UbiSite approach for comprehensive mapping of lysine and N-terminal ubiquitination sites

Performance Evaluation of the Q Exactive HF-X for Shotgun Proteomics

(2017) Christian D. Kelstrup et al.   JOURNAL OF PROTEOME RESEARCH

Quantitative Proteomics Reveals Extensive Changes in the Ubiquitinome after Perturbation of the Proteasome by Targeted dsRNA-Mediated Subunit Knockdown in Drosophila

(2017) Karen A. Sap et al.   JOURNAL OF PROTEOME RESEARCH

StUbEx PLUS—A Modified Stable Tagged Ubiquitin Exchange System for Peptide Level Purification and In-Depth Mapping of Ubiquitination Sites

(2017) Vyacheslav Akimov et al.   JOURNAL OF PROTEOME RESEARCH

Cylindromatosis Tumor Suppressor Protein (CYLD) Deubiquitinase is Necessary for Proper Ubiquitination and Degradation of the Epidermal Growth Factor Receptor

(2017) Virginia Sanchez-Quiles et al.   MOLECULAR & CELLULAR PROTEOMICS

Internally tagged ubiquitin: a tool to identify linear polyubiquitin-modified proteins by mass spectrometry

(2017) Katarzyna Kliza et al.   NATURE METHODS

Acute lymphoblastic leukemia cells are sensitive to disturbances in protein homeostasis induced by proteasome deubiquitinase inhibition

(2017) Magdalena Mazurkiewicz et al.   Oncotarget

An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes

(2017) Dorte B. Bekker-Jensen et al.   Cell Systems

The world of protein acetylation

(2016) Adrian Drazic et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

Drug developers delve into the cell's trash-disposal machinery

(2016) Kelly Rae Chi   NATURE REVIEWS DRUG DISCOVERY

Regulation of DNA double-strand break repair by ubiquitin and ubiquitin-like modifiers

(2016) Petra Schwertman et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Multilayered proteomics reveals molecular switches dictating ligand-dependent EGFR trafficking

(2016) Chiara Francavilla et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Multilayered proteomics reveals molecular switches dictating ligand-dependent EGFR trafficking

(2016) Chiara Francavilla et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Highly Multiplexed Quantitative Mass Spectrometry Analysis of Ubiquitylomes

(2016) Christopher M. Rose et al.   Cell Systems

Drug makers target ubiquitin proteasome pathway anew

(2015) Cormac Sheridan   NATURE BIOTECHNOLOGY

Substrate degradation by the proteasome: A single-molecule kinetic analysis

(2015) Y. Lu et al.   SCIENCE

Western Blotting Inaccuracies with Unverified Antibodies: Need for a Western Blotting Minimal Reporting Standard (WBMRS)

(2015) Jennifer E. Gilda et al.   PLoS One

AMBRA1 Interplay with Cullin E3 Ubiquitin Ligases Regulates Autophagy Dynamics

(2014) Manuela Antonioli et al.   DEVELOPMENTAL CELL

The role of the ubiquitin-proteasome pathway in cancer development and treatment

(2014) Fangbao Ding   Frontiers in Bioscience-Landmark

Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer

(2014) Christian D. Kelstrup et al.   JOURNAL OF PROTEOME RESEARCH

StUbEx: Stable Tagged Ubiquitin Exchange System for the Global Investigation of Cellular Ubiquitination

(2014) Vyacheslav Akimov et al.   JOURNAL OF PROTEOME RESEARCH

Off-Line High-pH Reversed-Phase Fractionation for In-Depth Phosphoproteomics

(2014) Tanveer S. Batth et al.   JOURNAL OF PROTEOME RESEARCH

Intrinsic disorder drives N-terminal ubiquitination by Ube2w

(2014) Vinayak Vittal et al.   Nature Chemical Biology

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

(2014) Peter V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

Phosphorylation Site Dynamics of Early T-cell Receptor Signaling

(2014) Lily A. Chylek et al.   PLoS One

Ubiquitin pathways in neurodegenerative disease

(2014) Graham Atkin et al.   Frontiers in Molecular Neuroscience

Induction of Tumor Cell Apoptosis by a Proteasome Deubiquitinase Inhibitor Is Associated with Oxidative Stress

(2013) Slavica Brnjic et al.   ANTIOXIDANTS & REDOX SIGNALING

Advances in characterizing ubiquitylation sites by mass spectrometry

(2013) Kathrine B Sylvestersen et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Status of Large-scale Analysis of Post-translational Modifications by Mass Spectrometry

(2013) Jesper V. Olsen et al.   MOLECULAR & CELLULAR PROTEOMICS

Protein Group Modification and Synergy in the SUMO Pathway as Exemplified in DNA Repair

(2012) Ivan Psakhye et al.   CELL

Using Guanidine-Hydrochloride for Fast and Efficient Protein Digestion and Single-step Affinity-purification Mass Spectrometry

(2012) Jon W. Poulsen et al.   JOURNAL OF PROTEOME RESEARCH

Synaptic Protein Ubiquitination in Rat Brain Revealed by Antibody-based Ubiquitome Analysis

(2012) Chan Hyun Na et al.   JOURNAL OF PROTEOME RESEARCH

Methods for Quantification ofin vivoChanges in Protein Ubiquitination following Proteasome and Deubiquitinase Inhibition

(2012) Namrata D. Udeshi et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteomic Analyses Reveal Divergent Ubiquitylation Site Patterns in Murine Tissues

(2012) Sebastian A. Wagner et al.   MOLECULAR & CELLULAR PROTEOMICS

Refined Preparation and Use of Anti-diglycine Remnant (K-ε-GG) Antibody Enables Routine Quantification of 10,000s of Ubiquitination Sites in Single Proteomics Experiments

(2012) Namrata D. Udeshi et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantitative phosphoproteomics to characterize signaling networks

(2012) Kristoffer T.G. Rigbolt et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Polyubiquitin Linkage Profiles in Three Models of Proteolytic Stress Suggest the Etiology of Alzheimer Disease

(2011) Eric B. Dammer et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

GProX, a User-Friendly Platform for Bioinformatics Analysis and Visualization of Quantitative Proteomics Data

(2011) Kristoffer T. G. Rigbolt et al.   MOLECULAR & CELLULAR PROTEOMICS

A Proteome-wide, Quantitative Survey of In Vivo Ubiquitylation Sites Reveals Widespread Regulatory Roles

(2011) Sebastian A. Wagner et al.   MOLECULAR & CELLULAR PROTEOMICS

Characterization of ubiquitination dependent dynamics in growth factor receptor signaling by quantitative proteomics

(2011) Vyacheslav Akimov et al.   Molecular BioSystems

Systematic and Quantitative Assessment of the Ubiquitin-Modified Proteome

(2011) Woong Kim et al.   MOLECULAR CELL

SHARPIN forms a linear ubiquitin ligase complex regulating NF-κB activity and apoptosis

(2011) Fumiyo Ikeda et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Inhibition of proteasome deubiquitinating activity as a new cancer therapy

(2011) Pádraig D'Arcy et al.   NATURE MEDICINE

MINT, the molecular interaction database: 2012 update

(2011) Luana Licata et al.   NUCLEIC ACIDS RESEARCH

Mass Spectrometric Analysis of Lysine Ubiquitylation Reveals Promiscuity at Site Level

(2010) Jannie M. R. Danielsen et al.   MOLECULAR & CELLULAR PROTEOMICS

Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling

(2010) Guoqiang Xu et al.   NATURE BIOTECHNOLOGY

Quantitative Proteomics Reveals the Function of Unconventional Ubiquitin Chains in Proteasomal Degradation

(2009) Ping Xu et al.   CELL

Efficient protection and isolation of ubiquitylated proteins using tandem ubiquitin-binding entities

(2009) Roland Hjerpe et al.   EMBO REPORTS

Improved visualization of protein consensus sequences by iceLogo

(2009) Niklaas Colaert et al.   NATURE METHODS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Ubiquitin-binding domains — from structures to functions

(2009) Ivan Dikic et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Inactivation of Effector Caspases through Nondegradative Polyubiquitylation

(2008) Mark Ditzel et al.   MOLECULAR CELL