Systematic optimization of long gradient chromatography mass spectrometry for deep analysis of brain proteome
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The development of high-resolution liquid chromatography (LC) is essential for improving the sensitivity and throughput of mass spectrometry (MS)-based proteomics. Here we present systematic optimization of a long gradient LC-MS/MS platform to enhance protein identification from a complex mixture. The platform employed an in-house fabricated, reverse-phase long column (100 μm × 150 cm, 5 μm C18 beads) coupled to Q Exactive MS. The column was capable of achieving a peak capacity of ∼700 in a 720 min gradient of 10-45% acetonitrile. The optimal loading level was ∼6 μg of peptides, although the column allowed loading as many as 20 μg. Gas-phase fractionation of peptide ions further increased the number of peptide identification by ∼10%. Moreover, the combination of basic pH LC prefractionation with the long gradient LC-MS/MS platform enabled the identification of 96,127 peptides and 10,544 proteins at 1% protein false discovery rate in a post-mortem brain sample of Alzheimer's disease. Because deep RNA sequencing of the same specimen suggested that ∼16,000 genes were expressed, the current analysis covered more than 60% of the expressed proteome. Further improvement strategies of the LC/LC-MS/MS platform were also discussed.
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The acquisition of rich proteomic information is largely attributed to access to high quality AD brain tissue and the strength of the optimized MS-based proteomics platform.
“The acquisition of such rich proteomic information is largely attributed to the access to high quality AD brain tissue (Beach et al., 2015) and the strength of the optimized mass spectrometry-based proteomics platform, including multiplex TMT isobaric labeling (Niu et al., 2017), extensive long gradient LC/LC coupled with high resolution MS/MS analysis (Wang et al., 2015), a refined phosphopeptide”
From Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer’s Disease Progression (2020) · cites this paper as Wang et al., 2015
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Cites
Mass spectrometry-based proteomics
Aebersold, R., & Mann, M. (2003) · Nature · doi:10.1038/nature01511 · Cited by 6,955 · see citing works
Eng, J. K., McCormack, A. L., & Yates, J. R. (1994) · Journal of the American Society for Mass Spectrometry · doi:10.1016/1044-0305(94)80016-2 · Cited by 6,484 · see citing works
Elias, J. E., & Gygi, S. P. (2007) · Nature Methods · doi:10.1038/nmeth1019 · Cited by 3,925 · see citing works
An anatomically comprehensive atlas of the adult human brain transcriptome
Hawrylycz, M. J., Lein, E. S., Guillozet-Bongaarts, A. L., Shen, E. H., Ng, L., Miller, J. A., van de Lagemaat, L. N., Smith, K. A., Ebbert, A., Riley, Z. L., et al. (2012) · Nature · doi:10.1038/nature11405 · Cited by 3,083 · see citing works
Self-citationA draft map of the human proteome
Kim, M.-S., Pinto, S. M., Getnet, D., Nirujogi, R. S., Manda, S. S., Chaerkady, R., Madugundu, A. K., Kelkar, D. S., Isserlin, R., Jain, S., et al. (2014) · Nature · doi:10.1038/nature13302 · Cited by 2,198 · see citing works
Analytical Properties of the Nanoelectrospray Ion Source
Wilm, M. S., & Mann, M. (1996) · Analytical Chemistry · doi:10.1021/ac9509519 · Cited by 1,866 · see citing works
Mass-spectrometry-based draft of the human proteome
Wilhelm, M., Schlegl, J., Hahne, H., Gholami, A. M., Lieberenz, M., Savitski, M. M., Ziegler, E., Butzmann, L., Gessulat, S., Marx, H., et al. (2014) · Nature · doi:10.1038/nature13319 · Cited by 1,820 · see citing works
Kulak, N. A., Pichler, G., Paron, I., Nagaraj, N., & Mann, M. (2014) · Nature Methods · doi:10.1038/nmeth.2834 · Cited by 1,719 · see citing works
Peng, J., Elias, J. E., Thoreen, C. C., Licklider, L., & Gygi, S. P. (2002) · Journal of Proteome Research · doi:10.1021/pr025556v · Cited by 1,652 · see citing works
Self-citationHYMAN, B. T., & TROJANOWSKI, J. Q. (1997) · Journal of Neuropathology and Experimental Neurology · doi:10.1097/00005072-199710000-00002 · Cited by 1,542 · see citing works
Protein 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
Xu, P., Duong, D. M., Seyfried, N. T., Cheng, D., Xie, Y., Robert, J., Rush, A. J., Hochstrasser, M., Finley, D. J., & Peng, J. (2009) · Cell · doi:10.1016/j.cell.2009.01.041 · Cited by 1,125 · see citing works
Self-citationDeep proteome and transcriptome mapping of a human cancer cell line
Nagaraj, N., Wisniewski, J. R., Geiger, T., Cox, J., Kircher, M., Kelso, J., Pääbo, S., & Mann, M. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.81 · Cited by 979 · see citing works
Geiger, T., Wehner, A., Schaab, C., Cox, J., & Mann, M. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.014050 · Cited by 797 · see citing works
Integrated proteomic analysis of post-translational modifications by serial enrichment
Mertins, P., Qiao, J., Patel, J., Udeshi, N. D., Clauser, K. R., Mani, D. R., Burgess, M. W., Gillette, M. A., Jaffe, J. D., & Carr, S. A. (2013) · Nature Methods · doi:10.1038/nmeth.2518 · Cited by 619 · see citing works
Wang, Y., Yang, F., Gritsenko, M. A., Wang, Y., Clauss, T. R., Liu, T., Shen, Y., Monroe, M. E., López‐Ferrer, D., Reno, T. A., et al. (2011) · PROTEOMICS · doi:10.1002/pmic.201000722 · Cited by 600 · see citing works
Self-citationHebert, A. S., Richards, A. L., Bailey, D. J., Ulbrich, A., Coughlin, E. E., Westphall, M. S., & Coon, J. J. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.034769 · Cited by 528 · see citing works
Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis
Griffin, N. M., Yu, J., Long, F., Oh, P., Shore, S., Li, Y., Koziol, J., & Schnitzer, J. E. (2009) · Nature Biotechnology · doi:10.1038/nbt.1592 · Cited by 400 · see citing works
Self-citationMaximum number of components resolvable by gel filtration and other elution chromatographic methods
Giddings, J. C. (1967) · Analytical Chemistry · doi:10.1021/ac60252a025 · Cited by 380 · see citing works
Michalski, A., Damoc, E., Lange, O., Denisov, E., Nolting, D., Müller, M., Viner, R., Schwartz, J., Remes, P., Belford, M., et al. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o111.013698 · Cited by 373 · see citing works
The Coming Age of Complete, Accurate, and Ubiquitous Proteomes
Mann, M., Kulak, N. A., Nagaraj, N., & Cox, J. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.01.029 · Cited by 350 · see citing works
U1 small nuclear ribonucleoprotein complex and RNA splicing alterations in Alzheimer’s disease
Bai, B., Hales, C. M., Chen, P.-C., Gozal, Y., Dammer, E. B., Fritz, J. J., Wang, X., Xia, Q., Duong, D. M., Street, C., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1310249110 · Cited by 335 · see citing works
Self-citationDeep and Highly Sensitive Proteome Coverage by LC-MS/MS Without Prefractionation
Thakur, S. S., Geiger, T., Chatterjee, B., Bandilla, P., Fröhlich, F., Cox, J., & Mann, M. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.003699 · Cited by 335 · see citing works
Shen, Y., Zhao, R., Berger, S. J., Anderson, G., Rodríguez, N., & Smith, R. D. (2002) · Analytical Chemistry · doi:10.1021/ac0202280 · Cited by 284 · see citing works
HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics
Branca, R. M., Orre, L. M., Johansson, H. J., Granholm, V., Huss, M., Pérez-Bercoff, Å., Forshed, J., Käll, L., & Lehtiö, J. (2013) · Nature Methods · doi:10.1038/nmeth.2732 · Cited by 264 · 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
Shen, Y., Zhang, R., Moore, R. J., Kim, J., Metz, T., Hixson, K. K., Zhao, R., Livesay, E. A., Udseth, H. R., & Smith, R. D. (2005) · Analytical Chemistry · doi:10.1021/ac0483062 · Cited by 230 · see citing works
The challenge of the proteome dynamic range and its implications for in‐depth proteomics
Zubarev, R. A. (2013) · PROTEOMICS · doi:10.1002/pmic.201200451 · Cited by 230 · see citing works
Systematical Optimization of Reverse-Phase Chromatography for Shotgun Proteomics
Xu, P., Duong, D. M., & Peng, J. (2009) · Journal of Proteome Research · doi:10.1021/pr900251d · Cited by 202 · see citing works
Self-citationMellors, J. S., & Jorgenson, J. W. (2004) · Analytical Chemistry · doi:10.1021/ac049643d · Cited by 178 · see citing works
Dwivedi, R. C., Spicer, V., Harder, M., Antonovici, M., Ens, W., Standing, K. G., Wilkins, J. A., & Krokhin, O. V. (2008) · Analytical Chemistry · doi:10.1021/ac800984n · Cited by 161 · see citing works
Song, C., Ye, M., Han, G., Jiang, X., Wang, F., Yu, Z., Chen, R., & Zou, H. (2009) · Analytical Chemistry · doi:10.1021/ac9023044 · Cited by 150 · see citing works
Rapid and Deep Human Proteome Analysis by Single-dimension Shotgun Proteomics
Pirmoradian, M., Budamgunta, H., Chingin, K., Zhang, B., Astorga-Wells, J., & Zubarev, R. A. (2013) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o113.028787 · Cited by 144 · see citing works
Wang, X., Stoll, D. R., Schellinger, A. P., & Carr, P. W. (2006) · Analytical Chemistry · doi:10.1021/ac0600149 · Cited by 141 · see citing works
Self-citationKöcher, T., Swart, R., & Mechtler, K. (2011) · Analytical Chemistry · doi:10.1021/ac103243t · Cited by 140 · see citing works
Synaptic Protein Ubiquitination in Rat Brain Revealed by Antibody-based Ubiquitome Analysis
Na, C. H., Jones, D. R., Yang, Y., Wang, X., Xu, Y., & Peng, J. (2012) · Journal of Proteome Research · doi:10.1021/pr300536k · Cited by 128 · see citing works
Self-citationLow, T. Y., van Heesch, S., van den Toorn, H., Giansanti, P., Cristobal, A., Toonen, P. W., Schäfer, S., Hübner, N., van Breukelen, B., Mohammed, S., et al. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.10.041 · Cited by 125 · see citing works
Köcher, T., Pichler, P., Swart, R., & Mechtler, K. (2012) · Nature Protocols · doi:10.1038/nprot.2012.036 · Cited by 107 · see citing works
Gozal, Y. M., Duong, D. M., Gearing, M., Cheng, D., Hanfelt, J., Funderburk, C. D., Peng, J., Lah, J. J., & Levey, A. I. (2009) · Journal of Proteome Research · doi:10.1021/pr900474t · Cited by 92 · see citing works
Self-citationGenome-scale proteome quantification by DEEP SEQ mass spectrometry
Zhou, F., Lu, Y., Ficarro, S. B., Adelmant, G., Jiang, W., Luckey, C. J., & Marto, J. A. (2013) · Nature Communications · doi:10.1038/ncomms3171 · Cited by 92 · see citing works
Scherl, A., Shaffer, S. A., Taylor, G. K., Kulasekara, H. D., Miller, S. I., & Goodlett, D. R. (2008) · Analytical Chemistry · doi:10.1021/ac701680f · Cited by 91 · see citing works
Hsieh, E. J., Bereman, M. S., Durand, S., Valaskovic, G. A., & MacCoss, M. J. (2012) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-012-0508-6 · Cited by 85 · see citing works
Eriksson, J., & Fenyö, D. (2007) · Nature Biotechnology · doi:10.1038/nbt1315 · Cited by 74 · see citing works
Burgess, M. W., Keshishian, H., Mani, D. R., Gillette, M. A., & Carr, S. A. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.034660 · Cited by 73 · see citing works
Zhou, F., Lu, Y., Ficarro, S. B., Webber, J. T., & Marto, J. A. (2012) · Analytical Chemistry · doi:10.1021/ac2031404 · Cited by 64 · see citing works
Zhang, B., Pirmoradian, M., Chernobrovkin, A. L., & Zubarev, R. A. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o114.038877 · Cited by 56 · see citing works
Simplified mass spectra by dual field ionization-electron impact source
Wanless, G. G., & Glock, G. A. (1967) · Analytical Chemistry · doi:10.1021/ac60245a010 · Cited by 48 · see citing works
Shi, T., Fillmore, T., Gao, Y., Zhao, R., He, J., Schepmoes, A., Nicora, C., Wu, C., Chambers, J., Moore, R., et al. (2013) · Analytical Chemistry · doi:10.1021/ac402105s · Cited by 43 · see citing works
Self-citationDayon, L., Sonderegger, B., & Kussmann, M. (2012) · Journal of Proteome Research · doi:10.1021/pr300519c · Cited by 32 · see citing works
Vincent, C. E., Potts, G. K., Ulbrich, A., Westphall, M. S., Atwood, J., Coon, J. J., & Weatherly, D. B. (2013) · Analytical Chemistry · doi:10.1021/ac303352n · Cited by 15 · see citing works
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Bai, B., Wang, X., Li, Y., Chen, P.-C., Yu, K., Dey, K. K., Yarbro, J. M., Han, X., Lutz, B. M., Rao, S., et al. (2020) · Neuron · doi:10.1016/j.neuron.2019.12.015 · Cited by 632 · see citing works
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MethodInfluentialSelf-citationTan, H., Yang, K., Li, Y., Shaw, T. I., Wang, Y., Blanco, D. B., Wang, X., Cho, J.-H., Wang, H., Rankin, S., et al. (2017) · Immunity · doi:10.1016/j.immuni.2017.02.010 · Cited by 372 · see citing works
Self-citationProteomic landscape of Alzheimer’s Disease: novel insights into pathogenesis and biomarker discovery
Bai, B., Vanderwall, D., Li, Y., Wang, X., Poudel, S., Wang, H., Dey, K. K., Chen, P., Yang, K., & Peng, J. (2021) · Molecular Neurodegeneration · doi:10.1186/s13024-021-00474-z · Cited by 252 · see citing works
Self-citationDeng, Z., Lim, J., Wang, Q., Purtell, K., Wu, S., Palomo, G. M., Tan, H., Manfredi, G., Zhao, Y., Peng, J., et al. (2019) · Autophagy · doi:10.1080/15548627.2019.1644076 · Cited by 232 · see citing works
Self-citationHippo/Mst signalling couples metabolic state and immune function of CD8α+ dendritic cells
Du, X., Wen, J., Wang, Y., Karmaus, P. W. F., Khatamian, A., Tan, H., Li, Y., Guy, C. S., Nguyen, T.-L. M., Dhungana, Y., et al. (2018) · Nature · doi:10.1038/s41586-018-0177-0 · Cited by 224 · see citing works
Self-citationGlobal quantitative analysis of the human brain proteome in Alzheimer’s and Parkinson’s Disease
Ping, L., Duong, D. M., Yin, L., Gearing, M., Lah, J. J., Levey, A. I., & Seyfried, N. T. (2018) · Scientific Data · doi:10.1038/sdata.2018.36 · Cited by 221 · see citing works
Wang, H., Dey, K. K., Chen, P.-C., Li, Y., Niu, M., Cho, J.-H., Wang, X., Bai, B., Jiao, Y., Chepyala, S. R., et al. (2020) · Molecular Neurodegeneration · doi:10.1186/s13024-020-00384-6 · Cited by 210 · see citing works
Self-citationStructural analysis of the full-length human LRRK2
Myasnikov, A. G., Zhu, H., Hixson, P. M., Xie, B., Yu, K., Pitre, A., Peng, J., & Sun, J. (2021) · Cell · doi:10.1016/j.cell.2021.05.004 · Cited by 193 · see citing works
Self-citationCheng, Y., Wang, Z., Tan, W., Wang, X., Li, Y., Bai, B., Li, Y., Zhang, S.-F., Yan, H., Chen, Z.-L., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0261-7 · Cited by 136 · see citing works
Self-citationDeep undepleted human serum proteome profiling toward biomarker discovery for Alzheimer’s disease
Dey, K. K., Wang, H., Niu, M., Bai, B., Wang, X., Li, Y., Cho, J.-H., Tan, H., Mishra, A., High, A. A., et al. (2019) · Clinical Proteomics · doi:10.1186/s12014-019-9237-1 · Cited by 135 · see citing works
Self-citationInsights into molecular therapy of glioma: current challenges and next generation blueprint
Rajesh, Y., Pal, I., Banik, P., Chakraborty, S., Borkar, S. A., Dey, G., Mukherjee, A., & Mandal, M. (2017) · Acta Pharmacologica Sinica · doi:10.1038/aps.2016.167 · Cited by 130 · see citing works
Bai, B., Tan, H., Pagala, V., High, A. A., Ichhaporia, V. P., Hendershot, L. M., & Peng, J. (2016) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2016.10.007 · Cited by 119 · see citing works
Self-citation27-Plex Tandem Mass Tag Mass Spectrometry for Profiling Brain Proteome in Alzheimer’s Disease
Wang, Z., Yu, K., Tan, H., Wu, Z., Cho, J.-H., Han, X., Sun, H., Beach, T. G., & Peng, J. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.0c00655 · Cited by 113 · see citing works
Self-citationNiu, M., Cho, J.-H., Kodali, K., Pagala, V., High, A. A., Wang, H., Wu, Z., Li, Y., Bi, W., Zhang, H., et al. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.6b04415 · Cited by 118 · see citing works
Self-citationA Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry
Ahrens, C. H., Wade, J. T., Champion, M. M., & Langer, J. D. (2021) · Journal of Bacteriology · doi:10.1128/jb.00353-21 · Cited by 97 · see citing works
Novel specialized cell state and spatial compartments within the germinal center
Kennedy, D. E., Okoreeh, M. K., Maienschein‐Cline, M., Ai, J., Veselits, M., McLean, K. C., Dhungana, Y., Wang, H., Peng, J., Chi, H., et al. (2020) · Nature Immunology · doi:10.1038/s41590-020-0660-2 · Cited by 95 · see citing works
Self-citationLi, Y., Wang, X., Cho, J.-H., Shaw, T. I., Wu, Z., Bai, B., Wang, H., Zhou, S., Beach, T. G., Wu, G., et al. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00344 · Cited by 88 · see citing works
Self-citationReversed-Phase Liquid Chromatography of Peptides for Bottom-Up Proteomics: A Tutorial
Lenčo, J., Jadeja, S., Naplekov, D. K., Krokhin, O. V., Khalikova, M. A., Chocholouš, P., Urban, J., Broeckhoven, K., Nováková, L., & Švec, F. (2022) · Journal of Proteome Research · doi:10.1021/acs.jproteome.2c00407 · Cited by 72 · see citing works
Wang, H., Diaz, A. K., Shaw, T. I., Li, Y., Niu, M., Cho, J.-H., Paugh, B. S., Zhang, Y., Sifford, J. M., Bai, B., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-11661-4 · Cited by 67 · see citing works
Self-citationLKB1 orchestrates dendritic cell metabolic quiescence and anti-tumor immunity
Wang, Y., Du, X., Wei, J., Long, L., Tan, H., Guy, C. S., Dhungana, Y., Qian, C., Neale, G. A. M., Fu, Y., et al. (2019) · Cell Research · doi:10.1038/s41422-019-0157-4 · Cited by 64 · see citing works
Self-citationAcute depletion of CTCF rewires genome-wide chromatin accessibility
Xu, B., Wang, H., Wright, S., Hyle, J. W., Zhang, Y., Shao, Y., Niu, M., Fan, Y., Rosikiewicz, W., Djekidel, M. N., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02466-0 · Cited by 57 · see citing works
Self-citationChen, P., Han, X., Shaw, T. I., Fu, Y., Sun, H., Niu, M., Wang, Z., Jiao, Y., Teubner, B. J. W., Eddins, D. M., et al. (2022) · Nature Aging · doi:10.1038/s43587-022-00290-0 · Cited by 60 · see citing works
Self-citationDetermination of local chromatin interactions using a combined CRISPR and peroxidase APEX2 system
Qiu, W., Xu, Z., Zhang, M., Zhang, D., Fan, H., Li, T., Wang, Q., Liu, P., Zhu, Z., Du, D., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz134 · Cited by 57 · see citing works
Niu, M., Dai, X., Zou, W., Yu, X., Teng, W., Chen, Q., Sun, X., Yu, W., Ma, H., & Liu, P. (2017) · Translational Neuroscience · doi:10.1515/tnsci-2017-0008 · Cited by 56 · see citing works
Song, G., Hsu, P. Y., & Walley, J. W. (2018) · PROTEOMICS · doi:10.1002/pmic.201800220 · Cited by 47 · see citing works
Zeng, H., Yu, M., Tan, H., Li, Y., Su, W., Shi, H., Dhungana, Y., Guy, C. S., Neale, G. A. M., Cloer, C., et al. (2018) · Science Advances · doi:10.1126/sciadv.aar5701 · Cited by 44 · see citing works
Self-citationTurnover atlas of proteome and phosphoproteome across mouse tissues and brain regions
Li, W., Dasgupta, A., Yang, K., Wang, S., Kumar, N. H., Chepyala, S. R., Yarbro, J. M., Hu, Z., Šalovská, B., Fornasiero, E. F., et al. (2025) · Cell · doi:10.1016/j.cell.2025.02.021 · Cited by 47 · see citing works
Self-citationMass spectrometry and the cellular surfaceome.
Pauwels, J., Fijałkowska, D., Eyckerman, S., & Gevaert, K. (2021) · Mass spectrometry reviews (Print) · doi:10.1002/mas.21690 · Cited by 38 · see citing works
Bwayi, M. N., Garcia-Maldonado, E., Chai, S. C., Xie, B., Chodankar, S., Huber, A. D., Wu, J., Annu, K., Wright, W. C., Lee, H.-M., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac133 · Cited by 42 · see citing works
Self-citationYarbro, J. M., Han, X., Dasgupta, A., Yang, K., Liu, D., Shrestha, H. K., Zaman, M., Wang, Z., Yu, K., Lee, D. G., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-56853-3 · Cited by 41 · see citing works
Self-citationMertz, J. L., Tan, H., Pagala, V., Bai, B., Chen, P., Li, Y., Cho, J., Shaw, T. I., Wang, X., & Peng, J. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.045898 · Cited by 40 · see citing works
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Ravichandran, R., Kodali, K., Peng, J., & Potts, P. R. (2019) · EMBO Reports · doi:10.15252/embr.201847352 · Cited by 39 · see citing works
Self-citationYu, K., Wang, Z., Wu, Z., Tan, H., Mishra, A., & Peng, J. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1024-4_15 · Cited by 38 · see citing works
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He, M.-H., Zong, X., Xu, B., Qi, W., Huang, W., Djekidel, M. N., Zhang, Y., Pagala, V., Li, J., Hao, X., et al. (2024) · The Journal of Experimental Medicine · doi:10.1084/jem.20232068 · Cited by 37 · see citing works
Self-citationHanna, J. A., Garcia, M. R., Go, J. C., Finkelstein, D., Kodali, K., Pagala, V., Wang, X., Peng, J., & Hatley, M. E. (2016) · Cell Death and Disease · doi:10.1038/cddis.2016.159 · Cited by 36 · see citing works
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Liu, D., Yang, S., Kavdia, K., Sifford, J. M., Wu, Z., Xie, B., Wang, Z., Pagala, V., Wang, H., Yu, K., et al. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00426 · Cited by 34 · see citing works
Self-citationHu, J., Jarusiewicz, J., Du, G., Nishiguchi, G., Yoshimura, S., Panetta, J. C., Li, Z., Min, J., Yang, L., Chepyala, D., et al. (2022) · Science Translational Medicine · doi:10.1126/scitranslmed.abo5228 · Cited by 35 · see citing works
Anderson, B. G., Raskind, A. B., Habra, H., Kennedy, R. T., & Evans, C. R. (2021) · Analytical Chemistry · doi:10.1021/acs.analchem.1c02149 · Cited by 31 · see citing works
WSTF nuclear autophagy regulates chronic but not acute inflammation
Wang, Y., Eapen, V. V., Liang, Y., Kournoutis, A., Sherman, M. S., Xu, Y., Onorati, A., Li, X., Zhou, X., Corey, K. E., et al. (2025) · Nature · doi:10.1038/s41586-025-09234-1 · Cited by 30 · see citing works
Self-citationOn-Chip Comparison of the Performance of First- and Second-Generation Micropillar Array Columns
Vankeerberghen, B., Beeck, J. O. D., & Desmet, G. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.3c01829 · Cited by 29 · see citing works
Genetic regulation of human brain proteome reveals proteins implicated in psychiatric disorders
Luo, J., Li, L., Niu, M., Kong, D., Jiang, Y. W., Poudel, S., Shieh, A. W., Cheng, L., Giase, G. M., Grennan, K. S., et al. (2024) · Molecular Psychiatry · doi:10.1038/s41380-024-02576-8 · Cited by 25 · see citing works
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Shen, J., Pagala, V., Breuer, A. M., Peng, J., Ma, B., & Wang, X. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00594 · Cited by 23 · see citing works
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Tu, L., Liu, S., Wang, Y., Zhang, C., & Li, P. (2019) · The Journal of Supercomputing · doi:10.1007/s11227-019-02773-1 · Cited by 22 · see citing works
Chepyala, S. R., Liu, X., Yang, K., Wu, Z., Breuer, A. M., Cho, J.-H., Li, Y., Mancieri, A., Jiao, Y., Zhang, H., et al. (2021) · Analytical Chemistry · doi:10.1021/acs.analchem.1c02309 · Cited by 18 · see citing works
Self-citationCapriotti, A. L., Cavaliere, C., Cavazzini, A., Gasparrini, F., Pierri, G., Piovesana, S., & Laganà, A. (2017) · Journal of Chromatography A · doi:10.1016/j.chroma.2017.03.032 · Cited by 20 · see citing works
Wang, Z., Kavdia, K., Dey, K. K., Pagala, V., Kodali, K., Liu, D., Lee, D. G., Sun, H., Chepyala, S. R., Cho, J.-H., et al. (2020) · Journal of Visualized Experiments · doi:10.3791/61684 · Cited by 22 · see citing works
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Jayathirtha, M., Dupree, E. J., Manzoor, Z., Larose, B., Sechrist, Z., Neagu, A.-N., Petre, B. A., & Darie, C. C. (2020) · Current Protein and Peptide Science · doi:10.2174/1389203721666200726223336 · Cited by 18 · see citing works
High, A. A., Tan, H., Pagala, V., Niu, M., Cho, J.-H., Wang, X., Bai, B., & Peng, J. (2017) · Journal of Visualized Experiments · doi:10.3791/56474 · Cited by 18 · see citing works
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Nguyen, R., Wang, H., Sun, M., Lee, D. G., Peng, J., & Thiele, C. J. (2022) · Neoplasia · doi:10.1016/j.neo.2022.100776 · Cited by 17 · see citing works
Self-citationJiang, W., Zhang, P., Yang, P. H., Kang, N., Liu, J., Aihemaiti, Y., & Tu, H. (2022) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2022.100222 · Cited by 16 · see citing works
Yu, K., Niu, M., Wang, H., Li, Y., Wu, Z., Zhang, B., Haroutunian, V. H., & Peng, J. (2021) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.0c00450 · Cited by 15 · see citing works
Self-citationMin, J., Yang, S., Cai, Y., Vanderwall, D., Wu, Z., Li, S., Liu, S., Liu, B., Wang, J., Ding, Y., et al. (2023) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-023-04803-x · Cited by 13 · see citing works
Self-citationVanderwall, D., Poudel, S., Fu, Y., Cho, J., Shaw, T. I., Mishra, A., High, A. A., Peng, J., & Li, Y. (2021) · Journal of Visualized Experiments · doi:10.3791/62796 · Cited by 16 · see citing works
Self-citationWright, S., Hu, J., Wang, H., Hyle, J. W., Zhang, Y., Du, G., Konopleva, M. Y., Kornblau, S. M., Djekidel, M. N., Rosikiewicz, W., et al. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2220134120 · Cited by 12 · see citing works
Self-citationAn optimization of the LC-MS/MS workflow for deep proteome profiling on an Orbitrap Fusion
Nie, L., Zhu, M., Sun, S., Zhai, L., Wu, Z., Qian, L., & Tan, M. (2015) · Analytical Methods · doi:10.1039/c5ay01900a · Cited by 14 · see citing works
Self-citationFerrari, E., Palma, A. D., & Mauri, P. (2017) · Expert Review of Proteomics · doi:10.1080/14789450.2017.1364629 · Cited by 12 · see citing works
An ABC Transporter Drives Medulloblastoma Pathogenesis by Regulating Sonic Hedgehog Signaling
Wijaya, J., Vo, B. T., Liu, J., Xu, B., Wu, G., Wang, Y., Peng, J., Zhang, J., Janke, L. J., Orr, B. A., et al. (2020) · Cancer Research · doi:10.1158/0008-5472.can-19-2054 · Cited by 13 · see citing works
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Wang, J., Tan, H., Fu, Y., Mishra, A., Sun, H., Wang, Z., Wu, Z., Wang, X., Serrano, G. E., Beach, T. G., et al. (2024) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.4c00067 · Cited by 11 · see citing works
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Zaman, M., Yang, S., Huang, Y., Yarbro, J. M., Hao, Y., Wang, Z., Liu, D., Harper, K. E., Soliman, H., Hemphill, A., et al. (2025) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01657-8 · Cited by 15 · see citing works
Self-citationCutrona, M. B., Wu, J., Yang, K., Peng, J., & Chen, T. (2024) · iScience · doi:10.1016/j.isci.2024.110289 · Cited by 10 · see citing works
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Jain, M., Dhariwal, R., Patil, N., Ojha, S., Tendulkar, R., Tendulkar, M., Dhanda, P. S., Yadav, A., & Kaushik, P. (2023) · Proteomes · doi:10.3390/proteomes11040033 · Cited by 10 · see citing works
Zhang, Y., Wen, Z., Washburn, M. P., & Florens, L. A. (2019) · Journal of Proteome Research · doi:10.1021/acs.jproteome.9b00036 · Cited by 9 · see citing works
de Beeck, J. O., Pauwels, J., Staes, A., Landuyt, N. V., Haver, D. V., de Malsche, W., Desmet, G., Argentini, A., Martens, L., Jacobs, P., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/472134 · Cited by 3 · see citing works
Ray, B., Liu, W., & Fenyö, D. (2017) · Cancer Informatics · doi:10.1177/1176935117725727 · Cited by 8 · see citing works
Fedorov, I. I., Protasov, S. A., Tarasova, I. A., & Gorshkov, M. V. (2024) · Biochemistry (Moscow) · doi:10.1134/s0006297924080017 · Cited by 8 · see citing works
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Erickson, A., Zhou, S., Luo, J., Li, L., Huang, X., Even, Z., Huang, H., Xu, H., Peng, J., Lu, L., et al. (2021) · BMC Genomics · doi:10.1186/s12864-021-08168-y · Cited by 7 · see citing works
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Hissong, R., Evans, K. R., & Evans, C. R. (2022) · Handbook of experimental pharmacology · doi:10.1007/164_2022_617 · Cited by 7 · see citing works
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Shrestha, H. K., Sun, H., Yarbro, J. M., Lee, D., Liu, D., Wang, E., McReynolds, M. G., Zhang, N., Xie, B., Yang, S., et al. (2026) · Cell · doi:10.1016/j.cell.2026.02.026 · Cited by 11 · see citing works
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Li, W., Dasgupta, A., Yang, K., Wang, S., Hemandhar-Kumar, N., Yarbro, J. M., Hu, Z., Šalovská, B., Fornasiero, E. F., Peng, J., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.15.618303 · Cited by 5 · see citing works
Self-citationSilvestre, D. D., Brambilla, F., Agnetti, G., & Mauri, P. (2016) · Springer eBooks · doi:10.1007/978-3-319-31828-8_7 · Cited by 3 · see citing works
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Yu, H., Biswas, P., Rideout, E. J., Cao, Y., & Huan, T. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.08.556930 · Cited by 3 · see citing works
Shrestha, H. K., Sun, H., Wang, J., & Peng, J. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-3934-4_10 · Cited by 2 · see citing works
Self-citationRaj, A., Aggarwal, S., Singh, P., Yadav, A. K., & Dash, D. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.12.033 · Cited by 2 · see citing works
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Zaman, M., Yang, S., Huang, Y., Yarbro, J. M., Hao, Y., Wang, Z., Liu, D., Harper, K. E., Soliman, H., Hemphill, A., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.03.20.644383 · Cited by 2 · see citing works
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Li, L., Wu, Z., Guarracino, A., Villani, F., Kong, D., Mancieri, A., Zhang, A., Saba, L. M., Chen, H., Brožka, H., et al. (2025) · iScience · doi:10.1016/j.isci.2025.112079 · Cited by 1 · see citing works
Self-citationEmekeeva, D. D., Kusainova, T. T., Garibova, L. A., Шелепчиков, А. А., Kononikhin, A. S., Tretyakov, A. V., Лаврухина, О. И., Николаев, Е. Н., Gorshkov, M. V., & Tarasova, I. A. (2025) · Biochemistry (Moscow) · doi:10.1134/s0006297925600930 · Cited by 1 · see citing works
Analysis of Brain Phosphoproteome Using Titanium Dioxide Enrichment and High-Resolution LC-MS/MS
Sifford, J. M., Tan, H., Wang, H., & Peng, J. (2017) · Neuromethods · doi:10.1007/978-1-4939-7119-0_9 · Cited by 1 · see citing works
Self-citationGovekar, R. B. (2022) · Biomedical Journal of Scientific & Technical Research · doi:10.26717/bjstr.2022.43.006944 · Cited by 1 · see citing works
Bayesian optimization of separation gradients to maximize the performance of untargeted LC-MSPreprint
Huan, T., Yu, H., Biswas, P., Rideout, E. J., & Cao, Y. (2023) · Research Square · doi:10.21203/rs.3.rs-3338667/v1 · Cited by 1 · see citing works
Chen, K., Chen, Y., Ren, Y., Wang, Z., Huang, Y., Pan, M., Li, Z., Casey, M. C., Qiao, W., Shi, J., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-78407-x
Self-citationWang, H. (2017) · doi:10.21007/etd.cghs.2017.0441
Self-citationJiang, W., Zhang, P., Yang, P. H., Kang, N., Liu, J., Aihemaiti, Y., & Tu, H. (2021) · SSRN Electronic Journal · doi:10.2139/ssrn.3940631
Tragedía y vida en la poesía de Garacía Rúa
Soler, J. B. (1998) · Alfa: revista de la Asociación Andaluza de Filosofía
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Huang, X., Li, L., Zhou, S., Kong, D., Luo, J., Lu, L., Xu, H., & Wang, X. (2022) · PROTEOMICS · doi:10.1002/pmic.202200120
Self-citationAdditional file 7 of Acute depletion of CTCF rewires genome-wide chromatin accessibility
Xu, B., Wang, H., Wright, S., Hyle, J. W., Zhang, Y., Shao, Y., Niu, M., Fan, Y., Rosikiewicz, W., Djekidel, M. N., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16435840
Self-citationAdditional file 6 of Acute depletion of CTCF rewires genome-wide chromatin accessibility
Xu, B., Wang, H., Wright, S., Hyle, J. W., Zhang, Y., Shao, Y., Niu, M., Fan, Y., Rosikiewicz, W., Djekidel, M. N., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16435837
Self-citationAdditional file 2 of Acute depletion of CTCF rewires genome-wide chromatin accessibility
Xu, B., Wang, H., Wright, S., Hyle, J. W., Zhang, Y., Shao, Y., Niu, M., Fan, Y., Rosikiewicz, W., Djekidel, M. N., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16435825
Self-citationAdditional file 5 of Acute depletion of CTCF rewires genome-wide chromatin accessibility
Xu, B., Wang, H., Wright, S., Hyle, J. W., Zhang, Y., Shao, Y., Niu, M., Fan, Y., Rosikiewicz, W., Djekidel, M. N., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16435834
Self-citationBai, B., Vanderwall, D., Li, Y., Wang, X., Poudel, S., Wang, H., Dey, K. K., Chen, P., Yang, K., & Peng, J. (2021) · Figshare · doi:10.6084/m9.figshare.15162179
Self-citationErickson, A., Zhou, S., Luo, J., Li, L. J., Huang, X., Even, Z., Huang, H., Xu, H., Peng, J., Lu, L., et al. (2021) · Figshare · doi:10.6084/m9.figshare.17126047
Self-citationAdditional file 8 of Acute depletion of CTCF rewires genome-wide chromatin accessibility
Xu, B., Wang, H., Wright, S., Hyle, J. W., Zhang, Y., Shao, Y., Niu, M., Fan, Y., Rosikiewicz, W., Djekidel, M. N., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16435843
Self-citationAdditional file 4 of Acute depletion of CTCF rewires genome-wide chromatin accessibility
Xu, B., Wang, H., Wright, S., Hyle, J. W., Zhang, Y., Shao, Y., Niu, M., Fan, Y., Rosikiewicz, W., Djekidel, M. N., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16435831
Self-citationAdditional file 3 of Acute depletion of CTCF rewires genome-wide chromatin accessibility
Xu, B., Wang, H., Wright, S., Hyle, J. W., Zhang, Y., Shao, Y., Niu, M., Fan, Y., Rosikiewicz, W., Djekidel, M. N., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16435828
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Gomaa, B., Lü, J., Abdelhamed, H., Banes, M. M., Pechanova, O., Pechan, T., Arick, M. A., Karsi, A., & Lawrence, M. L. (2024) · Foods · doi:10.3390/foods13091302
Proteomics for Novel Biomarker and Drug Target Discovery in Alzheimer Disease
Zhu, H., Cai, M., Chen, D., Sha, J., Du, L., Chen, Y., Liu, S., Zheng, Q., Wei, X., & Bai, B. (2025) · Springer eBooks · doi:10.1007/978-3-031-80849-4_12
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Xie, B., Ding, L., Zhang, Q., Chen, X., Wang, K., Lv, J., Wang, J., Xiang, L., Qu, J., & Chen, Q. (2025) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5c00363
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Kitano, E. S., Demyanenko, Y., & Mohammed, S. (2025) · Analytical Chemistry · doi:10.1021/acs.analchem.5c03073
Shliaha, P. V. (2025) · Journal of Chromatography A · doi:10.1016/j.chroma.2025.466484
- Authors
- Wang, H., Yang, Y., Li, Y., Bai, B., Wang, X., Tan, H., Liu, T., Beach, T. G., Peng, J., & Wu, Z.
- Affiliations
- University of Tennessee Health Science Center (US)
- St. Jude Children's Research Hospital (US)
- Pacific Northwest National Laboratory (US)
- Banner Sun Health Research Institute (US)
- Corresponding author
- Peng, Junmin
- Wu, Zhiping
- ORCID
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2014-12-12
- Volume
- 14
- Issue
- 2
- Pages
- 829-838
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- PMC
- PMC4324436
- OpenAlex
- W2037114174
- Cited by
- 96
- References
- 50
- Citations by year
- 2026: 3 · 2025: 12 · 2024: 8 · 2023: 7 · 2022: 10 · 2021: 15 · 2020: 8 · 2019: 8 · 2018: 7 · 2017: 11 · 2016: 4 · 2015: 2
- FWCI
- 2.43
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Journal of Proteome Research (publishedVersion, other-oa)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of Neurological Disorders and Stroke (R21NS081571, U24NS072026)
- Michael J. Fox Foundation for Parkinson's Research
- National Institute on Aging (P30AG19610, R21AG039764)
- American Lebanese Syrian Associated Charities
- Arizona Biomedical Research Commission, Arizona Department of Health Services (0011, 05-901, 1001, 4001)
- Arizona Department of Health Services (211002)
- 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
- brain proteome, peak capacity, gas-phase fractionation, postmortem brain, Alzheimer's disease, protein identification, peptide identification
- MeSH terms
- Alzheimer Disease, Animals, Brain, Brain Chemistry, Chromatography, Liquid, Humans, Proteome, Proteomics, Rats, Tandem Mass Spectrometry
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