Middle-down proteomics: a still unexploited resource for chromatin biology

Sensitive and Precise Characterization of Combinatorial Histone Modifications by Selective Derivatization Coupled with RPLC-EThcD-MS/MS

(2017) Rijing Liao et al.   JOURNAL OF PROTEOME RESEARCH

Histone H4 acetylation and the epigenetic reader Brd4 are critical regulators of pluripotency in embryonic stem cells

(2016) Michelle Gonzales-Cope et al.   BMC GENOMICS

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

(2016) Yupeng Zheng et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements

(2016) Michael R. Shortreed et al.   JOURNAL OF PROTEOME RESEARCH

Systems Level Analysis of Histone H3 Post-translational Modifications (PTMs) Reveals Features of PTM Crosstalk in Chromatin Regulation

(2016) Veit Schwämmle et al.   MOLECULAR & CELLULAR PROTEOMICS

Metabolic regulation of gene expression through histone acylations

(2016) Benjamin R. Sabari et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Dynamic changes of histone H3 marks during Caenorhabditis elegans lifecycle revealed by middle-down proteomics

(2016) Simone Sidoli et al.   PROTEOMICS

Single-molecule decoding of combinatorially modified nucleosomes

(2016) E. Shema et al.   SCIENCE

Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis

(2016) Simone Sidoli et al.   Jove-Journal of Visualized Experiments

Bottom-Up and Middle-Down Proteomics Have Comparable Accuracies in Defining Histone Post-Translational Modification Relative Abundance and Stoichiometry

(2015) Simone Sidoli et al.   ANALYTICAL CHEMISTRY

High Resolution Parallel Reaction Monitoring with Electron Transfer Dissociation for Middle-Down Proteomics

(2015) Michael J. Sweredoski et al.   ANALYTICAL CHEMISTRY

Progress in epigenetic histone modification analysis by mass spectrometry for clinical investigations

(2015) Özlem Önder et al.   Expert Review of Proteomics

Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin

(2015) Kirsty Jamieson et al.   GENOME RESEARCH

Mass Spectrometric Quantification of Histone Post-translational Modifications by a Hybrid Chemical Labeling Method

(2015) Tobias M. Maile et al.   MOLECULAR & CELLULAR PROTEOMICS

Top-down and Middle-down Protein Analysis Reveals that Intact and Clipped Human Histones Differ in Post-translational Modification Patterns

(2015) Andrey Tvardovskiy et al.   MOLECULAR & CELLULAR PROTEOMICS

Comprehensive Catalog of Currently Documented Histone Modifications

(2015) Yingming Zhao et al.   Cold Spring Harbor Perspectives in Biology

Histone variants: dynamic punctuation in transcription

(2014) C. M. Weber et al.   GENES & DEVELOPMENT

UpSet: Visualization of Intersecting Sets

(2014) Alexander Lex et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

The C-Score: A Bayesian Framework to Sharply Improve Proteoform Scoring in High-Throughput Top Down Proteomics

(2014) Richard D. LeDuc et al.   JOURNAL OF PROTEOME RESEARCH

Large Scale Analysis of Co-existing Post-translational Modifications in Histone Tails Reveals Global Fine Structure of Cross-talk

(2014) Veit Schwämmle et al.   MOLECULAR & CELLULAR PROTEOMICS

Middle-down hybrid chromatography/tandem mass spectrometry workflow for characterization of combinatorial post-translational modifications in histones

(2014) Simone Sidoli et al.   PROTEOMICS

Data-Dependent Middle-Down Nano-Liquid Chromatography–Electron Capture Dissociation-Tandem Mass Spectrometry: An Application for the Analysis of Unfractionated Histones

(2013) Anastasia Kalli et al.   ANALYTICAL CHEMISTRY

Precision Mapping of Coexisting Modifications in Histone H3 Tails from Embryonic Stem Cells by ETD-MS/MS

(2013) Hye Ryung Jung et al.   ANALYTICAL CHEMISTRY

Specific and Efficient N-Propionylation of Histones with Propionic Acid N-Hydroxysuccinimide Ester for Histone Marks Characterization by LC-MS

(2013) Rijing Liao et al.   ANALYTICAL CHEMISTRY

Comparing and Combining Capillary Electrophoresis Electrospray Ionization Mass Spectrometry and Nano–Liquid Chromatography Electrospray Ionization Mass Spectrometry for the Characterization of Post-translationally Modified Histones

(2013) Bettina Sarg et al.   MOLECULAR & CELLULAR PROTEOMICS

Discovery of Histone Modification Crosstalk Networks by Stable Isotope Labeling of Amino Acids in Cell Culture Mass Spectrometry (SILAC MS)

(2013) Xiaoyan Guan et al.   MOLECULAR & CELLULAR PROTEOMICS

The Histone Code of Toxoplasma gondii Comprises Conserved and Unique Posttranslational Modifications

(2013) S. C. Nardelli et al.   mBio

Separation of Variant Methylated Histone Tails by Differential Ion Mobility

(2012) Alexandre A. Shvartsburg et al.   ANALYTICAL CHEMISTRY

Asymmetrically Modified Nucleosomes

(2012) Philipp Voigt et al.   CELL

Proteomics in chromatin biology and epigenetics: Elucidation of post-translational modifications of histone proteins by mass spectrometry

(2012) Simone Sidoli et al.   Journal of Proteomics

Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer Formation

(2012) Tamir Chandra et al.   MOLECULAR CELL

Histone methylation: a dynamic mark in health, disease and inheritance

(2012) Eric L. Greer et al.   NATURE REVIEWS GENETICS

Enhanced top-down characterization of histone post-translational modifications

(2012) Zhixin Tian et al.   GENOME BIOLOGY

Readers of histone modifications

(2011) Miyong Yun et al.   CELL RESEARCH

H3K36 Methylation Antagonizes PRC2-mediated H3K27 Methylation

(2011) Wen Yuan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Language of Histone Crosstalk

(2010) Jung-Shin Lee et al.   CELL

Quantitative Interaction Proteomics and Genome-wide Profiling of Epigenetic Histone Marks and Their Readers

(2010) Michiel Vermeulen et al.   CELL

Covalent modifications of histones during mitosis and meiosis

(2010) Dazhong Xu et al.   CELL CYCLE

A chromodomain switch mediated by histone H3 Lys 4 acetylation regulates heterochromatin assembly

(2010) B. Xhemalce et al.   GENES & DEVELOPMENT

Mass spectrometry–based proteomics in cell biology

(2010) Tobias C. Walther et al.   JOURNAL OF CELL BIOLOGY

Deconvolution and Database Search of Complex Tandem Mass Spectra of Intact Proteins

(2010) Xiaowen Liu et al.   MOLECULAR & CELLULAR PROTEOMICS

Epigenetic modifications and human disease

(2010) Anna Portela et al.   NATURE BIOTECHNOLOGY

An assessment of histone-modification antibody quality

(2010) Thea A Egelhofer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) Peter A. DiMaggio et al.   MOLECULAR & CELLULAR PROTEOMICS

High Throughput Characterization of Combinatorial Histone Codes

(2009) Nicolas L. Young et al.   MOLECULAR & CELLULAR PROTEOMICS

Interpreting Top-Down Mass Spectra Using Spectral Alignment

(2008) Ari M. Frank et al.   ANALYTICAL CHEMISTRY

Sensitive and Specific Identification of Wild Type and Variant Proteins from 8 to 669 kDa Using Top-down Mass Spectrometry

(2008) N. Murat Karabacak et al.   MOLECULAR & CELLULAR PROTEOMICS

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS