, A. (2025) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2025.101465 · Cited by 3 · see citing works
Rogers, H. T., Melby, J. A., Ehlers, L. E., Fischer, M. S., Larson, E. J., Gao, Z., Rossler, K. J., Wang, D.-J., Alpert, A. J., & Ge, Y. (2024) · Analytical Chemistry · doi:10.1021/acs.analchem.3c05733 · Cited by 8 · see citing works
Centrifugal Gel Crushing Tips for Gel-Based Proteome Analysis
Nishida, H., Kanao, E., & Ishihama, Y. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.3c02527 · Cited by 5 · see citing works
Effects of obesity on the cardiac proteome
Vileigas, D., & Cicogna, A. (2021) · Endocrine and Metabolic Science · doi:10.1016/j.endmts.2020.100076 · Cited by 5 · see citing works
Synthesis and polymerase bypass studies of DNA-peptide and DNA-protein conjugates
Pujari, S. S., & Tretyakova, N. Y. (2021) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2021.09.005 · Cited by 4 · see citing works
Proteoform-predictor: Increasing the Phylogenetic Reach of Top-Down Proteomics
Su, T., Fellers, R. T., Greer, J. B., LeDuc, R., Thomas, P. M., & Kelleher, N. L. (2025) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00943 · Cited by 3 · see citing works
Comparative Analysis of Proteoform Clean‐Up Methods for In‐Depth Top‐Down Proteomics
Williams, A. A., Firenza, K. N., Carfagno, A., Kline, J. T., & Fornelli, L. (2025) · Proteomics · doi:10.1002/pmic.70067 · Cited by 3 · see citing works
Pujari, S. S., Wu, M., Thomforde, J., Wang, Z. A., Chao, C., Olson, N. M., Erber, L. N., Pomerantz, W. C. K., Cole, P. A., & Tretyakova, N. Y. (2021) · Angewandte Chemie · doi:10.1002/ange.202109418 · Cited by 3 · see citing works
Ramos, Y., Almeida, A., Carpio, J., Rodríguez‐Ulloa, A., Perera, Y., González, L. J., Wiśniewski, J. R., & Besada, V. (2022) · Journal of Separation Science · doi:10.1002/jssc.202100992 · Cited by 3 · see citing works
Liu, N., Zhang, M., Qin, H.-W., Zhao, H., Zhu, Y., Xie, Y., Liu, J., Wang, F.-J., Liu, Z.-Y., & Chang, C. (2026) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6c00159 · Cited by 1 · see citing works
Jakubec, P. J., & Doucette, A. A. (2021) · Analytical Chemistry · doi:10.1021/acs.analchem.1c03549 · Cited by 2 · see citing works
Pavek, J., Frey, B. L., Frost, D. C., Gu, T.-J., Li, L.-J., & Smith, L. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.3c02473 · Cited by 2 · see citing works
Advancements in Chemical Proteomics for Target Identification of Natural Products in Live Cells
Banday, A. H., Ashraf, I., Bashir, M., Yousuf, A., Qayoom, B., Bhat, M. A., Nabi, S., Maqbool, S., & Lone, M. A. (2024) · The Natural Products Journal · doi:10.2174/0122103155290163240528065607 · Cited by 2 · see citing works
Takemori, A., Kaulich, P. T., Tholey, A., & Takemori, N. (2025) · Proteomics · doi:10.1002/pmic.70007 · Cited by 2 · see citing works
Self-citationIntact Mass Proteomics using a Proteoform Atlas
Pavek, J., Whitworth, I. T., Nakayama, L., Scalf, M., Frey, B. L., & Smith, L. (2024) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00838
Proteoforms in Disease: Biomedical Applications of Top-Down Proteomics
Rogers, H. T., Gregorich, Z., Gant, M. S., Gao, Z., Chamot-Rooke, J., & Ge, Y. (2026) · Mass spectrometry reviews (Print) · doi:10.1002/mas.70042 · Cited by 1 · see citing works
Takemori, N. (2022) · SEIBUTSU BUTSURI KAGAKU · doi:10.2198/electroph.66.53
Self-citationCentrifugal Gel Crushing for Gel-based Proteome AnalysisPreprint
Nishida, H., Kanao, E., & Ishihama, Y. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.06.15.545122
Nanoproteomics: An Approach for the Identification of Molecular Targets Associated with Hypoxia
Priya, J. D. A., Malik, S., Khalid, M., & Gautam, A. (2023) · Smart nanomaterials technology · doi:10.1007/978-981-99-1718-1_8
Artificial Intelligence Applications for Producing Glycosylated Biopharmaceutical Drug Modalities
von Horsten, H. H. (2024) · Management for professionals · doi:10.1007/978-3-031-47768-3_4
Gel Electrophoresis in Protein and Peptide Analysis: History and Current Status
Kaplan, B. (2025) · Encyclopedia of Analytical Chemistry · doi:10.1002/9780470027318.a1613.pub2
Ma, N., Lan, Y., Ding, N., Ding, S., Wang, X., & Sun, L. (2025) · SSRN Electronic Journal · doi:10.2139/ssrn.5386896
Ma, N., Lan, Y., Nan, D., Ding, S., Wang, X., & Sun, L. (2025) · SSRN Electronic Journal · doi:10.2139/ssrn.5386899
Single-cell western blotting of cytoplasmic cytokeratin 8 proteoforms
Khartchenko, A. F., Lam, T., & Herr, A. E. (2025) · The Analyst · doi:10.1039/d5an00776c
Li, J., Shi, Z., Du, X., Dong, G., Pan, Y., Chen, R.-T., Qiu, M., Xu, Y., Xu, L., Liu, D., et al. (2025) · ACS Applied Polymer Materials · doi:10.1021/acsapm.5c03172
Bioactive peptides from plant-based proteins: Preparation, characterization, and health benefits
Aslam, R., & Kaur, G. (2026) · Elsevier eBooks · doi:10.1016/b978-0-443-32976-0.00001-1
Ma, N., Lan, Y., Ding, N., Ding, S., Gao, X., Gong, X., Wang, X., & Cui, Y. (2026) · Food Chemistry X · doi:10.1016/j.fochx.2026.103868
Selective prefractionation of fluorescent glycan samples by cathodic electrophoresisPreprint
Vater, V., Lankamp, F., Dallinger, T., Müller, B., & von Horsten, H. H. (2026) · SSRN Electronic Journal · doi:10.2139/ssrn.6840222
Protein Aggregation Capture for Top-down ProteomicsPreprint
Feltenstein, I. G., & Drown, B. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.07.02.736076
Mishra, K., Malathi, V. M., Behera, C., Fathima, R., Venkateswarlu, R., Satyavathi, C. T., & Krishnan, V. (2026) · Royal Society of Chemistry eBooks · doi:10.1039/9781837677405-00054
Fang, F., & Sun, L. (2026) · Methods in molecular biology · doi:10.1007/978-1-0716-5166-7_12
Takemori, A., Kline, J. T., Fornelli, L., & Takemori, N. (2026) · Methods in molecular biology · doi:10.1007/978-1-0716-5166-7_13
Self-citationThe Proteoform Landscape of Current Top-Down ProteomicsPreprint
Tholey, A., & Kaulich, P. T. (2026) · Research Square · doi:10.21203/rs.3.rs-10574514/v1
Wang, D., Wu, J., Zheng, X., Fan, Z., Li, Z., Peng, C., Xu, B., & Zheng, T. (2026) · Molecules · doi:10.3390/molecules31183307
Advances in Sample Preparation for Protein Top-Down Mass Spectrometry
ZHANG, M., Xue, J., Yang, S., Yongliang, Y. U., Zheyi, L. I. U., & Fangjun, W. A. N. G. (2026) · Analysis and Testing Technology and Instruments · doi:10.3724/j.1006-3757.2026.05.004
Protein Aggregation Capture for Top-Down Proteomics
Feltenstein, I. G., & Drown, B. (2026) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6c00583
Decoding Emerging Protein Post-Translational Modifications Through Chemical Biology
Symasek, A., Ma, X., & Zheng, Q. (2026) · Proteomes · doi:10.3390/proteomes14040054
Quantitative Top‐Down Proteomics: A Review
Cupp‐Sutton, K. A., Atallah, M. A., Zhao, Z., Anjum, S., Chowdhury, T., Sunny, A. T., Szamweber, P., & Wu, S. (2026) · Mass Spectrometry Reviews · doi:10.1002/mas.70051
- Authors
- Takemori, A., Butcher, D. S., Harman, V. M., Brownridge, P., Shima, K., Higo, D., Ishizaki, J., Hasegawa, H., Suzuki, J., Yamashita, M., Loo, J. A., Loo, R. R. O., Beynon, R. J., Anderson, L. C., & Takemori, N.
- Affiliations
- Ehime University (JP)
- Florida State University (US)
- University of Liverpool (GB)
- Shimadzu (Japan) (JP)
- Thermo Fisher Scientific (Japan) (JP)
- University of California, Los Angeles (US)
- Corresponding author
- Anderson, Lissa C.
- Takemori, Nobuaki
- ORCID
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2020-06-15
- Volume
- 19
- Issue
- 9
- Pages
- 3779-3791
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- PMC
- PMC8141340
- OpenAlex
- W3034535568
- Cited by
- 90
- References
- 61
- Citations by year
- 2026: 15 · 2025: 16 · 2024: 16 · 2023: 15 · 2022: 8 · 2021: 13 · 2020: 7
- FWCI
- 4.10
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Journal of Proteome Research (publishedVersion, other-oa)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- U.S. Department of Health and Human Services (R01GM103479, R01GM104610)
- National Science Foundation (DMR-1644779)
- Research Councils UK (BB/M025756/1, BB/R005311/1)
- Ministry of Education, Culture, Sports, Science and Technology (16K08937, 18H04559, 19K05526)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Keywords
- top-down proteomics, polyacrylamide gel electrophoresis, proteoforms, protein complexes, Coomassie blue staining, two-dimensional separation, reversed-phase liquid chromatography
- MeSH terms
- Polyacrylamides, Acrylic Resins, Electrophoresis, Polyacrylamide Gel, Mass Spectrometry
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