Garcia, B. A. et al. Chemical derivatization of histones for facilitated analysis by mass spectrometry. Nat. Protoc. 2, 933\u2013938 (2007).<\/p>\n
King, J., Patel, M. & Chandrasekaran, S. Metabolism, HDACs, and HDAC inhibitors: a systems biology perspective. Metabolites 11, 792 (2021).<\/p>\n Boumber, Y., Younes, A. & Garcia-Manero, G. Mocetinostat (MGCD0103): a review of an isotype-specific histone deacetylase inhibitor. Expert Opin. Investig. Drugs 20, 823\u2013829 (2011).<\/p>\n Shapiro, E., Biezuner, T. & Linnarsson, S. Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat. Rev. Genet. 14, 618\u2013630 (2013).<\/p>\n Meers, M. P., Llagas, G., Janssens, D. H., Codomo, C. A. & Henikoff, S. Multifactorial profiling of epigenetic landscapes at single-cell resolution using MulTI-Tag. Nat. Biotechnol. 41, 708\u2013716 (2023).<\/p>\n Orsburn, B. C., Yuan, Y. & Bumpus, N. N. Insights into protein post-translational modification landscapes of individual human cells by trapped ion mobility time-of-flight mass spectrometry. Nat. Commun. 13, 7237 (2022).<\/p>\n Orsburn, B. C. Metabolomic, proteomic, and single-cell proteomic analysis of cancer cells treated with the KRASG12D inhibitor MRTX1133. J. Proteome Res. 22, 3703\u20133713 (2023).<\/p>\n Specht, H. et al. Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2. Genome Biol. 22, 50 (2021).<\/p>\n Wi\u015bniewski, J. R., Hein, M. Y., Cox, J. & Mann, M. A \u2018proteomic ruler\u2019 for protein copy number and concentration estimation without spike-in standards. Mol. Cell. Proteomics 13, 3497\u20133506 (2014).<\/p>\n Lanz, M. C., Fuentes Valenzuela, L., Elias, J. E. & Skotheim, J. M. Cell size contributes to single-cell proteome variation. J. Proteome Res. 23, 221\u2013231 (2024).<\/p>\n Bache, N. et al. A novel LC system embeds analytes in pre-formed gradients for rapid, ultra-robust proteomics. Mol. Cell. Proteomics 17, 2284\u20132296 (2018).<\/p>\n Eberhard, C. D. & Orsburn, B. C. A. Multiplexed single-cell proteomic workflow applicable to drug treatment studies. in Proteomics for Drug Discovery (ed. Blonder, J.) 1\u201310 (Springer, 2024).<\/p>\n Gygi, J. P. et al. Web-based search tool for visualizing instrument performance using the triple knockout (TKO) proteome standard. J. Proteome Res. 18, 687\u2013693 (2019).<\/p>\n Paulo, J. A., O\u2019Connell, J. D. & Gygi, S. P. A Triple Knockout (TKO) Proteomics Standard for Diagnosing Ion Interference in Isobaric Labeling Experiments. J. Am. Soc. Mass Spectrom. 27, 1674\u20131681 (2016).<\/p>\n Yates, J. R., Ruse, C. I. & Nakorchevsky, A. Proteomics by mass spectrometry: approaches, advances, and applications. Annu. Rev. Biomed. Eng. 11, 49\u201379 (2009).<\/p>\n Bian, Y. et al. Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC\u2013MS\/MS. Nat. Commun. 11, 157 (2020).<\/p>\n Bruderer, R. et al. Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues. Mol. Cell. Proteomics 14, 1400\u20131410 (2015)<\/p>\n Peterson, A. C., Russell, J. D., Bailey, D. J., Westphall, M. S. & Coon, J. J. Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. Mol. Cell. Proteomics 11, 1475\u201388 (2012).<\/p>\n Singh, C., Zampronio, C. G., Creese, A. J. & Cooper, H. J. Higher energy collision dissociation (HCD) product ion-triggered electron transfer dissociation (ETD) mass spectrometry for the analysis of N-linked glycoproteins. J. Proteome Res. 11, 4517\u20134525 (2012).<\/p>\n Zolg, D. P. et al. ProteomeTools: systematic characterization of 21 post-translational protein modifications by liquid chromatography tandem mass spectrometry (LC-MS\/MS) using synthetic peptides. Mol. Cell. Proteomics 17, 1850\u20131863 (2018).<\/p>\n Armony, G. et al. The GlycoPaSER prototype as a real-time N-glycopeptide identification tool based on the PaSER parallel computing platform. Int. J. Mol. Sci. 24, 7869 (2023).<\/p>\n Toghi Eshghi, S. et al. Classification of tandem mass spectra for identification of N- and O-linked glycopeptides. Sci. Rep. 6, 37189 (2016).<\/p>\n Jenkins, C. & Orsburn, B. C. Simple tool for rapidly assessing the quality of multiplexed single cell proteomics data. J. Am. Soc. Mass Spectrom. 34, 1709\u20131711 (2023).<\/p>\n Gallia, J., Lavrich, K., Tan-Wilson, A. & Madden, P. H. Filtering of MS\/MS data for peptide identification. BMC Genomics 14, S2 (2013).<\/p>\n Chang, Y.-C. et al. Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomics. Cell Rep. 43, 113612 (2024).<\/p>\n Gatto, L. et al. Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments. Nat. Methods 20, 375\u2013386 (2023).<\/p>\n Sui, J. et al. Plasma levels of S100A8\/A9, histone\/DNA complexes, and cell-free DNA predict adverse outcomes of immune thrombotic thrombocytopenic purpura. J. Thromb. Haemost. 19, 370\u2013379 (2021).<\/p>\n Orsburn, B. C. An integrated method for single cell proteomics with simultaneous measurements of intracellular drug concentration implicates new mechanisms for adaptation to KRASG12D inhibitors. bioRxiv https:\/\/doi.org\/10.1101\/2023.11.18.567669<\/a> (2023).<\/p>\n Mardis, E. R. ChIP-seq: welcome to the new frontier. Nat. Methods 4, 613\u2013614 (2007).<\/p>\n Rotem, A. et al. Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat. Biotechnol. 33, 1165\u20131172 (2015).<\/p>\n Dickson, B. M., Kupai, A., Vaughan, R. M. & Rothbart, S. B. Streamlined quantitative analysis of histone modification abundance at nucleosome-scale resolution with siQ-ChIP version 2.0. Sci. Rep. 13, 7508 (2023).<\/p>\n Berendzen, K. W., Grefen, C., Sakamoto, T. & Slane, D. Analysis of chromatin accessibility, histone modifications, and transcriptional states in specific cell types using flow cytometry. In Plant Gene Regulatory Networks: Methods and Protocols (eds. Kaufmann, K. & Vandepoele, K.) 57\u201373 (Springer US, New York, NY, 2023).<\/p>\n Cheung, P. et al. Single-cell epigenetics\u2014chromatin modification atlas unveiled by mass cytometry. Clin. Immunol. 196, 40\u201348 (2018).<\/p>\n Mill\u00e1n-Zambrano, G., Burton, A., Bannister, A. J. & Schneider, R. Histone post-translational modifications \u2014 cause and consequence of genome function. Nat. Rev. Genet. 23, 563\u2013580 (2022).<\/p>\n Ctortecka, C. & Mechtler, K. The rise of single-cell proteomics. Anal. Sci. Adv. 2, 240\u2013254 (2021).<\/p>\n Schoof, E. M. et al. Quantitative single-cell proteomics as a tool to characterize cellular hierarchies. Nat. Commun. 12, 3341 (2021).<\/p>\n Doerr, A. DIA mass spectrometry. Nat. Methods https:\/\/doi.org\/10.1038\/nmeth.3234<\/a> (2014).<\/p>\n Szyrwiel, L., Sinn, L., Ralser, M. & Demichev, V. Slice-PASEF: fragmenting all ions for maximum sensitivity in proteomics. bioRxiv https:\/\/doi.org\/10.1101\/2022.10.31.514544<\/a> (2022).<\/p>\n Kreimer, S. et al. High-throughput single-cell proteomic analysis of organ-derived heterogeneous cell populations by nanoflow dual-trap single-column liquid chromatography. Anal. Chem. 95, 9145\u20139150 (2023).<\/p>\n
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