Published in Anal Chem on February 09, 2015
A generalizable platform for interrogating target- and signal-specific consequences of electrophilic modifications in redox-dependent cell signaling. J Am Chem Soc (2015) 0.90
A capture method based on the VC1 domain reveals new binding properties of the human receptor for advanced glycation end products (RAGE). Redox Biol (2016) 0.89
On-Demand Targeting: Investigating Biology with Proximity-Directed Chemistry. J Am Chem Soc (2016) 0.86
Chemical proteomics approaches for identifying the cellular targets of natural products. Nat Prod Rep (2016) 0.83
Protein lipoxidation: Detection strategies and challenges. Redox Biol (2015) 0.79
The Die Is Cast: Precision Electrophilic Modifications Contribute to Cellular Decision Making. Chem Res Toxicol (2016) 0.77
T-REX on-demand redox targeting in live cells. Nat Protoc (2016) 0.77
Specificity of Protein Covalent Modification by the Electrophilic Proteasome Inhibitor Carfilzomib in Human Cells. Mol Cell Proteomics (2016) 0.76
Histone adduction and its functional impact on epigenetics. Chem Res Toxicol (2016) 0.75
Quantitative Analysis and Discovery of Lysine and Arginine Modifications (QuARKMod). Anal Chem (2016) 0.75
Click Chemistry Reagent for Identification of Sites of Covalent Ligand Incorporation in Integral Membrane Proteins. Anal Chem (2017) 0.75
Cross-talk between lipid and protein carbonylation in a dynamic cardiomyocyte model of mild nitroxidative stress. Redox Biol (2016) 0.75
Chemoproteomic profiling of targets of lipid-derived electrophiles by bioorthogonal aminooxy probe. Redox Biol (2017) 0.75
Signaling by 4-hydroxy-2-nonenal: Exposure protocols, target selectivity and degradation. Arch Biochem Biophys (2016) 0.75
Systematic and Quantitative Assessment of Hydrogen Peroxide Reactivity With Cysteines Across Human Proteomes. Mol Cell Proteomics (2017) 0.75
Chemoproteomics Reveals Chemical Diversity and Dynamics of 4-Oxo-2-nonenal Modifications in Cells. Mol Cell Proteomics (2017) 0.75
Higher-energy C-trap dissociation for peptide modification analysis. Nat Methods (2007) 5.04
IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering. J Proteome Res (2009) 3.72
Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation. Mol Cell Proteomics (2012) 2.66
Disparate proteome reactivity profiles of carbon electrophiles. Nat Chem Biol (2008) 2.25
Click chemistry for drug development and diverse chemical-biology applications. Chem Rev (2013) 2.08
Global analysis of protein damage by the lipid electrophile 4-hydroxy-2-nonenal. Mol Cell Proteomics (2008) 1.89
Identification of protein targets of 4-hydroxynonenal using click chemistry for ex vivo biotinylation of azido and alkynyl derivatives. Chem Res Toxicol (2008) 1.82
Transduction of redox signaling by electrophile-protein reactions. Sci Signal (2009) 1.62
pLogo: a probabilistic approach to visualizing sequence motifs. Nat Methods (2013) 1.55
An azido-biotin reagent for use in the isolation of protein adducts of lipid-derived electrophiles by streptavidin catch and photorelease. Mol Cell Proteomics (2009) 1.52
TagRecon: high-throughput mutation identification through sequence tagging. J Proteome Res (2010) 1.49
A chemoproteomic platform to quantitatively map targets of lipid-derived electrophiles. Nat Methods (2013) 1.48
Reversibility of covalent electrophile-protein adducts and chemical toxicity. Chem Res Toxicol (2008) 1.38
Covalent modification of epithelial fatty acid-binding protein by 4-hydroxynonenal in vitro and in vivo. Evidence for a role in antioxidant biology. J Biol Chem (2002) 1.36
Molecular basis of enzyme inactivation by an endogenous electrophile 4-hydroxy-2-nonenal: identification of modification sites in glyceraldehyde-3-phosphate dehydrogenase. Biochemistry (2003) 1.30
Quinone electrophiles selectively adduct "electrophile binding motifs" within cytochrome c. Biochemistry (2007) 1.25
Cell death and diseases related to oxidative stress: 4-hydroxynonenal (HNE) in the balance. Cell Death Differ (2013) 1.23
Reactive aldehyde modification of thioredoxin-1 activates early steps of inflammation and cell adhesion. Am J Pathol (2007) 1.21
Site-specific mapping and quantification of protein S-sulphenylation in cells. Nat Commun (2014) 1.19
Actin Cys374 as a nucleophilic target of alpha,beta-unsaturated aldehydes. Free Radic Biol Med (2006) 1.18
Alkylation damage by lipid electrophiles targets functional protein systems. Mol Cell Proteomics (2014) 1.13
NetGestalt: integrating multidimensional omics data over biological networks. Nat Methods (2013) 1.13
The lipid peroxidation product 4-hydroxy-2-nonenal: Advances in chemistry and analysis. Redox Biol (2013) 1.10
Supporting tool suite for production proteomics. Bioinformatics (2011) 1.08
Posttranslational modification and regulation of glutamate-cysteine ligase by the α,β-unsaturated aldehyde 4-hydroxy-2-nonenal. Free Radic Biol Med (2010) 0.99
Relating protein adduction to gene expression changes: a systems approach. Mol Biosyst (2011) 0.99
Protein-selective capture to analyze electrophile adduction of hsp90 by 4-hydroxynonenal. Chem Res Toxicol (2011) 0.96
Redox proteomic identification of HNE-bound mitochondrial proteins in cardiac tissues reveals a systemic effect on energy metabolism after doxorubicin treatment. Free Radic Biol Med (2014) 0.93
The reactivity of human serum albumin toward trans-4-hydroxy-2-nonenal. J Mass Spectrom (2012) 0.87
Role of 4-hydroxynonenal-protein adducts in human diseases. Antioxid Redox Signal (2015) 0.86
Protein alkylation by the α,β-unsaturated aldehyde acrolein. A reversible mechanism of electrophile signaling? FEBS Lett (2013) 0.85
The concerted action of a positive charge and hydrogen bonds dynamically regulates the pKa of the nucleophilic cysteine in the NrdH-redoxin family. Protein Sci (2013) 0.81
Informatics of protein and posttranslational modification detection via shotgun proteomics. Methods Mol Biol (2013) 0.80
Covalent binding of 4-hydroxy-2-nonenal to lactate dehydrogenase decreases NADH formation and metmyoglobin reducing activity. J Agric Food Chem (2014) 0.79
RNA-seq data analysis at the gene and CDS levels provides a comprehensive view of transcriptome responses induced by 4-hydroxynonenal. Mol Biosyst (2013) 0.79
Covalent binding of 4-hydroxynonenal to matrix metalloproteinase 13 studied by liquid chromatography-mass spectrometry. Chem Res Toxicol (2014) 0.77
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics (2010) 13.35
Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotechnol (2009) 9.67
Glucose-independent glutamine metabolism via TCA cycling for proliferation and survival in B cells. Cell Metab (2012) 4.80
Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. J Proteome Res (2010) 3.08
Identification of S-nitrosylation motifs by site-specific mapping of the S-nitrosocysteine proteome in human vascular smooth muscle cells. Proc Natl Acad Sci U S A (2006) 2.58
Sample preparation and digestion for proteomic analyses using spin filters. Proteomics (2005) 2.49
Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance. Mol Cell Proteomics (2009) 2.39
Specific patterns of electrophile adduction trigger Keap1 ubiquitination and Nrf2 activation. J Biol Chem (2005) 2.37
Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Mol Cell Proteomics (2014) 2.37
Control of oxygenation in lipoxygenase and cyclooxygenase catalysis. Chem Biol (2007) 2.29
Identification of sensor cysteines in human Keap1 modified by the cancer chemopreventive agent sulforaphane. Chem Res Toxicol (2005) 2.22
Free radical lipid peroxidation: mechanisms and analysis. Chem Rev (2011) 2.17
Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses. Mol Cell Proteomics (2009) 2.09
Global analysis of protein damage by the lipid electrophile 4-hydroxy-2-nonenal. Mol Cell Proteomics (2008) 1.89
Identification of protein targets of 4-hydroxynonenal using click chemistry for ex vivo biotinylation of azido and alkynyl derivatives. Chem Res Toxicol (2008) 1.82
Routes to 4-hydroxynonenal: fundamental issues in the mechanisms of lipid peroxidation. J Biol Chem (2008) 1.76
Cytosolic and nuclear protein targets of thiol-reactive electrophiles. Chem Res Toxicol (2006) 1.69
Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis. Mol Cell Proteomics (2009) 1.66
P-Mod: an algorithm and software to map modifications to peptide sequences using tandem MS data. J Proteome Res (2005) 1.65
Discovery of lipid peroxidation products formed in vivo with a substituted tetrahydrofuran ring (isofurans) that are favored by increased oxygen tension. Proc Natl Acad Sci U S A (2002) 1.63
Protein identification using customized protein sequence databases derived from RNA-Seq data. J Proteome Res (2011) 1.62
Rate constants for peroxidation of polyunsaturated fatty acids and sterols in solution and in liposomes. J Am Chem Soc (2009) 1.58
Global shifts in protein sumoylation in response to electrophile and oxidative stress. Chem Res Toxicol (2004) 1.57
Proteomic analysis of exosomes from mutant KRAS colon cancer cells identifies intercellular transfer of mutant KRAS. Mol Cell Proteomics (2012) 1.55
Evaluation of strong cation exchange versus isoelectric focusing of peptides for multidimensional liquid chromatography-tandem mass spectrometry. J Proteome Res (2008) 1.55
Methods for peptide and protein quantitation by liquid chromatography-multiple reaction monitoring mass spectrometry. Mol Cell Proteomics (2011) 1.54
An azido-biotin reagent for use in the isolation of protein adducts of lipid-derived electrophiles by streptavidin catch and photorelease. Mol Cell Proteomics (2009) 1.52
Depletion of abundant plasma proteins and limitations of plasma proteomics. J Proteome Res (2010) 1.52
Covalent modification at Cys151 dissociates the electrophile sensor Keap1 from the ubiquitin ligase CUL3. Chem Res Toxicol (2008) 1.47
Biological activities of 7-dehydrocholesterol-derived oxysterols: implications for Smith-Lemli-Opitz syndrome. J Lipid Res (2010) 1.44
Comparative shotgun proteomics using spectral count data and quasi-likelihood modeling. J Proteome Res (2010) 1.43
New insights regarding the autoxidation of polyunsaturated fatty acids. Antioxid Redox Signal (2005) 1.42
Diagnostic accuracy of MALDI mass spectrometric analysis of unfractionated serum in lung cancer. J Thorac Oncol (2007) 1.40
Reversibility of covalent electrophile-protein adducts and chemical toxicity. Chem Res Toxicol (2008) 1.38
Proteomic identification of ubiquitinated proteins from human cells expressing His-tagged ubiquitin. Proteomics (2005) 1.37
A bioinformatics workflow for variant peptide detection in shotgun proteomics. Mol Cell Proteomics (2011) 1.34
Protein targets of reactive electrophiles in human liver microsomes. Chem Res Toxicol (2007) 1.34
Identification of proteins adducted by lipid peroxidation products in plasma and modifications of apolipoprotein A1 with a novel biotinylated phospholipid probe. J Proteome Res (2008) 1.28
Oxysterols from free radical chain oxidation of 7-dehydrocholesterol: product and mechanistic studies. J Am Chem Soc (2010) 1.27
An oxysterol biomarker for 7-dehydrocholesterol oxidation in cell/mouse models for Smith-Lemli-Opitz syndrome. J Lipid Res (2011) 1.25
Formation of F-ring isoprostane-like compounds (F3-isoprostanes) in vivo from eicosapentaenoic acid. J Biol Chem (2006) 1.25
Theoretical calculations of carbon-oxygen bond dissociation enthalpies of peroxyl radicals formed in the autoxidation of lipids. J Am Chem Soc (2003) 1.23
Use of dimedone-based chemical probes for sulfenic acid detection methods to visualize and identify labeled proteins. Methods Enzymol (2010) 1.23
Spin filter-based sample preparation for shotgun proteomics. Nat Methods (2009) 1.21
Connecting genomic alterations to cancer biology with proteomics: the NCI Clinical Proteomic Tumor Analysis Consortium. Cancer Discov (2013) 1.20
Statistical design for biospecimen cohort size in proteomics-based biomarker discovery and verification studies. J Proteome Res (2013) 1.20
Network-assisted protein identification and data interpretation in shotgun proteomics. Mol Syst Biol (2009) 1.19
DNA-protein cross-linking by 1,2,3,4-diepoxybutane. J Proteome Res (2010) 1.17
Covalent adduction of human serum albumin by 4-hydroxy-2-nonenal: kinetic analysis of competing alkylation reactions. Biochemistry (2006) 1.16
Formation of highly reactive cyclopentenone isoprostane compounds (A3/J3-isoprostanes) in vivo from eicosapentaenoic acid. J Biol Chem (2008) 1.15
Transforming thymidine into a magnetic resonance imaging probe for monitoring gene expression. J Am Chem Soc (2013) 1.15
Efficacy of cetuximab in the treatment of Menetrier's disease. Sci Transl Med (2009) 1.14
Alkylation damage by lipid electrophiles targets functional protein systems. Mol Cell Proteomics (2014) 1.13
Peroxyl radical clocks. J Org Chem (2006) 1.13
Mitochondrial protein targets of thiol-reactive electrophiles. Chem Res Toxicol (2008) 1.12
Enzymatic synthesis of a bicyclobutane fatty acid by a hemoprotein lipoxygenase fusion protein from the cyanobacterium Anabaena PCC 7120. Proc Natl Acad Sci U S A (2007) 1.12
Formation of prostaglandins E2 and D2 via the isoprostane pathway: a mechanism for the generation of bioactive prostaglandins independent of cyclooxygenase. J Biol Chem (2003) 1.11
The development of selected reaction monitoring methods for targeted proteomics via empirical refinement. Proteomics (2012) 1.10
Analytical validation of protein-based multiplex assays: a workshop report by the NCI-FDA interagency oncology task force on molecular diagnostics. Clin Chem (2009) 1.10
Urinary prostaglandin F2alpha is generated from the isoprostane pathway and not the cyclooxygenase in humans. J Biol Chem (2006) 1.09
QuaMeter: multivendor performance metrics for LC-MS/MS proteomics instrumentation. Anal Chem (2012) 1.08
Supporting tool suite for production proteomics. Bioinformatics (2011) 1.08
Formation of 4-hydroxynonenal from cardiolipin oxidation: Intramolecular peroxyl radical addition and decomposition. Free Radic Biol Med (2010) 1.08
Ex vivo oxidation in tissue and plasma assays of hydroxyoctadecadienoates: Z,E/E,E stereoisomer ratios. Chem Res Toxicol (2010) 1.07
Protein-based multiplex assays: mock presubmissions to the US Food and Drug Administration. Clin Chem (2009) 1.07
Conversion of 7-dehydrocholesterol to 7-ketocholesterol is catalyzed by human cytochrome P450 7A1 and occurs by direct oxidation without an epoxide intermediate. J Biol Chem (2011) 1.07
In-depth proteomic analysis of nonsmall cell lung cancer to discover molecular targets and candidate biomarkers. Mol Cell Proteomics (2012) 1.06
DHCEO accumulation is a critical mediator of pathophysiology in a Smith-Lemli-Opitz syndrome model. Neurobiol Dis (2011) 1.05
Label-free quantitation of protein modifications by pseudo selected reaction monitoring with internal reference peptides. J Proteome Res (2012) 1.05
Lipid biomarkers of oxidative stress in a genetic mouse model of Smith-Lemli-Opitz syndrome. J Inherit Metab Dis (2012) 1.04
Fibrinogen beta-chain tyrosine nitration is a prothrombotic risk factor. J Biol Chem (2008) 1.04
Mass spectrometry of intracellular and membrane proteins using cleavable detergents. Anal Chem (2003) 1.03
Proteomic analysis of DNA-protein cross-linking by antitumor nitrogen mustards. Chem Res Toxicol (2009) 1.03
Metabolism of oxysterols derived from nonenzymatic oxidation of 7-dehydrocholesterol in cells. J Lipid Res (2013) 1.02
Autoxidative transformation of chiral omega6 hydroxy linoleic and arachidonic acids to chiral 4-hydroxy-2E-nonenal. Chem Res Toxicol (2004) 1.01
Combination detergent/MALDI matrix: functional cleavable detergents for mass spectrometry. Anal Chem (2005) 1.01
Free radical oxidation of polyunsaturated lipids: New mechanistic insights and the development of peroxyl radical clocks. Acc Chem Res (2011) 1.01
Regiochemistry of neuroprostanes generated from the peroxidation of docosahexaenoic acid in vitro and in vivo. J Biol Chem (2005) 1.01
Proteomic consequences of a single gene mutation in a colorectal cancer model. J Proteome Res (2011) 1.01
Sequence tagging reveals unexpected modifications in toxicoproteomics. Chem Res Toxicol (2011) 1.00
Novel oxysterols observed in tissues and fluids of AY9944-treated rats: a model for Smith-Lemli-Opitz syndrome. J Lipid Res (2011) 0.99
Relating protein adduction to gene expression changes: a systems approach. Mol Biosyst (2011) 0.99
Formation of highly reactive A-ring and J-ring isoprostane-like compounds (A4/J4-neuroprostanes) in vivo from docosahexaenoic acid. J Biol Chem (2002) 0.99
Small amounts of isotope-reinforced polyunsaturated fatty acids suppress lipid autoxidation. Free Radic Biol Med (2012) 0.99
Quantitative analysis of modified proteins by LC-MS/MS of peptides labeled with phenyl isocyanate. J Proteome Res (2003) 0.99
Capture and release of alkyne-derivatized glycerophospholipids using cobalt chemistry. Nat Chem Biol (2010) 0.99
Factors influencing the autoxidation of fatty acids: effect of olefin geometry of the nonconjugated diene. J Am Chem Soc (2004) 0.98
Increased protein nitration burden in the atherosclerotic lesions and plasma of apolipoprotein A-I deficient mice. Circ Res (2007) 0.98
Mechlorethamine-induced DNA-protein cross-linking in human fibrosarcoma (HT1080) cells. J Proteome Res (2011) 0.98