Proteomic approaches to study ubiquitinomics.

[1]  J. Rain,et al.  Isolation and Mass Spectrometry Identification of K48 and K63 Ubiquitin Proteome Using Chain-Specific Nanobodies. , 2023, Methods in molecular biology.

[2]  B. Schulman,et al.  An expanded lexicon for the ubiquitin code , 2022, Nature Reviews Molecular Cell Biology.

[3]  Daniel R. Squair,et al.  A new dawn beyond lysine ubiquitination , 2022, Nature Chemical Biology.

[4]  J. Cox,et al.  Deubiquitinating enzymes and the proteasome regulate preferential sets of ubiquitin substrates , 2022, Nature Communications.

[5]  H. Daub,et al.  Time-resolved in vivo ubiquitinome profiling by DIA-MS reveals USP7 targets on a proteome-wide scale , 2021, Nature Communications.

[6]  A. Peterson,et al.  Antibody toolkit reveals N-terminally ubiquitinated substrates of UBE2W , 2021, Nature Communications.

[7]  G. Glauser,et al.  Eight key rules for successful data‐dependent acquisition in mass spectrometry‐based metabolomics , 2021, Mass spectrometry reviews.

[8]  S. Satpathy,et al.  Automating UbiFast for High-throughput and Multiplexed Ubiquitin Enrichment , 2021, bioRxiv.

[9]  Christoph B. Messner,et al.  Ultra-fast proteomics with Scanning SWATH , 2021, Nature Biotechnology.

[10]  S. Rothbart,et al.  Chromatin Regulation through Ubiquitin and Ubiquitin-like Histone Modifications. , 2020, Trends in biochemical sciences.

[11]  Ben C. Collins,et al.  diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition , 2020, Nature Methods.

[12]  M. Mann,et al.  Data-independent acquisition method for ubiquitinome analysis reveals regulation of circadian biology , 2020, bioRxiv.

[13]  S. Eyles,et al.  Quantitative Middle-Down MS Analysis of Parkin-Mediated Ubiquitin Chain Assembly. , 2020, Journal of the American Society for Mass Spectrometry.

[14]  Michelle S. Scott,et al.  UBB pseudogene 4 encodes functional ubiquitin variants , 2020, Nature Communications.

[15]  S. Carr,et al.  Rapid and deep-scale ubiquitylation profiling for biology and translational research , 2020, Nature Communications.

[16]  Christoph B. Messner,et al.  DIA-NN: Neural networks and interference correction enable deep proteome coverage in high throughput , 2019, Nature Methods.

[17]  J. Pruneda,et al.  Insights into ubiquitin chain architecture using Ub-clipping , 2019, Nature.

[18]  Dorte B. Bekker-Jensen,et al.  UbiSite approach for comprehensive mapping of lysine and N-terminal ubiquitination sites , 2018, Nature Structural & Molecular Biology.

[19]  M. Komada,et al.  Ub-ProT reveals global length and composition of protein ubiquitylation in cells , 2018, Nature Communications.

[20]  Y. Saeki,et al.  K63 ubiquitylation triggers proteasomal degradation by seeding branched ubiquitin chains , 2018, Proceedings of the National Academy of Sciences.

[21]  J. Harper,et al.  Building and decoding ubiquitin chains for mitophagy , 2018, Nature Reviews Molecular Cell Biology.

[22]  Blagoy Blagoev,et al.  StUbEx PLUS-A Modified Stable Tagged Ubiquitin Exchange System for Peptide Level Purification and In-Depth Mapping of Ubiquitination Sites. , 2018, Journal of proteome research.

[23]  V. Dixit,et al.  Assembly and Function of Heterotypic Ubiquitin Chains in Cell-Cycle and Protein Quality Control , 2017, Cell.

[24]  D. Komander,et al.  Ubiquitin Linkage-Specific Affimers Reveal Insights into K6-Linked Ubiquitin Signaling , 2017, Molecular cell.

[25]  Ambar S J B Rana,et al.  Ubiquitin Chain Enrichment Middle-Down Mass Spectrometry (UbiChEM-MS) Reveals Cell-Cycle Dependent Formation of Lys11/Lys48 Branched Ubiquitin Chains. , 2017, Journal of proteome research.

[26]  Filomena Esteves,et al.  Affimer proteins are versatile and renewable affinity reagents , 2017, eLife.

[27]  E. Strieter,et al.  Ubiquitin Chain Enrichment Middle-Down Mass Spectrometry Enables Characterization of Branched Ubiquitin Chains in Cellulo. , 2017, Analytical chemistry.

[28]  Boris Macek,et al.  Internally tagged ubiquitin: a tool to identify linear polyubiquitin-modified proteins by mass spectrometry , 2017, Nature Methods.

[29]  A. Knebel,et al.  A single MIU motif of MINDY‐1 recognizes K48‐linked polyubiquitin chains , 2017, EMBO reports.

[30]  I. Matic,et al.  Phosphoribosylation of Ubiquitin Promotes Serine Ubiquitination and Impairs Conventional Ubiquitination , 2016, Cell.

[31]  S. Gygi,et al.  Highly Multiplexed Quantitative Mass Spectrometry Analysis of Ubiquitylomes. , 2016, Cell systems.

[32]  J. Rain,et al.  NaLi-H1: A universal synthetic library of humanized nanobodies providing highly functional antibodies and intrabodies , 2016, eLife.

[33]  Zhao‐Qing Luo,et al.  Ubiquitination independent of E1 and E2 enzymes by bacterial effectors , 2016, Nature.

[34]  David Komander,et al.  Ubiquitin modifications , 2016, Cell Research.

[35]  S. Gygi,et al.  USP14 deubiquitinates proteasome-bound substrates that are ubiquitinated at multiple sites , 2016, Nature.

[36]  Ming Yan,et al.  Identification and characterization of a novel ISG15-ubiquitin mixed chain and its role in regulating protein homeostasis , 2015, Scientific Reports.

[37]  D. Campbell,et al.  K29-Selective Ubiquitin Binding Domain Reveals Structural Basis of Specificity and Heterotypic Nature of K29 Polyubiquitin , 2015, Molecular cell.

[38]  M. Mann,et al.  Uncovering Global SUMOylation Signaling Networks in a Site-Specific Manner , 2014, Nature Structural &Molecular Biology.

[39]  E. Strieter,et al.  Middle-Down Mass Spectrometry Enables Characterization of Branched Ubiquitin Chains , 2014, Biochemistry.

[40]  D. A. Stein,et al.  Unanchored K48-linked polyubiquitin synthesized by the E3-ubiquitin ligase TRIM6 stimulates the interferon-IKKε kinase-mediated antiviral response. , 2014, Immunity.

[41]  Christopher M Rose,et al.  NeuCode Labels for Relative Protein Quantification * , 2014, Molecular & Cellular Proteomics.

[42]  Mathias Laga,et al.  A COFRADIC protocol to study protein ubiquitination. , 2014, Journal of proteome research.

[43]  T. Hirokawa,et al.  Ubiquitin is phosphorylated by PINK1 to activate parkin , 2014, Nature.

[44]  K. Hofmann,et al.  Parkin is activated by PINK1-dependent phosphorylation of ubiquitin at Ser65 , 2014, The Biochemical journal.

[45]  A. Philpott,et al.  Non-canonical ubiquitylation: mechanisms and consequences. , 2013, The international journal of biochemistry & cell biology.

[46]  S. Fields,et al.  Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation , 2013, Nature Methods.

[47]  S. Freund,et al.  Assembly, analysis and architecture of atypical ubiquitin chains , 2013, Nature Structural &Molecular Biology.

[48]  Derek J. Bailey,et al.  Neutron-encoded mass signatures for multi-plexed proteome quantification , 2013, Nature Methods.

[49]  R. Kelley,et al.  Engineering and structural characterization of a linear polyubiquitin-specific antibody. , 2012, Journal of molecular biology.

[50]  D. Lane.  Stress, specificity and the NEDD8 proteome , 2012, Cell cycle.

[51]  Keiichi I Nakayama,et al.  Proteome-wide identification of ubiquitylation sites by conjugation of engineered lysine-less ubiquitin. , 2012, Journal of proteome research.

[52]  Ludovic C. Gillet,et al.  Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis* , 2012, Molecular & Cellular Proteomics.

[53]  Edward L. Huttlin,et al.  Systematic and quantitative assessment of the ubiquitin-modified proteome. , 2011, Molecular cell.

[54]  Sebastian A. Wagner,et al.  A Proteome-wide, Quantitative Survey of In Vivo Ubiquitylation Sites Reveals Widespread Regulatory Roles* , 2011, Molecular & Cellular Proteomics.

[55]  T. Shaler,et al.  Protein standard absolute quantification (PSAQ) method for the measurement of cellular ubiquitin pools , 2011, Nature Methods.

[56]  M. Mann,et al.  Quantitative, high-resolution proteomics for data-driven systems biology. , 2011, Annual review of biochemistry.

[57]  L. Hendershot,et al.  Ubiquitylation of an ERAD substrate occurs on multiple types of amino acids. , 2010, Molecular cell.

[58]  L. Jensen,et al.  Mass Spectrometric Analysis of Lysine Ubiquitylation Reveals Promiscuity at Site Level* , 2010, Molecular & Cellular Proteomics.

[59]  R. Kelley,et al.  Improved Quantitative Mass Spectrometry Methods for Characterizing Complex Ubiquitin Signals , 2010, Molecular & Cellular Proteomics.

[60]  J. Guatelli,et al.  Serine-Threonine Ubiquitination Mediates Downregulation of BST-2/Tetherin and Relief of Restricted Virion Release by HIV-1 Vpu , 2010, Journal of Virology.

[61]  N. Seyfried,et al.  A Novel Strategy to Isolate Ubiquitin Conjugates Reveals Wide Role for Ubiquitination during Neural Development , 2010, Molecular & Cellular Proteomics.

[62]  Matthias Mann,et al.  Mass spectrometry–based proteomics in cell biology , 2010, The Journal of cell biology.

[63]  Christine Yu,et al.  K11-linked polyubiquitination in cell cycle control revealed by a K11 linkage-specific antibody. , 2010, Molecular cell.

[64]  Samie R Jaffrey,et al.  Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling , 2010, Nature Biotechnology.

[65]  Kay Hofmann,et al.  Two-sided ubiquitin binding explains specificity of the TAB2 NZF domain , 2009, Nature Structural &Molecular Biology.

[66]  V. Lang,et al.  Efficient protection and isolation of ubiquitylated proteins using tandem ubiquitin‐binding entities , 2009, EMBO reports.

[67]  M. Mann,et al.  Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions , 2009, Science.

[68]  John Rush,et al.  Quantitative Proteomics Reveals the Function of Unconventional Ubiquitin Chains in Proteasomal Degradation , 2009, Cell.

[69]  A. Philpott,et al.  Ubiquitylation on Canonical and Non-canonical Sites Targets the Transcription Factor Neurogenin for Ubiquitin-mediated Proteolysis* , 2009, The Journal of Biological Chemistry.

[70]  Nobuhiro Suzuki,et al.  Specific Recognition of Linear Ubiquitin Chains by NEMO Is Important for NF-κB Activation , 2009, Cell.

[71]  Christine Yu,et al.  Ubiquitin Chain Editing Revealed by Polyubiquitin Linkage-Specific Antibodies , 2008, Cell.

[72]  B. Warscheid,et al.  Members of the E2D (UbcH5) Family Mediate the Ubiquitination of the Conserved Cysteine of Pex5p, the Peroxisomal Import Receptor* , 2008, Journal of Biological Chemistry.

[73]  Junmin Peng,et al.  Characterization of polyubiquitin chain structure by middle-down mass spectrometry. , 2008, Analytical chemistry.

[74]  M. Fransen,et al.  Ubiquitination of Mammalian Pex5p, the Peroxisomal Import Receptor* , 2007, Journal of Biological Chemistry.

[75]  M. van den Berg,et al.  A Conserved Cysteine Is Essential for Pex4p-dependent Ubiquitination of the Peroxisomal Import Receptor Pex5p* , 2007, Journal of Biological Chemistry.

[76]  E. Wiertz,et al.  Ubiquitination of serine, threonine, or lysine residues on the cytoplasmic tail can induce ERAD of MHC-I by viral E3 ligase mK3 , 2007, The Journal of cell biology.

[77]  S. Subramani,et al.  A Conserved Cysteine Residue of Pichia pastoris Pex20p Is Essential for Its Recycling from the Peroxisome to the Cytosol* , 2007, Journal of Biological Chemistry.

[78]  Aaron Ciechanover,et al.  The polycomb protein Ring1B generates self atypical mixed ubiquitin chains required for its in vitro histone H2A ligase activity. , 2006, Molecular cell.

[79]  Keiji Tanaka,et al.  A ubiquitin ligase complex assembles linear polyubiquitin chains , 2006, The EMBO journal.

[80]  S. Gygi,et al.  Quantitative analysis of in vitro ubiquitinated cyclin B1 reveals complex chain topology , 2006, Nature Cell Biology.

[81]  Pierre Baldi,et al.  A Tandem Affinity Tag for Two-step Purification under Fully Denaturing Conditions , 2006, Molecular & Cellular Proteomics.

[82]  G. Wider,et al.  Ubiquitin-Binding Domains in Y-Family Polymerases Regulate Translesion Synthesis , 2005, Science.

[83]  M. Komada,et al.  Regulation of epidermal growth factor receptor down-regulation by UBPY-mediated deubiquitination at endosomes. , 2005, Molecular biology of the cell.

[84]  E. Borden,et al.  Proteomic identification of proteins conjugated to ISG15 in mouse and human cells. , 2005, Biochemical and biophysical research communications.

[85]  Steven P. Gygi,et al.  Weighing in on ubiquitin: the expanding role of mass-spectrometry-based proteomics , 2005, Nature Cell Biology.

[86]  K. Cadwell,et al.  Ubiquitination on Nonlysine Residues by a Viral E3 Ubiquitin Ligase , 2005, Science.

[87]  A. J. Gandolfi,et al.  Proteomic identification of ubiquitinated proteins from human cells expressing His‐tagged ubiquitin , 2005, Proteomics.

[88]  K. Parker,et al.  Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents*S , 2004, Molecular & Cellular Proteomics.

[89]  A. Ciechanover,et al.  The Tumor Suppressor Protein p16INK4a and the Human Papillomavirus Oncoprotein-58 E7 Are Naturally Occurring Lysine-less Proteins That Are Degraded by the Ubiquitin System , 2004, Journal of Biological Chemistry.

[90]  Steven P Gygi,et al.  A proteomics approach to understanding protein ubiquitination , 2003, Nature Biotechnology.

[91]  S. Gygi,et al.  Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[92]  Andrew H. Thompson,et al.  Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. , 2003, Analytical chemistry.

[93]  Boris Pfander,et al.  RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO , 2002, Nature.

[94]  M. Mann,et al.  Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics* , 2002, Molecular & Cellular Proteomics.

[95]  E. Hol,et al.  Mutant ubiquitin found in neurodegenerative disorders is a ubiquitin fusion degradation substrate that blocks proteasomal degradation , 2002, The Journal of cell biology.

[96]  A. Ciechanover,et al.  The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction. , 2002, Physiological reviews.

[97]  S. Gygi,et al.  Proteomics: the move to mixtures. , 2001, Journal of mass spectrometry : JMS.

[98]  C. Pickart,et al.  Inhibition of the ubiquitin-proteasome system in Alzheimer's disease. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[99]  L. Hicke,et al.  A function for monoubiquitination in the internalization of a G protein-coupled receptor. , 1998, Molecular cell.

[100]  L L Needham,et al.  Isotope dilution--mass spectrometric quantification of specific proteins: model application with apolipoprotein A-I. , 1996, Clinical chemistry.

[101]  Tom Maniatis,et al.  The ubiquitinproteasome pathway is required for processing the NF-κB1 precursor protein and the activation of NF-κB , 1994, Cell.

[102]  A. Ciechanover,et al.  Mechanisms of intracellular protein breakdown. , 1982, Annual review of biochemistry.