Recent advances in quantitative and chemical proteomics for autophagy studies

No abstract is available for this paper.

• Publication year

  2017

• Venue

  Autophagy

• Publication date

  2017-08-18

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1080/15548627.2017.1313944PMID 28820289PMCID PMC5612287
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• ATG9A loss confers resistance to trastuzumab via c-Cbl mediated Her2 degradation

  2016cited by this paper
• Global Analysis of Cellular Protein Flux Quantifies the Selectivity of Basal Autophagy

  2016cited by this paper
• Ubiquitin-Dependent And Independent Signals In Selective Autophagy.

  2016cited by this paper
• Redox proteomics: Methods for the identification and enrichment of redox‐modified proteins and their applications

  2016cited by this paper
• Probes of Ubiquitin E3 ligases distinguish different stages of Parkin activation

  2016cited by this paper
• Assessing the Mitochondrial Membrane Potential in Cells and In Vivo using Targeted Click Chemistry and Mass Spectrometry

  2016cited by this paper
• Proteome-wide Changes in Protein Turnover Rates in C. elegans Models of Longevity and Age-Related Disease.

  2016cited by this paper
• BONLAC: A combinatorial proteomic technique to measure stimulus-induced translational profiles in brain slices.

  2016cited by this paper
• Global Liver Proteome Analysis Using iTRAQ Reveals AMPK-mTOR-Autophagy Signaling Is Altered by Intrauterine Growth Restriction in Newborn Piglets.

  2016cited by this paper
• Assessing the Delivery of Molecules to the Mitochondrial Matrix Using Click Chemistry

  2016cited by this paper
• Target identification of natural and traditional medicines with quantitative chemical proteomics approaches.

  2016cited by this paper
• Phosphorylation of Atg9 regulates movement to the phagophore assembly site and the rate of autophagosome formation

  2016cited by this paper
• Kinetic Analysis of Protein Stability Reveals Age-Dependent Degradation.

  2016cited by this paper
• Global analysis of cellular protein flux quantifies the selectivity of basal autophagy

  2016cited by this paper
• Quantitative chemical proteomics profiling of de novo protein synthesis during starvation-mediated autophagy

  2016cited by this paper
• Quantitative Chemical Proteomic Profiling of Ubiquitin Specific Proteases in Intact Cancer Cells.

  2016cited by this paper
• Chemical proteomics approaches for identifying the cellular targets of natural products

  2016cited by this paper
• Phosphorylation of OPTN by TBK1 enhances its binding to Ub chains and promotes selective autophagy of damaged mitochondria

  2016cited by this paper
• Nutrient-regulated Phosphorylation of ATG13 Inhibits Starvation-induced Autophagy*

  2016cited by this paper
• Target identification of covalently binding drugs by activity-based protein profiling (ABPP).

  2016cited by this paper
• The role of protein and peptide separation before mass spectrometry analysis in clinical proteomics.

  2015cited by this paper
• Loss of neuronal Miro1 disrupts mitophagy and induces hyperactivation of the integrated stress response

  2015cited by this paper
• Chemical methods for the proteome-wide identification of posttranslationally modified proteins.

  2015cited by this paper
• TXNDC17 promotes paclitaxel resistance via inducing autophagy in ovarian cancer

  2015cited by this paper
• Precision autophagy: Will the next wave of selective autophagy markers and specific autophagy inhibitors feed clinical pipelines?

  2015cited by this paper
• K-Profiles: A Nonlinear Clustering Method for Pattern Detection in High Dimensional Data

  2015cited by this paper
• Mapping sites of aspirin-induced acetylations in live cells by quantitative acid-cleavable activity-based protein profiling (QA-ABPP)

  2015cited by this paper
• Amino Acid Activation of mTORC1 by a PB1-Domain-Driven Kinase Complex Cascade.

  2015cited by this paper
• Dynamics of zebrafish fin regeneration using a pulsed SILAC approach

  2015cited by this paper
• Autophagy-Related Deubiquitinating Enzymes Involved in Health and Disease

  2015cited by this paper
• Regulation of autophagy by protein post-translational modification

  2015cited by this paper
• Posttranslational modification of autophagy-related proteins in macroautophagy

  2015cited by this paper
• Autophagy signal transduction by ATG proteins: from hierarchies to networks

  2015cited by this paper
• Autophagy machinery in the context of mammalian mitophagy.

  2015cited by this paper
• Elaborating the Role of Natural Products-Induced Autophagy in Cancer Treatment: Achievements and Artifacts in the State of the Art

  2015cited by this paper
• The PINK1-PARKIN Mitochondrial Ubiquitylation Pathway Drives a Program of OPTN/NDP52 Recruitment and TBK1 Activation to Promote Mitophagy.

  2015cited by this paper
• Quantitative shotgun proteomics: considerations for a high-quality workflow in immunology

  2014cited by this paper
• Early Steps in Autophagy Depend on Direct Phosphorylation of Atg9 by the Atg1 Kinase

  2014cited by this paper
• In-Depth Quantitative Proteomic Analysis of de Novo Protein Synthesis Induced by Brain-Derived Neurotrophic Factor

  2014cited by this paper
• Organelle-specific activity-based protein profiling in living cells.

  2014cited by this paper
• Phosphoproteomics Reveals Resveratrol-Dependent Inhibition of Akt/mTORC1/S6K1 Signaling

  2014cited by this paper
• Kinetics of precursor labeling in stable isotope labeling in cell cultures (SILAC) experiments.

  2014cited by this paper
• Development of a novel method for quantification of autophagic protein degradation by AHA labeling

  2014cited by this paper
• Chemical proteomic strategies for the discovery and development of anticancer drugs

  2014cited by this paper
• Caloric restriction mimetics: natural/physiological pharmacological autophagy inducers

  2014cited by this paper
• A roadmap to evaluate the proteome-wide selectivity of covalent kinase inhibitors

  2014cited by this paper
• Quantitative proteomics reveal a feedforward mechanism for mitochondrial PARKIN translocation and ubiquitin chain synthesis.

  2014cited by this paper
• USP8 regulates mitophagy by removing K6‐linked ubiquitin conjugates from parkin

  2014cited by this paper
• At the end of the autophagic road: an emerging understanding of lysosomal functions in autophagy.

  2014cited by this paper
• Identifying specific receptors for cargo-mediated autophagy

  2014cited by this paper
• Quantitative proteomics identifies NCOA4 as the cargo receptor mediating ferritinophagy

  2014cited by this paper
• 2DE: the phoenix of proteomics.

  2014cited by this paper
• Functional role of autophagy-mediated proteome remodeling in cell survival signaling and innate immunity.

  2014cited by this paper
• Characterization of early autophagy signaling by quantitative phosphoproteomics

  2014cited by this paper
• Affinity purification–mass spectrometry and network analysis to understand protein-protein interactions

  2014cited by this paper
• Combining pulsed SILAC labeling and click-chemistry for quantitative secretome analysis.

  2014cited by this paper
• Target identification for small bioactive molecules: finding the needle in the haystack.

  2013cited by this paper
• The LIR motif – crucial for selective autophagy

  2013cited by this paper
• Neutron encoded labeling for peptide identification.

  2013cited by this paper
• Proteomics analysis of autophagy-deficient Atg7-/- MEFs reveals a close relationship between F-actin and autophagy.

  2013cited by this paper
• Emerging roles of E3 ubiquitin ligases in autophagy.

  2013cited by this paper
• Status of Large-scale Analysis of Post-translational Modifications by Mass Spectrometry*

  2013cited by this paper
• Post-translational modifications and mass spectrometry detection.

  2013cited by this paper
• Autophagy and human diseases

  2013cited by this paper
• Why should autophagic flux be assessed?

  2013cited by this paper
• Quantitative Proteomics Reveals the Induction of Mitophagy in Tumor Necrosis Factor-α-activated (TNFα) Macrophages*

  2013cited by this paper
• Exploiting the bad eating habits of Ras-driven cancers

  2013cited by this paper
• Stable isotope labeling methods in protein profiling.

  2013cited by this paper
• Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization

  2013cited by this paper
• Inducing autophagy

  2013cited by this paper
• Identification of Autophagosome-associated Proteins and Regulators by Quantitative Proteomic Analysis and Genetic Screens

  2012cited by this paper
• Supplemental material Identification of autophagosome-associated proteins and regulators by quantitative proteomic analysis and genetic screens

  2012cited by this paper
• Fluorescence-based active site probes for profiling deubiquitinating enzymes.

  2012cited by this paper
• The proteomic analysis of endogenous FAT10 substrates identifies p62/SQSTM1 as a substrate of FAT10ylation

  2012cited by this paper
• Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present

  2012cited by this paper
• Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics*

  2012cited by this paper
• Development of a Protein Standard Absolute Quantification (PSAQ™) assay for the quantification of Staphylococcus aureus enterotoxin A in serum.

  2012cited by this paper
• Affinity‐purification coupled to mass spectrometry: Basic principles and strategies

  2012cited by this paper
• Mass spectrometry‐based targeted quantitative proteomics: Achieving sensitive and reproducible detection of proteins

  2012cited by this paper
• Proteome Dynamics: Revisiting Turnover with a Global Perspective*

  2012cited by this paper
• Quantitative phosphoproteomics to characterize signaling networks.

  2012cited by this paper
• Phosphoproteomic analysis of cells treated with longevity-related autophagy inducers

  2012cited by this paper
• Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics

  2011cited by this paper
• Protein identification using MS/MS data.

  2011cited by this paper
• Global quantification of mammalian gene expression control

  2011cited by this paper
• Autophagy in protein and organelle turnover.

  2011cited by this paper
• The role of Atg proteins in autophagosome formation.

  2011cited by this paper
• A Protein Epitope Signature Tag (PrEST) Library Allows SILAC-based Absolute Quantification and Multiplexed Determination of Protein Copy Numbers in Cell Lines*

  2011cited by this paper
• Spermidine and resveratrol induce autophagy by distinct pathways converging on the acetylproteome

  2011cited by this paper
• Longevity-relevant regulation of autophagy at the level of the acetylproteome

  2011cited by this paper
• Quantitative proteomic analysis by iTRAQ® for the identification of candidate biomarkers in ovarian cancer serum

  2010cited by this paper
• Quantitative proteomics for the analysis of spatio-temporal protein dynamics during autophagy

  2010cited by this paper
• Network organization of the human autophagy system

  2010cited by this paper
• Ubiquitin C-terminal electrophiles are activity-based probes for identification and mechanistic study of ubiquitin conjugating machinery.

  2009cited by this paper
• Target profiling of small molecules by chemical proteomics.

  2009cited by this paper
• Mapping the phosphorylation sites of Ulk1.

  2009cited by this paper
• FLEXIQuant: a novel tool for the absolute quantification of proteins, and the simultaneous identification and quantification of potentially modified peptides.

  2009cited by this paper
• Mass Spectrometry-Based Label-Free Quantitative Proteomics

  2009cited by this paper
• Defining the human deubiquitinating enzyme interaction landscape.

  2009cited by this paper
• A comparison of labeling and label-free mass spectrometry-based proteomics approaches.

  2009cited by this paper

• Activity-based protein profiling: A graphical review

  2023cites this paper
• Studying Autophagy Using a TMT-Based Quantitative Proteomics Approach.

  2022cites this paper
• Oxidative Stress and Autophagy Are Important Processes in Post Ripeness and Brown Film Formation in Mycelium of Lentinula edodes

  2022cites this paper
• Plant Chemical Genomics: Methods and Protocols

  2021cites this paper
• Tetra-arylborate lipophilic anions as targeting groups

  2021cites this paper
• Exosomes Produced by Adipose-derived Stem Cells Inhibit Schwann Cells Autophagy and Promote the Regeneration of the Myelin Sheath.

  2021cites this paper
• Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1

  2021cites this paper
• Enhancing Comprehensive Analysis of Newly Synthesized Proteins Based on Cleavable Bioorthogonal Tagging.

  2021cites this paper
• Hepatitis B Surface Antigen Suppresses the Activation of Nuclear Factor Kappa B Pathway via Interaction With the TAK1-TAB2 Complex

  2021cites this paper
• ANXA6 suppresses the tumorigenesis of cervical cancer through autophagy induction

  2020cites this paper
• Quantitative Mitochondrial Proteomics Reveals ANXA7 as a Crucial Factor in Mitophagy.

  2020cites this paper
• Identification of HO-1 as a novel biomarker for graft acute cellular rejection and prognosis prediction after liver transplantation

  2020cites this paper
• Fishing for newly synthesized proteins with phosphonate-handles

  2020cites this paper
• Recent advances in autophagic machinery: a proteomic perspective

  2020cites this paper
• Target Profiling of an Anticancer Drug Curcumin by an In Situ Chemical Proteomics Approach.

  2020cites this paper
• TIME-DEPENDENT EFFECTS ON HOST AUTOPHAGY PROMOTE THE INTRACELLULAR SURVIVAL OF LEISHMANIA

  2019cites this paper
• Recent Developments in Cell Permeable Deubiquitinating Enzyme Activity-Based Probes

  2019cites this paper
• Guidelines for evaluating myocardial cell death.

  2019cites this paper
• Triptolide Induces Glioma Cell Autophagy and Apoptosis via Upregulating the ROS/JNK and Downregulating the Akt/mTOR Signaling Pathways

  2019cites this paper
• Diurnal Rhythms Spatially and Temporally Organize Autophagy

  2019cites this paper
• Understanding and exploiting the roles of autophagy in plants through multi-omics approaches.

  2018cites this paper
• Cornification of nail keratinocytes requires autophagy for bulk degradation of intracellular proteins while sparing components of the cytoskeleton

  2018cites this paper