Comprehensive quantification of the modified proteome reveals oxidative heart damage in mitochondrial heteroplasmy
暂无分享,去创建一个
Spiros Michalakopoulos | Jesús Vázquez | Iakes Ezkurdia | Marco Trevisan-Herraz | Navratan Bagwan | Elena Bonzon-Kulichenko | J. Rodriguez | I. Ezkurdia | J. Enríquez | E. Bonzón-Kulichenko | E. Calvo | J. Vázquez | A. Latorre-Pellicer | Marco Trevisan-Herraz | Enrique Calvo | A. V. Lechuga-Vieco | José Antonio Enríquez | Ana Latorre-Pellicer | Ana Victoria Lechuga-Vieco | José Manuel Rodríguez | Ricardo Magni | Navratan Bagwan | Spiros Michalakopoulos | Ricardo Magni | Iakes Ezkurdia | J. Rodríguez | Ana Latorre-Pellicer | Elena Bonzón-Kulichenko
[1] E. Bonzón-Kulichenko,et al. Revisiting peptide identification by high-accuracy mass spectrometry: problems associated with the use of narrow mass precursor windows. , 2015, Journal of proteome research.
[2] Alexey I Nesvizhskii,et al. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. , 2002, Analytical chemistry.
[3] Ting-Yi Sung,et al. Phosphoproteomics Reveals HMGA1, a CK2 Substrate, as a Drug-Resistant Target in Non-Small Cell Lung Cancer , 2017, Scientific Reports.
[4] Brian L. Frey,et al. Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search , 2015, Journal of proteome research.
[5] L. Beamer,et al. Compromised Catalysis and Potential Folding Defects in in Vitro Studies of Missense Mutants Associated with Hereditary Phosphoglucomutase 1 Deficiency* , 2014, The Journal of Biological Chemistry.
[6] Hyungwon Choi,et al. Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics. , 2008, Journal of Proteome Research.
[7] Itay Mayrose,et al. ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules , 2016, Nucleic Acids Res..
[8] Edward L. Huttlin,et al. An ultra-tolerant database search reveals that a myriad of modified peptides contributes to unassigned spectra in shotgun proteomics , 2015, Nature Biotechnology.
[9] Yu-Chao Wang,et al. Temporal Phosphoproteome Dynamics Induced by an ATP Synthase Inhibitor Citreoviridin* , 2015, Molecular & Cellular Proteomics.
[10] J. Redondo,et al. A Novel Systems-Biology Algorithm for the Analysis of Coordinated Protein Responses Using Quantitative Proteomics* , 2016, Molecular & Cellular Proteomics.
[11] J. Yates,et al. Direct analysis of protein complexes using mass spectrometry , 1999, Nature Biotechnology.
[12] E. P. Patallo,et al. Flavin-dependent halogenases involved in secondary metabolism in bacteria , 2006, Applied Microbiology and Biotechnology.
[13] Concha Gil,et al. General statistical framework for quantitative proteomics by stable isotope labeling. , 2014, Journal of proteome research.
[14] P. Pérez,et al. Activation of the Phosphatidylinositol 3-Kinase/Akt Signaling Pathway by Retinoic Acid Is Required for Neural Differentiation of SH-SY5Y Human Neuroblastoma Cells* , 2002, The Journal of Biological Chemistry.
[15] Pedro Navarro,et al. A refined method to calculate false discovery rates for peptide identification using decoy databases. , 2009, Journal of proteome research.
[16] Zhiping Weng,et al. Genome-wide decoding of hierarchical modular structure of transcriptional regulation by cis-element and expression clustering , 2005, ECCB/JBI.
[17] Edward L. Huttlin,et al. A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression , 2010, Cell.
[18] J. Vázquez,et al. A Novel Strategy for Global Analysis of the Dynamic Thiol Redox Proteome* , 2012, Molecular & Cellular Proteomics.
[19] P. Ellonen,et al. mtDNA Mutagenesis Disrupts Pluripotent Stem Cell Function by Altering Redox Signaling , 2015, Cell reports.
[20] David Goldberg,et al. Lookup peaks: a hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry. , 2007, Analytical chemistry.
[21] Neil L Kelleher,et al. Illuminating the dark matter of shotgun proteomics , 2015, Nature Biotechnology.
[22] Steven P Gygi,et al. Phosphoproteomic Analysis of the Developing Mouse Brain*S , 2004, Molecular & Cellular Proteomics.
[23] P. Pilch,et al. PTRF/Cavin-1 promotes efficient ribosomal RNA transcription in response to metabolic challenges , 2016, eLife.
[24] M. Sharpley,et al. Heteroplasmy of Mouse mtDNA Is Genetically Unstable and Results in Altered Behavior and Cognition , 2012, Cell.
[25] Heiko Horn,et al. In Vivo Phosphoproteomics Analysis Reveals the Cardiac Targets of β-Adrenergic Receptor Signaling , 2013, Science Signaling.
[26] Johannes Griss,et al. Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets , 2016, Nature Methods.
[27] Henry Lam,et al. Hunting for unexpected post-translational modifications by spectral library searching with tier-wise scoring. , 2014, Journal of proteome research.
[28] Peter R Baker,et al. In-depth Analysis of Tandem Mass Spectrometry Data from Disparate Instrument Types*S , 2008, Molecular & Cellular Proteomics.
[29] Alexey I Nesvizhskii,et al. MSFragger: ultrafast and comprehensive peptide identification in shotgun proteomics , 2017, Nature Methods.
[30] Pavel A. Pevzner,et al. Universal database search tool for proteomics , 2014, Nature Communications.
[31] Patrick F Chinnery,et al. Pronuclear transfer in human embryos to prevent transmission of mitochondrial DNA disease , 2010, Nature.
[32] Andrew R. Jones,et al. Evaluation of Parameters for Confident Phosphorylation Site Localization Using an Orbitrap Fusion Tribrid Mass Spectrometer. , 2017, Journal of proteome research.
[33] E. Shoubridge,et al. Random genetic drift in the female germline explains the rapid segregation of mammalian mitochondrial DNA , 1996, Nature Genetics.
[34] Matthias Mann,et al. High recovery FASP applied to the proteomic analysis of microdissected formalin fixed paraffin embedded cancer tissues retrieves known colon cancer markers. , 2011, Journal of proteome research.
[35] M. Mann,et al. System-Wide Temporal Characterization of the Proteome and Phosphoproteome of Human Embryonic Stem Cell Differentiation , 2011, Science Signaling.
[36] L. Neckers,et al. Post-translational modifications of Hsp90 and their contributions to chaperone regulation. , 2012, Biochimica et biophysica acta.
[37] I. Ezkurdia,et al. Mechanism of super-assembly of respiratory complexes III and IV , 2016, Nature.
[38] R. Zeng,et al. Protein phosphorylation and expression profiling by Yin-yang multidimensional liquid chromatography (Yin-yang MDLC) mass spectrometry. , 2007, Journal of proteome research.
[39] Michael J MacCoss,et al. A Deeper Look into Comet—Implementation and Features , 2015, Journal of The American Society for Mass Spectrometry.
[40] Rong Zeng,et al. Phosphoproteome analysis of mouse liver using immobilized metal affinity purification and linear ion trap mass spectrometry. , 2004, Rapid communications in mass spectrometry : RCM.
[41] S. Mitalipov,et al. Mitochondrial replacement therapy in reproductive medicine. , 2015, Trends in molecular medicine.
[42] A. Suomalainen,et al. Tissue- and cell-type–specific manifestations of heteroplasmic mtDNA 3243A>G mutation in human induced pluripotent stem cell-derived disease model , 2013, Proceedings of the National Academy of Sciences.
[43] Johannes Söding,et al. Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling , 2015, PLoS Comput. Biol..
[44] J. Eng,et al. Comet: An open‐source MS/MS sequence database search tool , 2013, Proteomics.
[45] Yingming Zhao,et al. PTMap—A sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites , 2009, Proceedings of the National Academy of Sciences.