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Critical Reviews in Biochemistry and Molecular Biology Volume 46, 2011 - Issue 4
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Review Article

Revealing histone variant induced changes via quantitative proteomics

Anna M. ArnaudoDepartment of Molecular Biology, Princeton University, Princeton, NJ, USA
,
Rosalynn C. MoldenDepartment of Chemistry, Princeton University, Princeton, NJ, USA
&
Benjamin A. GarciaDepartment of Molecular Biology, Princeton University, Princeton, NJ, USA;Department of Chemistry, Princeton University, Princeton, NJ, USA;Quantitative and Computational Biology Program, Princeton University, Princeton, NJ, USACorrespondence[email protected]
Pages 284-294 | Received 01 Feb 2011, Accepted 29 Mar 2011, Published online: 25 Jul 2011

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Ping Jin, Kui Wang, Canhua Huang & Edouard C. Nice. (2017) Mining the fecal proteome: from biomarkers to personalised medicine. Expert Review of Proteomics 14:5, pages 445-459.
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Juan Sandoval, Lorena Peiró-Chova, Federico V Pallardó & José Luis García-Giménez. (2013) Epigenetic biomarkers in laboratory diagnostics: emerging approaches and opportunities. Expert Review of Molecular Diagnostics 13:5, pages 457-471.
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Articles from other publishers (27)

Kim Pham, Long Ho, Claudio Peter D'Incal, Andrée De Cock, Wim Vanden Berghe & Peter Goethals. (2023) Epigenetic analytical approaches in ecotoxicological aquatic research. Environmental Pollution 330, pages 121737.
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Faith M. Joseph & Nicolas L. Young. (2023) Histone variant-specific post-translational modifications. Seminars in Cell & Developmental Biology 135, pages 73-84.
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Giulia Robusti, Alessandro Vai, Tiziana Bonaldi & Roberta Noberini. (2022) Investigating pathological epigenetic aberrations by epi-proteomics. Clinical Epigenetics 14:1.
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Roberta Noberini, Giulia Robusti & Tiziana Bonaldi. (2021) Mass spectrometry‐based characterization of histones in clinical samples: applications, progress, and challenges. The FEBS Journal 289:5, pages 1191-1213.
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Arthur Grimaud, Frederik Haugaard Holck, Louise Marie Buur, Rebecca Kirsch & Veit Schwämmle. 2022. Computational Methods for Predicting Post-Translational Modification Sites. Computational Methods for Predicting Post-Translational Modification Sites 261 273 .
Niamat Khan, Sidra Shahid & Abdul R. Asif. (2021) Current Analytical Strategies in Studying Chromatin-Associated-Proteome (Chromatome). Molecules 26:21, pages 6694.
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Irena Dapic, Lucia Baljeu‐Neuman, Naomi Uwugiaren, Jesper Kers, David R. Goodlett & Garry L. Corthals. (2019) Proteome analysis of tissues by mass spectrometry. Mass Spectrometry Reviews 38:4-5, pages 403-441.
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Luana Granada, Marco F.L. Lemos, Henrique N. Cabral, Peter Bossier & Sara C. Novais. (2017) Epigenetics in aquaculture – the last frontier. Reviews in Aquaculture 10:4, pages 994-1013.
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Johayra Simithy, Simone Sidoli & Benjamin A. Garcia. (2018) Integrating Proteomics and Targeted Metabolomics to Understand Global Changes in Histone Modifications. PROTEOMICS 18:18, pages 1700309.
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Hongde Liu, Weiheng Ma, Jiahao Xie, Huamei Li, Kun Luo, Donghui Luo, Lei Liu & Xiao Sun. 2018. The Yeast Role in Medical Applications. The Yeast Role in Medical Applications.
Anna M. Arnaudo, A. James Link & Benjamin A. Garcia. (2016) Bioorthogonal Chemistry for the Isolation and Study of Newly Synthesized Histones and Their Modifications. ACS Chemical Biology 11:3, pages 782-791.
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Hao Yang, Ning Yang & Tai Wang. (2016) Proteomic analysis reveals the differential histone programs between male germline cells and vegetative cells in Lilium davidii . The Plant Journal 85:5, pages 660-674.
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Lissa C. Anderson, Kelly R. Karch, Scott A. Ugrin, Mariel Coradin, A. Michelle English, Simone Sidoli, Jeffrey Shabanowitz, Benjamin A. Garcia & Donald F. Hunt. (2016) Analyses of Histone Proteoforms Using Front-end Electron Transfer Dissociation-enabled Orbitrap Instruments. Molecular & Cellular Proteomics 15:3, pages 975-988.
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L.A. Farrelly, B.D. Dill, H. Molina, M.R. Birtwistle & I. Maze. 2016. Enzymes of Epigenetics, Part B. Enzymes of Epigenetics, Part B 331 354 .
Michael J. Sweredoski, Tonya Pekar Second, Jenny Broeker, Annie Moradian & Sonja Hess. (2015) High resolution data-independent acquisition with electron transfer dissociation mass spectrometry: Multiplexed analysis of post-translationally modified proteins. International Journal of Mass Spectrometry 390, pages 155-162.
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Michael J. Sweredoski, Annie Moradian, Matthias Raedle, Catarina Franco & Sonja Hess. (2015) High Resolution Parallel Reaction Monitoring with Electron Transfer Dissociation for Middle-Down Proteomics. Analytical Chemistry 87:16, pages 8360-8366.
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Zuo-Fei Yuan, Shu Lin, Rosalynn C. Molden, Xing-Jun Cao, Natarajan V. Bhanu, Xiaoshi Wang, Simone Sidoli, Shichong Liu & Benjamin A. Garcia. (2015) EpiProfile Quantifies Histone Peptides With Modifications by Extracting Retention Time and Intensity in High-resolution Mass Spectra*. Molecular & Cellular Proteomics 14:6, pages 1696-1707.
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He Huang, Shu Lin, Benjamin A. Garcia & Yingming Zhao. (2015) Quantitative Proteomic Analysis of Histone Modifications. Chemical Reviews 115:6, pages 2376-2418.
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Xiaoshi Wang, Simone Sidoli & Benjamin A. Garcia. 2015. Epigenetic Technological Applications. Epigenetic Technological Applications 55 78 .
Zuo-Fei YuanAnna M. Arnaudo & Benjamin A. Garcia. (2014) Mass Spectrometric Analysis of Histone Proteoforms. Annual Review of Analytical Chemistry 7:1, pages 113-128.
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Annie Moradian, Anastasia Kalli, Michael J. Sweredoski & Sonja Hess. (2014) The top-down, middle-down, and bottom-up mass spectrometry approaches for characterization of histone variants and their post-translational modifications. PROTEOMICS 14:4-5, pages 489-497.
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Natarajan V. Bhanu & Benjamin A. Garcia. 2014. Systems Analysis of Chromatin-Related Protein Complexes in Cancer. Systems Analysis of Chromatin-Related Protein Complexes in Cancer 149 175 .
Chunchao Zhang, Yifan Liu & Philip C. Andrews. (2013) Quantification of histone modifications using 15N metabolic labeling. Methods 61:3, pages 236-243.
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Anastasia Kalli, Michael J. Sweredoski & Sonja Hess. (2013) Data-Dependent Middle-Down Nano-Liquid Chromatography–Electron Capture Dissociation-Tandem Mass Spectrometry: An Application for the Analysis of Unfractionated Histones. Analytical Chemistry 85:7, pages 3501-3507.
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Melania Scarpa & Eleni Stylianou. (2012) Epigenetics: Concepts and relevance to IBD pathogenesis. Inflammatory Bowel Diseases 18:10, pages 1982-1996.
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Andrea M. Brunner, Ry Y. Tweedie-Cullen & Isabelle M. Mansuy. (2012) Epigenetic modifications of the neuroproteome. PROTEOMICS 12:15-16, pages 2404-2420.
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Simone Sidoli, Lei Cheng & Ole N. Jensen. (2012) Proteomics in chromatin biology and epigenetics: Elucidation of post-translational modifications of histone proteins by mass spectrometry. Journal of Proteomics 75:12, pages 3419-3433.
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