Literature DB >> 27371874

Epiproteomics: quantitative analysis of histone marks and codes by mass spectrometry.

Yupeng Zheng1, Xiaoxiao Huang2, Neil L Kelleher3.   

Abstract

Histones are a group of proteins with a high number of post-translational modifications, including methylation, acetylation, phosphorylation, and monoubiquitination, which play critical roles in every chromatin-templated activity. The quantitative analysis of these modifications using mass spectrometry (MS) has seen significant improvements over the last decade. It is now possible to perform large-scale surveys of dozens of histone marks and hundreds of their combinations on global chromatin. Here, we review the development of three MS strategies for analyzing histone modifications that have come to be known as Bottom Up, Middle Down, and Top Down. We also discuss challenges and innovative solutions for characterizing and quantifying complicated isobaric species arising from multiple modifications on the same histone molecule.
Copyright © 2016. Published by Elsevier Ltd.

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Year:  2016        PMID: 27371874      PMCID: PMC5129744          DOI: 10.1016/j.cbpa.2016.06.007

Source DB:  PubMed          Journal:  Curr Opin Chem Biol        ISSN: 1367-5931            Impact factor:   8.822


  50 in total

1.  Quantitative analysis of modified proteins and their positional isomers by tandem mass spectrometry: human histone H4.

Authors:  James J Pesavento; Craig A Mizzen; Neil L Kelleher
Journal:  Anal Chem       Date:  2006-07-01       Impact factor: 6.986

2.  Gene-specific characterization of human histone H2B by electron capture dissociation.

Authors:  Nertila Siuti; Michael J Roth; Craig A Mizzen; Neil L Kelleher; James J Pesavento
Journal:  J Proteome Res       Date:  2006-02       Impact factor: 4.466

3.  Chemical derivatization of histones for facilitated analysis by mass spectrometry.

Authors:  Benjamin A Garcia; Sahana Mollah; Beatrix M Ueberheide; Scott A Busby; Tara L Muratore; Jeffrey Shabanowitz; Donald F Hunt
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

4.  Pervasive combinatorial modification of histone H3 in human cells.

Authors:  Benjamin A Garcia; James J Pesavento; Craig A Mizzen; Neil L Kelleher
Journal:  Nat Methods       Date:  2007-05-21       Impact factor: 28.547

5.  A mixed integer linear optimization framework for the identification and quantification of targeted post-translational modifications of highly modified proteins using multiplexed electron transfer dissociation tandem mass spectrometry.

Authors:  Peter A DiMaggio; Nicolas L Young; Richard C Baliban; Benjamin A Garcia; Christodoulos A Floudas
Journal:  Mol Cell Proteomics       Date:  2009-08-07       Impact factor: 5.911

6.  EpiProfile Quantifies Histone Peptides With Modifications by Extracting Retention Time and Intensity in High-resolution Mass Spectra.

Authors:  Zuo-Fei Yuan; Shu Lin; Rosalynn C Molden; Xing-Jun Cao; Natarajan V Bhanu; Xiaoshi Wang; Simone Sidoli; Shichong Liu; Benjamin A Garcia
Journal:  Mol Cell Proteomics       Date:  2015-03-24       Impact factor: 5.911

7.  Data-dependent middle-down nano-liquid chromatography-electron capture dissociation-tandem mass spectrometry: an application for the analysis of unfractionated histones.

Authors:  Anastasia Kalli; Michael J Sweredoski; Sonja Hess
Journal:  Anal Chem       Date:  2013-03-12       Impact factor: 6.986

8.  Absolute quantification of histone PTM marks by MRM-based LC-MS/MS.

Authors:  Jun Gao; Rijing Liao; Yanyan Yu; Huili Zhai; Yingqi Wang; Ragna Sack; Antoine H F M Peters; Jiajia Chen; Haiping Wu; Zheng Huang; Min Hu; Wei Qi; Chris Lu; Peter Atadja; Counde Oyang; En Li; Wei Yi; Shaolian Zhou
Journal:  Anal Chem       Date:  2014-09-08       Impact factor: 6.986

9.  Bottom-up and middle-down proteomics have comparable accuracies in defining histone post-translational modification relative abundance and stoichiometry.

Authors:  Simone Sidoli; Shu Lin; Kelly R Karch; Benjamin A Garcia
Journal:  Anal Chem       Date:  2015-03-03       Impact factor: 6.986

10.  Evaluation of proteomic search engines for the analysis of histone modifications.

Authors:  Zuo-Fei Yuan; Shu Lin; Rosalynn C Molden; Benjamin A Garcia
Journal:  J Proteome Res       Date:  2014-09-07       Impact factor: 4.466

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  34 in total

1.  EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data.

Authors:  Zuo-Fei Yuan; Simone Sidoli; Dylan M Marchione; Johayra Simithy; Kevin A Janssen; Mary R Szurgot; Benjamin A Garcia
Journal:  J Proteome Res       Date:  2018-05-30       Impact factor: 4.466

2.  Mutant-IDH1-dependent chromatin state reprogramming, reversibility, and persistence.

Authors:  Sevin Turcan; Vladimir Makarov; Julian Taranda; Yuxiang Wang; Armida W M Fabius; Wei Wu; Yupeng Zheng; Nour El-Amine; Sara Haddock; Gouri Nanjangud; H Carl LeKaye; Cameron Brennan; Justin Cross; Jason T Huse; Neil L Kelleher; Pavel Osten; Craig B Thompson; Timothy A Chan
Journal:  Nat Genet       Date:  2017-11-27       Impact factor: 38.330

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

Authors:  Mariel Coradin; Mariel R Mendoza; Simone Sidoli; Andrew J Alpert; Congcong Lu; Benjamin A Garcia
Journal:  Methods       Date:  2020-02-15       Impact factor: 3.608

Review 4.  Mass-spectrometric exploration of proteome structure and function.

Authors:  Ruedi Aebersold; Matthias Mann
Journal:  Nature       Date:  2016-09-15       Impact factor: 49.962

Review 5.  Proteins and Proteoforms: New Separation Challenges.

Authors:  Fred E Regnier; JinHee Kim
Journal:  Anal Chem       Date:  2017-12-18       Impact factor: 6.986

6.  Mass Spectrometry-Based Methodology for Identification of Native Histone Variant Modifications From Mammalian Tissues and Solid Tumors.

Authors:  A G Nuccio; M Bui; Y Dalal; A Nita-Lazar
Journal:  Methods Enzymol       Date:  2016-11-02       Impact factor: 1.600

7.  Proteomic approaches for cancer epigenetics research.

Authors:  Dylan M Marchione; Benjamin A Garcia; John Wojcik
Journal:  Expert Rev Proteomics       Date:  2018-11-27       Impact factor: 3.940

Review 8.  Unravelling the biology of chromatin in health and cancer using proteomic approaches.

Authors:  Cassandra G Eubanks; Gerald Dayebgadoh; Xingyu Liu; Michael P Washburn
Journal:  Expert Rev Proteomics       Date:  2017-09-20       Impact factor: 3.940

9.  Toward a Universal Sample Preparation Method for Denaturing Top-Down Proteomics of Complex Proteomes.

Authors:  Zhichang Yang; Xiaojing Shen; Daoyang Chen; Liangliang Sun
Journal:  J Proteome Res       Date:  2020-05-29       Impact factor: 4.466

10.  Proteomics in Non-model Organisms: A New Analytical Frontier.

Authors:  Michelle Heck; Benjamin A Neely
Journal:  J Proteome Res       Date:  2020-08-20       Impact factor: 4.466

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