Published in Anal Chem on April 24, 2008
Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation. Cell (2009) 6.16
The mitochondrial deubiquitinase USP30 opposes parkin-mediated mitophagy. Nature (2014) 3.26
Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. Mol Cell Proteomics (2012) 1.58
Systematical optimization of reverse-phase chromatography for shotgun proteomics. J Proteome Res (2009) 1.53
Polyubiquitin linkage profiles in three models of proteolytic stress suggest the etiology of Alzheimer disease. J Biol Chem (2011) 1.48
USP19 deubiquitinating enzyme supports cell proliferation by stabilizing KPC1, a ubiquitin ligase for p27Kip1. Mol Cell Biol (2008) 1.44
A perturbed ubiquitin landscape distinguishes between ubiquitin in trafficking and in proteolysis. Mol Cell Proteomics (2011) 1.25
A data set of human endogenous protein ubiquitination sites. Mol Cell Proteomics (2010) 1.18
Characterization of cell cycle specific protein interaction networks of the yeast 26S proteasome complex by the QTAX strategy. J Proteome Res (2010) 1.14
Uncovering ubiquitin and ubiquitin-like signaling networks. Chem Rev (2011) 1.06
Applications of proteomics in the study of inflammatory bowel diseases: Current status and future directions with available technologies. Inflamm Bowel Dis (2009) 1.05
Synaptic protein ubiquitination in rat brain revealed by antibody-based ubiquitome analysis. J Proteome Res (2012) 1.05
Quantitative analysis of the detergent-insoluble brain proteome in frontotemporal lobar degeneration using SILAC internal standards. J Proteome Res (2012) 1.05
Coaggregation of RNA-binding proteins in a model of TDP-43 proteinopathy with selective RGG motif methylation and a role for RRM1 ubiquitination. PLoS One (2012) 1.05
Ubiquitin ligase substrate identification through quantitative proteomics at both the protein and peptide levels. J Biol Chem (2011) 1.04
Characterizing ubiquitination sites by peptide-based immunoaffinity enrichment. Mol Cell Proteomics (2012) 1.00
A novel strategy to isolate ubiquitin conjugates reveals wide role for ubiquitination during neural development. Mol Cell Proteomics (2010) 0.99
Analysis of a membrane-enriched proteome from postmortem human brain tissue in Alzheimer's disease. Proteomics Clin Appl (2012) 0.98
Molecular and proteomic analyses highlight the importance of ubiquitination for the stress resistance, metabolic adaptation, morphogenetic regulation and virulence of Candida albicans. Mol Microbiol (2011) 0.95
Characterizing the connectivity of poly-ubiquitin chains by selected reaction monitoring mass spectrometry. Mol Biosyst (2010) 0.94
Proteasome protease mediated regulation of cytokine induction and inflammation. Biochim Biophys Acta (2012) 0.88
Coupling of septins to the axial landmark by Bud4 in budding yeast. J Cell Sci (2013) 0.88
A bimolecular affinity purification method under denaturing conditions for rapid isolation of a ubiquitinated protein for mass spectrometry analysis. Nat Protoc (2010) 0.87
Ubiquitinated proteome: ready for global? Mol Cell Proteomics (2011) 0.87
Exploring the potential of the platelet membrane proteome as a source of peripheral biomarkers for Alzheimer's disease. Alzheimers Res Ther (2013) 0.84
E3Net: a system for exploring E3-mediated regulatory networks of cellular functions. Mol Cell Proteomics (2011) 0.84
Disruption of SUMO-targeted ubiquitin ligases Slx5-Slx8/RNF4 alters RecQ-like helicase Sgs1/BLM localization in yeast and human cells. DNA Repair (Amst) (2014) 0.82
Efficient mRNA polyadenylation requires a ubiquitin-like domain, a zinc knuckle, and a RING finger domain, all contained in the Mpe1 protein. Mol Cell Biol (2014) 0.81
Integrated approaches for analyzing U1-70K cleavage in Alzheimer's disease. J Proteome Res (2014) 0.79
Aggregation properties of the small nuclear ribonucleoprotein U1-70K in Alzheimer disease. J Biol Chem (2014) 0.79
A bird's-eye view of post-translational modifications in the spliceosome and their roles in spliceosome dynamics. Mol Biosyst (2010) 0.78
Quantitative proteomics to decipher ubiquitin signaling. Amino Acids (2012) 0.77
Deciphering tissue-specific ubiquitylation by mass spectrometry. Methods Mol Biol (2012) 0.76
Analysis of ubiquitinated proteome by quantitative mass spectrometry. Methods Mol Biol (2012) 0.76
Application of quantitative proteomics to the integrated analysis of the ubiquitylated and global proteomes of xenograft tumor tissues. Clin Proteomics (2015) 0.76
Enhanced Purification of Ubiquitinated Proteins by Engineered Tandem Hybrid Ubiquitin-binding Domains (ThUBDs). Mol Cell Proteomics (2016) 0.75
Ubiquitylation as a Rheostat for TCR Signaling: From Targeted Approaches Toward Global Profiling. Front Immunol (2015) 0.75
Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal Chem (1996) 45.70
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom (1994) 45.51
The ubiquitin system. Annu Rev Biochem (1998) 43.36
A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem (2004) 19.20
Mechanisms underlying ubiquitination. Annu Rev Biochem (2001) 18.87
Molecular weight determination of protein-dodecyl sulfate complexes by gel electrophoresis in a discontinuous buffer system. J Biol Chem (1971) 16.34
Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J Proteome Res (2003) 11.96
A proteomics approach to understanding protein ubiquitination. Nat Biotechnol (2003) 10.51
Protein degradation and protection against misfolded or damaged proteins. Nature (2003) 10.19
A genomic and functional inventory of deubiquitinating enzymes. Cell (2005) 9.36
Themes and variations on ubiquitylation. Nat Rev Mol Cell Biol (2001) 8.68
Regulation of membrane protein transport by ubiquitin and ubiquitin-binding proteins. Annu Rev Cell Dev Biol (2003) 8.13
Ubiquitin signalling in the NF-kappaB pathway. Nat Cell Biol (2005) 8.06
Mass spectrometry and protein analysis. Science (2006) 8.05
Polyubiquitin chains: polymeric protein signals. Curr Opin Chem Biol (2004) 7.10
Functional and quantitative proteomics using SILAC. Nat Rev Mol Cell Biol (2006) 6.25
Toxic proteins in neurodegenerative disease. Science (2002) 5.82
A ubiquitin ligase complex assembles linear polyubiquitin chains. EMBO J (2006) 4.95
Proteomics: the move to mixtures. J Mass Spectrom (2001) 3.95
Quantitative proteomics analysis of the secretory pathway. Cell (2006) 3.63
A tandem affinity tag for two-step purification under fully denaturing conditions: application in ubiquitin profiling and protein complex identification combined with in vivocross-linking. Mol Cell Proteomics (2006) 3.62
Proteomics of organelles and large cellular structures. Nat Rev Mol Cell Biol (2005) 2.98
Ubiquitination and deubiquitination: targeting of proteins for degradation by the proteasome. Semin Cell Dev Biol (2000) 2.85
Regulated protein degradation. Trends Biochem Sci (2005) 2.80
Lingering mysteries of ubiquitin-chain assembly. Cell (2006) 2.69
Weighing in on ubiquitin: the expanding role of mass-spectrometry-based proteomics. Nat Cell Biol (2005) 2.62
Large-scale analysis of the human ubiquitin-related proteome. Proteomics (2005) 2.00
The proteasome and proteasome inhibitors in cancer therapy. Annu Rev Pharmacol Toxicol (2006) 1.99
Analysis of polyubiquitin conjugates reveals that the Rpn10 substrate receptor contributes to the turnover of multiple proteasome targets. Mol Cell Proteomics (2005) 1.65
Molecular determinants of polyubiquitin linkage selection by an HECT ubiquitin ligase. EMBO J (2006) 1.64
Multidimensional protein identification technology (MudPIT) analysis of ubiquitinated proteins in plants. Mol Cell Proteomics (2007) 1.57
Quantitative profiling of ubiquitylated proteins reveals proteasome substrates and the substrate repertoire influenced by the Rpn10 receptor pathway. Mol Cell Proteomics (2007) 1.53
Tryptic digestion of ubiquitin standards reveals an improved strategy for identifying ubiquitinated proteins by mass spectrometry. Proteomics (2007) 1.43
Proteomic identification of ubiquitinated proteins from human cells expressing His-tagged ubiquitin. Proteomics (2005) 1.37
Proteomic analysis of ubiquitinated proteins from human MCF-7 breast cancer cells by immunoaffinity purification and mass spectrometry. J Proteome Res (2005) 1.34
Dissecting the ubiquitin pathway by mass spectrometry. Biochim Biophys Acta (2006) 1.32
Direct identification of a G protein ubiquitination site by mass spectrometry. Biochemistry (2002) 1.22
A proteomics approach to identify the ubiquitinated proteins in mouse heart. Biochem Biophys Res Commun (2007) 1.18
Global approaches to understanding ubiquitination. Genome Biol (2005) 1.03
Methods for the purification of ubiquitinated proteins. Proteomics (2007) 0.93
Human plasma proteome analysis by reversed sequence database search and molecular weight correlation based on a bacterial proteome analysis. Proteomics (2006) 0.92
Proteomic analysis of ubiquitin conjugates in yeast. Methods Enzymol (2005) 0.87
Molecular weight assessment of proteins in total proteome profiles using 1D-PAGE and LC/MS/MS. Proteome Sci (2005) 0.83
A proteomics approach to understanding protein ubiquitination. Nat Biotechnol (2003) 10.51
Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation. Cell (2009) 6.16
Complete genome sequence of the apicomplexan, Cryptosporidium parvum. Science (2004) 5.64
Rapid chemotherapy-induced acute endothelial progenitor cell mobilization: implications for antiangiogenic drugs as chemosensitizing agents. Cancer Cell (2008) 4.51
Derivation of pre-X inactivation human embryonic stem cells under physiological oxygen concentrations. Cell (2010) 4.32
Relative and absolute quantification of postsynaptic density proteome isolated from rat forebrain and cerebellum. Mol Cell Proteomics (2006) 3.56
Randomized trial using gonadotropin-releasing hormone agonist triptorelin for the preservation of ovarian function during (neo)adjuvant chemotherapy for breast cancer. J Clin Oncol (2012) 3.51
Soy isoflavones in the prevention of menopausal bone loss and menopausal symptoms: a randomized, double-blind trial. Arch Intern Med (2011) 3.11
Lysine propionylation and butyrylation are novel post-translational modifications in histones. Mol Cell Proteomics (2007) 3.09
MicroRNA miR-137 regulates neuronal maturation by targeting ubiquitin ligase mind bomb-1. Stem Cells (2010) 2.89
A genome-wide association study identifies two new lung cancer susceptibility loci at 13q12.12 and 22q12.2 in Han Chinese. Nat Genet (2011) 2.85
Semiquantitative proteomic analysis of rat forebrain postsynaptic density fractions by mass spectrometry. J Biol Chem (2004) 2.84
Comparative impact of trastuzumab and cyclophosphamide on HER-2-positive human breast cancer xenografts. Clin Cancer Res (2009) 2.79
Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes. J Biol Chem (2010) 2.72
Midbody accumulation through evasion of autophagy contributes to cellular reprogramming and tumorigenicity. Nat Cell Biol (2011) 2.65
Prolyl 4-hydroxylation regulates Argonaute 2 stability. Nature (2008) 2.51
Mouse models of advanced spontaneous metastasis for experimental therapeutics. Nat Rev Cancer (2011) 2.42
Anticancer therapies combining antiangiogenic and tumor cell cytotoxic effects reduce the tumor stem-like cell fraction in glioma xenograft tumors. Cancer Res (2007) 2.35
Regulation of estrogen receptor alpha by the SET7 lysine methyltransferase. Mol Cell (2008) 2.35
Genome-wide association analysis identifies new lung cancer susceptibility loci in never-smoking women in Asia. Nat Genet (2012) 2.26
Analysis of the large inactive P-TEFb complex indicates that it contains one 7SK molecule, a dimer of HEXIM1 or HEXIM2, and two P-TEFb molecules containing Cdk9 phosphorylated at threonine 186. J Biol Chem (2005) 2.24
Automation of nanoscale microcapillary liquid chromatography-tandem mass spectrometry with a vented column. Anal Chem (2002) 2.22
Cdk5-mediated inhibition of the protective effects of transcription factor MEF2 in neurotoxicity-induced apoptosis. Neuron (2003) 2.19
The deubiquitinating enzyme ataxin-3, a polyglutamine disease protein, edits Lys63 linkages in mixed linkage ubiquitin chains. J Biol Chem (2008) 2.09
Site-specific ubiquitination exposes a linear motif to promote interferon-alpha receptor endocytosis. J Cell Biol (2007) 2.07
C3PO, an endoribonuclease that promotes RNAi by facilitating RISC activation. Science (2009) 2.04
Autophosphorylated CaMKIIalpha acts as a scaffold to recruit proteasomes to dendritic spines. Cell (2010) 2.02
Development of a preclinical model of spontaneous human melanoma central nervous system metastasis. Cancer Res (2008) 1.99
Glypican-3 inhibits Hedgehog signaling during development by competing with patched for Hedgehog binding. Dev Cell (2008) 1.94
Enhanced 2,3-butanediol production by Klebsiella pneumoniae SDM. Appl Microbiol Biotechnol (2008) 1.92
The 5p15.33 locus is associated with risk of lung adenocarcinoma in never-smoking females in Asia. PLoS Genet (2010) 1.90
Essential role of sequestosome 1/p62 in regulating accumulation of Lys63-ubiquitinated proteins. J Biol Chem (2008) 1.83
Orphan receptor small heterodimer partner suppresses tumorigenesis by modulating cyclin D1 expression and cellular proliferation. Hepatology (2008) 1.83
Vascular endothelial growth factor-mediated decrease in plasma soluble vascular endothelial growth factor receptor-2 levels as a surrogate biomarker for tumor growth. Cancer Res (2008) 1.78
Ogg1 knockout-associated lung tumorigenesis and its suppression by Mth1 gene disruption. Cancer Res (2003) 1.75
Human LSD2/KDM1b/AOF1 regulates gene transcription by modulating intragenic H3K4me2 methylation. Mol Cell (2010) 1.73
Acetoin metabolism in bacteria. Crit Rev Microbiol (2007) 1.73
Adenosine production by human B cells and B cell-mediated suppression of activated T cells. Blood (2013) 1.70
Nuclear Akt associates with PKC-phosphorylated Ebp1, preventing DNA fragmentation by inhibition of caspase-activated DNase. EMBO J (2006) 1.67
Molecular determinants of polyubiquitin linkage selection by an HECT ubiquitin ligase. EMBO J (2006) 1.64
Structure dissection of human progranulin identifies well-folded granulin/epithelin modules with unique functional activities. Protein Sci (2008) 1.60
Proteomic characterization of postmortem amyloid plaques isolated by laser capture microdissection. J Biol Chem (2004) 1.58
Quantum teleportation and entanglement distribution over 100-kilometre free-space channels. Nature (2012) 1.56
Activated expression of an Arabidopsis HD-START protein confers drought tolerance with improved root system and reduced stomatal density. Plant Cell (2008) 1.53
Systematical optimization of reverse-phase chromatography for shotgun proteomics. J Proteome Res (2009) 1.53
Genetic inactivation of p62 leads to accumulation of hyperphosphorylated tau and neurodegeneration. J Neurochem (2008) 1.51
Adhesion molecule-dependent mechanisms regulate the rate of macrophage clearance during the resolution of peritoneal inflammation. J Exp Med (2002) 1.51
Racial ethnic differences in rates and determinants of deceased donor kidney transplantation. J Am Soc Nephrol (2011) 1.48
Polyubiquitin linkage profiles in three models of proteolytic stress suggest the etiology of Alzheimer disease. J Biol Chem (2011) 1.48
Non-sterilized fermentative production of polymer-grade L-lactic acid by a newly isolated thermophilic strain Bacillus sp. 2-6. PLoS One (2009) 1.46
The cotranslational function of ribosome-associated Hsp70 in eukaryotic protein homeostasis. Cell (2013) 1.46
USP19 deubiquitinating enzyme supports cell proliferation by stabilizing KPC1, a ubiquitin ligase for p27Kip1. Mol Cell Biol (2008) 1.44
Physicochemical properties of cross-linked poly-gamma-glutamic acid and its flocculating activity against kaolin suspension. J Biosci Bioeng (2005) 1.43
Polyubiquitination of prolactin receptor stimulates its internalization, postinternalization sorting, and degradation via the lysosomal pathway. Mol Cell Biol (2008) 1.41
The lysine 48 and lysine 63 ubiquitin conjugates are processed differently by the 26 s proteasome. J Biol Chem (2009) 1.39
Efficient internalization of MHC I requires lysine-11 and lysine-63 mixed linkage polyubiquitin chains. Traffic (2009) 1.39
Loss of LR11/SORLA enhances early pathology in a mouse model of amyloidosis: evidence for a proximal role in Alzheimer's disease. J Neurosci (2008) 1.39
Evening versus morning dosing regimen drug therapy for hypertension. Cochrane Database Syst Rev (2011) 1.38
A novel gene, encoding 6-hydroxy-3-succinoylpyridine hydroxylase, involved in nicotine degradation by Pseudomonas putida strain S16. Appl Environ Microbiol (2008) 1.38
Ube2w and ataxin-3 coordinately regulate the ubiquitin ligase CHIP. Mol Cell (2011) 1.37
Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol (2007) 1.34
Characterization of environmentally friendly nicotine degradation by Pseudomonas putida biotype A strain S16. Microbiology (2007) 1.34
Novel nicotine oxidoreductase-encoding gene involved in nicotine degradation by Pseudomonas putida strain S16. Appl Environ Microbiol (2008) 1.33
Dissecting the ubiquitin pathway by mass spectrometry. Biochim Biophys Acta (2006) 1.32
ELMOD2 is an Arl2 GTPase-activating protein that also acts on Arfs. J Biol Chem (2007) 1.31
Production of 2,3-butanediol from corncob molasses, a waste by-product in xylitol production. Appl Microbiol Biotechnol (2010) 1.31
Biotechnological routes based on lactic acid production from biomass. Biotechnol Adv (2011) 1.31
A novel whole-cell biocatalyst with NAD+ regeneration for production of chiral chemicals. PLoS One (2010) 1.31
A novel NADH-dependent and FAD-containing hydroxylase is crucial for nicotine degradation by Pseudomonas putida. J Biol Chem (2011) 1.30
Potent preclinical impact of metronomic low-dose oral topotecan combined with the antiangiogenic drug pazopanib for the treatment of ovarian cancer. Mol Cancer Ther (2010) 1.30
Proteomics analysis reveals novel components in the detergent-insoluble subproteome in Alzheimer's disease. J Proteome Res (2009) 1.27