Mass Spectrometry-Based Proteomics for the Analysis of Chromatin Structure and Dynamics

The Proteomic Investigation of Chromatin Functional Domains Reveals Novel Synergisms among Distinct Heterochromatin Components

(2013) Monica Soldi et al.   MOLECULAR & CELLULAR PROTEOMICS

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

Quantitative Chemical Proteomics Approach To Identify Post-translational Modification-Mediated Protein–Protein Interactions

(2012) Xiang Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Quantitative Assessment of Chromatin Immunoprecipitation Grade Antibodies Directed against Histone Modifications Reveals Patterns of Co-occurring Marks on Histone Protein Molecules

(2012) Sally E. Peach et al.   MOLECULAR & CELLULAR PROTEOMICS

PCGF Homologs, CBX Proteins, and RYBP Define Functionally Distinct PRC1 Family Complexes

(2012) Zhonghua Gao et al.   MOLECULAR CELL

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

(2012) Paola Picotti et al.   NATURE METHODS

Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions

(2012) Marion Scheibe et al.   NUCLEIC ACIDS RESEARCH

ChAP-MS: A Method for Identification of Proteins and Histone Posttranslational Modifications at a Single Genomic Locus

(2012) Stephanie D. Byrum et al.   Cell Reports

Histone variants and epigenetic inheritance

(2011) Gang Yuan et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Towards cracking the epigenetic code using a combination of high-throughput epigenomics and quantitative mass spectrometry-based proteomics

(2011) Hendrik G. Stunnenberg et al.   BIOESSAYS

Matrix-Assisted Laser Desorption/Ionization Imaging Mass Spectrometry: A Promising Technique for Reproductive Research1

(2011) Mélanie Lagarrigue et al.   BIOLOGY OF REPRODUCTION

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

Breaking the histone code with quantitative mass spectrometry

(2011) Laura-Mae P Britton et al.   Expert Review of Proteomics

The Epigenotype

(2011) C. H. Waddington   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Analysis of Intact Protein Isoforms by Mass Spectrometry

(2011) Jeremiah D. Tipton et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Studying the epigenome using next generation sequencing

(2011) C. S. Ku et al.   JOURNAL OF MEDICAL GENETICS

Quantitative Profiling ofIn Vivo-assembled RNA-Protein Complexes Using a Novel Integrated Proteomic Approach

(2011) Becky Pinjou Tsai et al.   MOLECULAR & CELLULAR PROTEOMICS

Chromatin Affinity Purification and Quantitative Mass Spectrometry Defining the Interactome of Histone Modification Patterns

(2011) Miroslav Nikolov et al.   MOLECULAR & CELLULAR PROTEOMICS

Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics

(2011) Tamar Geiger et al.   Nature Protocols

Silencing chromatin: comparing modes and mechanisms

(2011) Christian Beisel et al.   NATURE REVIEWS GENETICS

Developmental regulation of N-terminal H2B methylation in Drosophila melanogaster

(2011) Ana Villar-Garea et al.   NUCLEIC ACIDS RESEARCH

Histone Variants and Their Post-Translational Modifications in Primary Human Fat Cells

(2011) Åsa Jufvas et al.   PLoS One

Proteomic Interrogation of Human Chromatin

(2011) Mariana P. Torrente et al.   PLoS One

A SILAC-Based Screen for Methyl-CpG Binding Proteins Identifies RBP-J as a DNA Methylation and Sequence-Specific Binding Protein

(2011) Stefanie J. J. Bartels et al.   PLoS One

An improved method for the construction of decoy peptide MS/MS spectra suitable for the accurate estimation of false discovery rates

(2011) Erik Ahrné et al.   PROTEOMICS

Quantitative mass spectrometry of DENV-2 RNA-interacting proteins reveals that the DEAD-box RNA helicase DDX6 binds the DB1 and DB2 3’ UTR structures

(2011) Alex Michael Ward et al.   RNA Biology

SILAC-based proteomic analysis to dissect the “histone modification signature” of human breast cancer cells

(2010) Alessandro Cuomo et al.   AMINO ACIDS

The Protein Composition of Mitotic Chromosomes Determined Using Multiclassifier Combinatorial Proteomics

(2010) Shinya Ohta et al.   CELL

Nucleosome-Interacting Proteins Regulated by DNA and Histone Methylation

(2010) Till Bartke et al.   CELL

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

(2010) Michiel Vermeulen et al.   CELL

Quantitative Proteomics for Epigenetics

(2010) H. Christian Eberl et al.   CHEMBIOCHEM

Influence of Combinatorial Histone Modifications on Antibody and Effector Protein Recognition

(2010) Stephen M. Fuchs et al.   CURRENT BIOLOGY

A domesticated transposon mediates the effects of a single-nucleotide polymorphism responsible for enhanced muscle growth

(2010) Falk Butter et al.   EMBO REPORTS

Epigenetics meets next-generation sequencing

(2010) Peter J. Park   Epigenetics

A Modified “Cross-talk” between Histone H2B Lys-120 Ubiquitination and H3 Lys-79 Methylation

(2010) Agus Darwanto et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Kinetics of Re-establishing H3K79 Methylation Marks in Global Human Chromatin

(2010) Steve M. M. Sweet et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mass spectrometry–based proteomics in cell biology

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

Histone H1 phosphorylation is associated with transcription by RNA polymerases I and II

(2010) Yupeng Zheng et al.   JOURNAL OF CELL BIOLOGY

Systematic Identification of Methyllysine-Driven Interactions for Histone and Nonhistone Targets

(2010) Huadong Liu et al.   JOURNAL OF PROTEOME RESEARCH

A Novel Approach for Untargeted Post-translational Modification Identification Using Integer Linear Optimization and Tandem Mass Spectrometry

(2010) Richard C. Baliban et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantitative Proteomics: Comparison of the Macular Bruch Membrane/Choroid Complex from Age-related Macular Degeneration and Normal Eyes

(2010) Xianglin Yuan et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantitative Mass Spectrometry of Histones H3.2 and H3.3 inSuz12-deficient Mouse Embryonic Stem Cells Reveals Distinct, Dynamic Post-translational Modifications at Lys-27 and Lys-36

(2010) Hye Ryung Jung et al.   MOLECULAR & CELLULAR PROTEOMICS

High Resolution Electron Transfer Dissociation Studies of Unfractionated Intact Histones from Murine Embryonic Stem Cells Using On-line Capillary LC Separation

(2010) Shannon M. Eliuk et al.   MOLECULAR & CELLULAR PROTEOMICS

CDK2AP1/DOC-1 is a bona fide subunit of the Mi-2/NuRD complex

(2010) Cornelia G. Spruijt et al.   Molecular BioSystems

Short RNAs Are Transcribed from Repressed Polycomb Target Genes and Interact with Polycomb Repressive Complex-2

(2010) Aditi Kanhere et al.   MOLECULAR CELL

Super-SILAC mix for quantitative proteomics of human tumor tissue

(2010) Tamar Geiger et al.   NATURE METHODS

Chromatin structure and the inheritance of epigenetic information

(2010) Raphaël Margueron et al.   NATURE REVIEWS GENETICS

Two-dimensional liquid chromatography system for online top-down mass spectrometry

(2010) Zhixin Tian et al.   PROTEOMICS

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

Histone H1 variant-specific lysine methylation by G9a/KMT1C and Glp1/KMT1D

(2010) Thomas Weiss et al.   Epigenetics & Chromatin

Global turnover of histone post-translational modifications and variants in human cells

(2010) Barry M Zee et al.   Epigenetics & Chromatin

Proteomics by Mass Spectrometry: Approaches, Advances, and Applications

(2009) John R. Yates et al.   Annual Review of Biomedical Engineering

RNA regulation of epigenetic processes

(2009) John S. Mattick et al.   BIOESSAYS

Purification of Proteins Associated with Specific Genomic Loci

(2009) Jérôme Déjardin et al.   CELL

Site-specifically phosphorylated forms of H1.5 and H1.2 localized at distinct regions of the nucleus are related to different processes during the cell cycle

(2009) Heribert Talasz et al.   CHROMOSOMA

An operational definition of epigenetics

(2009) S. L. Berger et al.   GENES & DEVELOPMENT

In VivoResidue-specific Histone Methylation Dynamics

(2009) Barry M. Zee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

One-Pot Shotgun Quantitative Mass Spectrometry Characterization of Histones

(2009) Mariana D. Plazas-Mayorca et al.   JOURNAL OF PROTEOME RESEARCH

Global Histone Analysis by Mass Spectrometry Reveals a High Content of Acetylated Lysine Residues in the Malaria ParasitePlasmodium falciparum

(2009) Morten B. Trelle et al.   JOURNAL OF PROTEOME RESEARCH

What does the future hold for top down mass spectrometry?

(2009) Benjamin A. Garcia   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

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

Data Processing Algorithms for Analysis of High Resolution MSMS Spectra of Peptides with Complex Patterns of Posttranslational Modifications

(2009) Shenheng Guan et al.   MOLECULAR & CELLULAR PROTEOMICS

Global Effects of Kinase Inhibitors on Signaling Networks Revealed by Quantitative Phosphoproteomics

(2009) Cuiping Pan et al.   MOLECULAR & CELLULAR PROTEOMICS

High Throughput Characterization of Combinatorial Histone Codes

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

Mass spectrometry analysis of dynamic post-translational modifications of TH2B during spermatogenesis

(2009) Shuang Lu et al.   MOLECULAR HUMAN REPRODUCTION

Epigenetic inheritance during the cell cycle

(2009) Aline V. Probst et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Barrier-to-Autointegration Factor Proteome Reveals Chromatin-Regulatory Partners

(2009) Rocío Montes de Oca et al.   PLoS One

Unbiased RNA-protein interaction screen by quantitative proteomics

(2009) F. Butter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ZBED6, a Novel Transcription Factor Derived from a Domesticated DNA Transposon Regulates IGF2 Expression and Muscle Growth

(2009) Ellen Markljung et al.   PLOS BIOLOGY

Sequential Interval Motif Search: Unrestricted Database Surveys of Global MS/MS Data Sets for Detection of Putative Post-Translational Modifications

(2008) Jian Liu et al.   ANALYTICAL CHEMISTRY

Interpreting Top-Down Mass Spectra Using Spectral Alignment

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

High-Resolution Mass Spectrometers

(2008) Alan G. Marshall et al.   Annual Review of Analytical Chemistry

Histones: Annotating Chromatin

(2008) Eric I. Campos et al.   Annual Review of Genetics

Temporal Profiling of the Chromatin Proteome Reveals System-wide Responses to Replication Inhibition

(2008) Guennadi A. Khoudoli et al.   CURRENT BIOLOGY

A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements

(2008) G. Mittler et al.   GENOME RESEARCH

Tissue-Specific Expression and Post-Translational Modification of Histone H3 Variants

(2008) Benjamin A. Garcia et al.   JOURNAL OF PROTEOME RESEARCH

A Novel Proteomics Approach for the Discovery of Chromatin-associated Protein Networks

(2008) Jean-Philippe Lambert et al.   MOLECULAR & CELLULAR PROTEOMICS

Monomethylation of Lysine 20 on Histone H4 Facilitates Chromatin Maturation

(2008) A. N. D. Scharf et al.   MOLECULAR AND CELLULAR BIOLOGY

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Iodoacetamide-induced artifact mimics ubiquitination in mass spectrometry

(2008) Michael L Nielsen et al.   NATURE METHODS

Fine Mapping of Posttranslational Modifications of the Linker Histone H1 from Drosophila melanogaster

(2008) Ana Villar-Garea et al.   PLoS One

A phosphorylated subpopulation of the histone variant macroH2A1 is excluded from the inactive X chromosome and enriched during mitosis

(2008) E. Bernstein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Eukaryotic Genome as an RNA Machine

(2008) P. P. Amaral et al.   SCIENCE