A Quantitative Tissue-Specific Landscape of Protein Redox Regulation during Aging

[1]  Edward T Chouchani,et al.  H+ Transport is an Integral Function of the Mitochondrial ADP/ATP Carrier , 2019, Nature.

[2]  Ramin Rad,et al.  Full-featured, real-time database searching platform enables fast and accurate multiplexed quantitative proteomics , 2019, bioRxiv.

[3]  Do Young Hyeon,et al.  Evolution of the multi-tRNA synthetase complex and its role in cancer , 2019, The Journal of Biological Chemistry.

[4]  E. Weerapana,et al.  Cysteine reactivity across the subcellular universe. , 2019, Current opinion in chemical biology.

[5]  Susan E. Abbatiello,et al.  Characterization and Optimization of Multiplexed Quantitative Analyses Using High-Field Asymmetric-Waveform Ion Mobility Mass Spectrometry. , 2019, Analytical chemistry.

[6]  The UniProt Consortium,et al.  UniProt: a worldwide hub of protein knowledge , 2018, Nucleic Acids Res..

[7]  Martin Eisenacher,et al.  The PRIDE database and related tools and resources in 2019: improving support for quantification data , 2018, Nucleic Acids Res..

[8]  Direct cysteine sulfenylation drives activation of the Src kinase , 2018, Nature Communications.

[9]  Alexander S. Banks,et al.  Accumulation of succinate controls activation of adipose tissue thermogenesis , 2018, Nature.

[10]  Steven P Gygi,et al.  Streamlined Tandem Mass Tag (SL-TMT) Protocol: An Efficient Strategy for Quantitative (Phospho)proteome Profiling Using Tandem Mass Tag-Synchronous Precursor Selection-MS3. , 2018, Journal of proteome research.

[11]  E. Gottlieb,et al.  Proteome-wide analysis of cysteine oxidation reveals metabolic sensitivity to redox stress , 2018, Nature Communications.

[12]  Alison R Erickson,et al.  An Internal Standard for Assessing Phosphopeptide Recovery from Metal Ion/Oxide Enrichment Strategies , 2018, Journal of The American Society for Mass Spectrometry.

[13]  Shuhong Zhao,et al.  Proteomic Analyses of Cysteine Redox in High-Fat-Fed and Fasted Mouse Livers: Implications for Liver Metabolic Homeostasis. , 2018, Journal of proteome research.

[14]  Devin K Schweppe,et al.  BioPlex Display: An Interactive Suite for Large-Scale AP-MS Protein-Protein Interaction Data. , 2018, Journal of proteome research.

[15]  B. Warscheid,et al.  Quantitative proteomics identifies redox switches for global translation modulation by mitochondrially produced reactive oxygen species , 2018, Nature Communications.

[16]  Steven P Gygi,et al.  Improved Method for Determining Absolute Phosphorylation Stoichiometry Using Bayesian Statistics and Isobaric Labeling. , 2017, Journal of proteome research.

[17]  Edward T Chouchani,et al.  Mitochondrial reactive oxygen species and adipose tissue thermogenesis: Bridging physiology and mechanisms , 2017, The Journal of Biological Chemistry.

[18]  B. Erickson,et al.  Identification and quantification of protein S-nitrosation by nitrite in the mouse heart during ischemia , 2017, The Journal of Biological Chemistry.

[19]  Devin P. Sullivan,et al.  A subcellular map of the human proteome , 2017, Science.

[20]  Devin K. Schweppe,et al.  Architecture of the human interactome defines protein communities and disease networks , 2017, Nature.

[21]  J. Vinh,et al.  Quantitative analysis of the cysteine redoxome by iodoacetyl tandem mass tags , 2017, Analytical and Bioanalytical Chemistry.

[22]  M. Larsen,et al.  Simultaneous Enrichment of Cysteine-containing Peptides and Phosphopeptides Using a Cysteine-specific Phosphonate Adaptable Tag (CysPAT) in Combination with titanium dioxide (TiO2) Chromatography* , 2016, Molecular & Cellular Proteomics.

[23]  A. Holmgren,et al.  Cellular Redox Systems Impact the Aggregation of Cu,Zn Superoxide Dismutase Linked to Familial Amyotrophic Lateral Sclerosis* , 2016, The Journal of Biological Chemistry.

[24]  Kate S. Carroll,et al.  Reactivity, Selectivity, and Stability in Sulfenic Acid Detection: A Comparative Study of Nucleophilic and Electrophilic Probes. , 2016, Bioconjugate chemistry.

[25]  A. Olson,et al.  Proteome-wide covalent ligand discovery in native biological systems , 2016, Nature.

[26]  B. Spiegelman,et al.  Mitochondrial ROS regulate thermogenic energy expenditure and sulfenylation of UCP1 , 2016, Nature.

[27]  Gary D. Bader,et al.  Cytoscape.js: a graph theory library for visualisation and analysis , 2015, Bioinform..

[28]  The Expanding Landscape of the Thiol Redox Proteome* , 2015, Molecular & Cellular Proteomics.

[29]  Edward L. Huttlin,et al.  The BioPlex Network: A Systematic Exploration of the Human Interactome , 2015, Cell.

[30]  L. Partridge,et al.  Fasting, but Not Aging, Dramatically Alters the Redox Status of Cysteine Residues on Proteins in Drosophila melanogaster , 2015, Cell reports.

[31]  Núria Queralt-Rosinach,et al.  DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes , 2015, Database J. Biol. Databases Curation.

[32]  N. Chandel,et al.  ROS-dependent signal transduction. , 2015, Current opinion in cell biology.

[33]  L. Poole The basics of thiols and cysteines in redox biology and chemistry. , 2015, Free radical biology & medicine.

[34]  Corey Gough,et al.  Characterization and Optimization , 2015 .

[35]  M. Ristow,et al.  Unraveling the Truth About Antioxidants: Mitohormesis explains ROS-induced health benefits , 2014, Nature Medicine.

[36]  Edward L. Huttlin,et al.  MultiNotch MS3 Enables Accurate, Sensitive, and Multiplexed Detection of Differential Expression across Cancer Cell Line Proteomes , 2014, Analytical chemistry.

[37]  T. Finkel,et al.  Cellular mechanisms and physiological consequences of redox-dependent signalling , 2014, Nature Reviews Molecular Cell Biology.

[38]  N. Chandel,et al.  ROS Function in Redox Signaling and Oxidative Stress , 2014, Current Biology.

[39]  K. Khoo,et al.  Mass spectrometry-based quantitative proteomics for dissecting multiplexed redox cysteine modifications in nitric oxide-protected cardiomyocyte under hypoxia. , 2014, Antioxidants & redox signaling.

[40]  A. Aharoni,et al.  Mapping the diatom redox-sensitive proteome provides insight into response to nitrogen stress in the marine environment , 2014, Proceedings of the National Academy of Sciences.

[41]  George M Church,et al.  pLogo: a probabilistic approach to visualizing sequence motifs , 2013, Nature Methods.

[42]  Manuel Serrano,et al.  The Hallmarks of Aging , 2013, Cell.

[43]  Linda Partridge,et al.  Cardioprotection by S-nitrosation of a cysteine switch on mitochondrial complex I , 2013, Nature Medicine.

[44]  Kate S. Carroll,et al.  Cysteine-Mediated Redox Signaling: Chemistry, Biology, and Tools for Discovery , 2013, Chemical reviews.

[45]  R. Banerjee,et al.  Time line of redox events in aging postmitotic cells , 2013, eLife.

[46]  Edward T Chouchani,et al.  Inactivation of Pyruvate Dehydrogenase Kinase 2 by Mitochondrial Reactive Oxygen Species* , 2012, The Journal of Biological Chemistry.

[47]  S. Gygi,et al.  MS3 eliminates ratio distortion in isobaric labeling-based multiplexed quantitative proteomics , 2011, Nature Methods.

[48]  Linda Partridge,et al.  Unraveling the biological roles of reactive oxygen species. , 2011, Cell metabolism.

[49]  Edward T Chouchani,et al.  Proteomic approaches to the characterization of protein thiol modification , 2011, Current opinion in chemical biology.

[50]  Dean P. Jones,et al.  Protein Cysteines Map to Functional Networks According to Steady-state Level of Oxidation. , 2011, Journal of proteomics & bioinformatics.

[51]  Edward L. Huttlin,et al.  A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression , 2010, Cell.

[52]  T. Hurd,et al.  Cysteine residues exposed on protein surfaces are the dominant intramitochondrial thiol and may protect against oxidative damage , 2010, The FEBS journal.

[53]  Peng Huang,et al.  Role of mitochondria-associated hexokinase II in cancer cell death induced by 3-bromopyruvate. , 2009, Biochimica et biophysica acta.

[54]  J. Winther,et al.  Quantifying the global cellular thiol–disulfide status , 2009, Proceedings of the National Academy of Sciences.

[55]  Israel Steinfeld,et al.  BMC Bioinformatics BioMed Central , 2008 .

[56]  Catherine Overy,et al.  The mechanism of transport by mitochondrial carriers based on analysis of symmetry , 2008, Proceedings of the National Academy of Sciences.

[57]  H. Schägger,et al.  Identification of the Mitochondrial ND3 Subunit as a Structural Component Involved in the Active/Deactive Enzyme Transition of Respiratory Complex I* , 2008, Journal of Biological Chemistry.

[58]  J. Strahler,et al.  Quantifying changes in the thiol redox proteome upon oxidative stress in vivo , 2008, Proceedings of the National Academy of Sciences.

[59]  L. Herzenberg,et al.  N-Acetylcysteine--a safe antidote for cysteine/glutathione deficiency. , 2007, Current opinion in pharmacology.

[60]  P. S. Ray,et al.  Macromolecular complexes as depots for releasable regulatory proteins. , 2007, Trends in biochemical sciences.

[61]  Steven P Gygi,et al.  Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry , 2007, Nature Methods.

[62]  Zohar Yakhini,et al.  Discovering Motifs in Ranked Lists of DNA Sequences , 2007, PLoS Comput. Biol..

[63]  Edward L Huttlin,et al.  Prediction of error associated with false-positive rate determination for peptide identification in large-scale proteomics experiments using a combined reverse and forward peptide sequence database strategy. , 2007, Journal of proteome research.

[64]  Steven P Gygi,et al.  A probability-based approach for high-throughput protein phosphorylation analysis and site localization , 2006, Nature Biotechnology.

[65]  Kap-Seok Yang,et al.  Reversible oxidation and inactivation of the tumor suppressor PTEN in cells stimulated with peptide growth factors. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[66]  Sunghoon Kim,et al.  Aminoacyl-tRNA synthetase complexes: beyond translation , 2004, Journal of Cell Science.

[67]  A. Wollenberger,et al.  Eine einfache Technik der extrem schnellen Abkühlung größerer Gewebestücke , 1960, Pflüger's Archiv für die gesamte Physiologie des Menschen und der Tiere.

[68]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[69]  Joshua E. Elias,et al.  Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. , 2003, Journal of proteome research.

[70]  A. Halestrap,et al.  Role of critical thiol groups on the matrix surface of the adenine nucleotide translocase in the mechanism of the mitochondrial permeability transition pore. , 2002, The Biochemical journal.

[71]  P. Pedersen,et al.  Glucose catabolism in the rabbit VX2 tumor model for liver cancer: characterization and targeting hexokinase. , 2001, Cancer letters.

[72]  S. Gygi,et al.  Quantitative analysis of complex protein mixtures using isotope-coded affinity tags , 1999, Nature Biotechnology.

[73]  J. Yates,et al.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database , 1994, Journal of the American Society for Mass Spectrometry.

[74]  D. Wessel,et al.  A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. , 1984, Analytical biochemistry.

[75]  D. Harman Aging: a theory based on free radical and radiation chemistry. , 1956, Journal of gerontology.