Building ProteomeTools based on a complete synthetic human proteome
暂无分享,去创建一个
Mathias Wilhelm | Ruedi Aebersold | Stephan Aiche | Ulf Reimer | Eric W Deutsch | Bernhard Kuster | Maximilian Weininger | Robert L Moritz | Ulrike Kusebauch | Siegfried Gessulat | Derek J. Bailey | Bernard Delanghe | Hans-Christian Ehrlich | Johannes Zerweck | Derek J Bailey | Karsten Schnatbaum | Holger Wenschuh | Tobias Knaute | R. Aebersold | B. Kuster | U. Kusebauch | R. Moritz | Mathias Wilhelm | E. Deutsch | J. Schlegl | Siegfried Gessulat | K. Schnatbaum | U. Reimer | H. Wenschuh | Tobias Schmidt | Karl Kramer | Hans-Christian Ehrlich | Stephan Aiche | J. Zerweck | T. Moehring | A. Huhmer | B. Delanghe | Judith Schlegl | T. Knaute | Tobias Schmidt | Karl Kramer | Daniel P Zolg | Peng Yu | Thomas Moehring | Andreas Huhmer | Peng Yu | D. P. Zolg | Maximilian Weininger
[1] Ole N Jensen,et al. Utility of immonium ions for assignment of epsilon-N-acetyllysine-containing peptides by tandem mass spectrometry. , 2008, Analytical chemistry.
[2] P. Pevzner,et al. The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search* , 2010, Molecular & Cellular Proteomics.
[3] Yan‐Mei Li,et al. Synthesis of Site-Specifically Dimethylated and Trimethylated Peptides Derived from Histone H3 N-Terminal Tail , 2006, International Journal of Peptide Research and Therapeutics.
[4] M. Mann,et al. Analysis of Tyrosine Phosphorylation Sites in Signaling Molecules by a Phosphotyrosine-Specific Immonium Ion Scanning Method , 2002, Science's STKE.
[5] Takehiro Suzuki,et al. Global mapping of post-translational modifications on histone H3 variants in mouse testes , 2017, Biochemistry and biophysics reports.
[6] Jian Wang,et al. MSPLIT-DIA: sensitive peptide identification for data-independent acquisition , 2015, Nature Methods.
[7] G. McAlister,et al. Supplemental activation method for high-efficiency electron-transfer dissociation of doubly protonated peptide precursors. , 2007, Analytical chemistry.
[8] Lennart Martens,et al. Machine learning applications in proteomics research: How the past can boost the future , 2014, Proteomics.
[9] J. Schneider-Mergener,et al. Coherent membrane supports for parallel microsynthesis and screening of bioactive peptides. , 2000, Biopolymers.
[10] B. Domon,et al. Targeted Proteomic Quantification on Quadrupole-Orbitrap Mass Spectrometer* , 2012, Molecular & Cellular Proteomics.
[11] 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.
[12] Patricia Stadtmüller,et al. A technique for the specific enrichment of citrulline-containing peptides. , 2010, Analytical biochemistry.
[13] Manfred Kansy,et al. Predicting and Tuning Physicochemical Properties in Lead Optimization: Amine Basicities , 2007, ChemMedChem.
[14] José A. Dianes,et al. 2016 update of the PRIDE database and its related tools , 2016, Nucleic Acids Res..
[15] Daniel B. Martin,et al. Computational prediction of proteotypic peptides for quantitative proteomics , 2007, Nature Biotechnology.
[16] Alexey I. Nesvizhskii,et al. Using MSFragger for ultrafast database searching , 2017 .
[17] B. Kuster,et al. Mass-spectrometry-based draft of the human proteome , 2014, Nature.
[18] Yingming Zhao,et al. Lysine glutarylation is a protein posttranslational modification regulated by SIRT5. , 2014, Cell metabolism.
[19] P. Dedon,et al. Quantitative Analysis of Histone Modifications: Formaldehyde Is a Source of Pathological N6-Formyllysine That Is Refractory to Histone Deacetylases , 2013, PLoS genetics.
[20] Andrew R. Jones,et al. ProteomeXchange provides globally co-ordinated proteomics data submission and dissemination , 2014, Nature Biotechnology.
[21] Ping Liu,et al. Global Profiling of Protein Lysine Malonylation in Escherichia coli Reveals Its Role in Energy Metabolism. , 2016, Journal of proteome research.
[22] S. Mohammed,et al. Phosphopeptide fragmentation and analysis by mass spectrometry. , 2009, Journal of mass spectrometry : JMS.
[23] M. Mann,et al. A large synthetic peptide and phosphopeptide reference library for mass spectrometry–based proteomics , 2013, Nature Biotechnology.
[24] J. Yates,et al. Protein analysis by shotgun/bottom-up proteomics. , 2013, Chemical reviews.
[25] B. Searle,et al. “Plug-and-play” investigation of the human phosphoproteome by targeted high-resolution mass spectrometry , 2016, Nature Methods.
[26] B. Kuster,et al. Mining the Human Tissue Proteome for Protein Citrullination * , 2018, Molecular & Cellular Proteomics.
[27] Henk W. P. van den Toorn,et al. An Augmented Multiple-Protease-Based Human Phosphopeptide Atlas. , 2015, Cell reports.
[28] Nicholas W. Kwiecien,et al. A Calibration Routine for Efficient ETD in Large-Scale Proteomics , 2015, Journal of The American Society for Mass Spectrometry.
[29] Alexey I Nesvizhskii,et al. Effective Leveraging of Targeted Search Spaces for Improving Peptide Identification in Tandem Mass Spectrometry Based Proteomics. , 2015, Journal of proteome research.
[30] Zhike Lu,et al. Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification , 2011, Cell.
[31] Chris Sander,et al. Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome , 2016, Cell.
[32] M. Mann,et al. Andromeda: a peptide search engine integrated into the MaxQuant environment. , 2011, Journal of proteome research.
[33] O. Krokhin,et al. Sequence-specific retention calculator. Algorithm for peptide retention prediction in ion-pair RP-HPLC: application to 300- and 100-A pore size C18 sorbents. , 2006, Analytical chemistry.
[34] Jürgen Cox,et al. A systematic investigation into the nature of tryptic HCD spectra. , 2012, Journal of proteome research.
[35] K. Resing,et al. Mapping protein post-translational modifications with mass spectrometry , 2007, Nature Methods.
[36] S. Gross,et al. Neutral loss of isocyanic acid in peptide CID spectra: A novel diagnostic marker for mass spectrometric identification of protein citrullination , 2009, Journal of the American Society for Mass Spectrometry.
[37] John Chilton,et al. Using iRT, a normalized retention time for more targeted measurement of peptides , 2012, Proteomics.
[38] Ludovic C. Gillet,et al. Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps , 2015, Nature Medicine.
[39] Yingming Zhao,et al. Modification‐specific proteomics: Strategies for characterization of post‐translational modifications using enrichment techniques , 2009, Proteomics.
[40] Derek J. Bailey,et al. Intelligent Data Acquisition Blends Targeted and Discovery Methods , 2014, Journal of proteome research.
[41] Stephen E. Stein,et al. Interconversion of Peptide Mass Spectral Libraries Derivatized with iTRAQ or TMT Labels. , 2016, Journal of proteome research.
[42] Yingming Zhao,et al. Metabolic Regulation by Lysine Malonylation, Succinylation, and Glutarylation* , 2015, Molecular & Cellular Proteomics.
[43] R. Aebersold,et al. Generating and navigating proteome maps using mass spectrometry , 2010, Nature Reviews Molecular Cell Biology.
[44] Hangjun Sun,et al. First comprehensive proteome analysis of lysine crotonylation in seedling leaves of Nicotiana tabacum , 2017, Scientific Reports.
[45] M. Moran,et al. A mass spectrometry based method for distinguishing between symmetrically and asymmetrically dimethylated arginine residues. , 2004, Rapid communications in mass spectrometry : RCM.
[46] Ruedi Aebersold,et al. Conserved Peptide Fragmentation as a Benchmarking Tool for Mass Spectrometers and a Discriminating Feature for Targeted Proteomics* , 2014, Molecular & Cellular Proteomics.
[47] M. Mann,et al. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.
[48] Johannes Griss,et al. Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets , 2016, Nature Methods.
[49] M. Wilkins,et al. Immonium ion scanning for the discovery of post-translational modifications and its application to histones. , 2008, Journal of proteome research.
[50] Yi Zhang,et al. The First Identification of Lysine Malonylation Substrates and Its Regulatory Enzyme* , 2011, Molecular & Cellular Proteomics.
[51] Mathias Wilhelm,et al. A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets , 2015, Molecular & Cellular Proteomics.
[52] T. Osawa,et al. Formation of Nϵ-(succinyl)lysine in vivo: a novel marker for docosahexaenoic acid-derived protein modification Published, JLR Papers in Press, April 1, 2006. , 2006, Journal of Lipid Research.
[53] M. Mann,et al. Proteomic analysis of post-translational modifications , 2003, Nature Biotechnology.
[54] Jüergen Cox,et al. The MaxQuant computational platform for mass spectrometry-based shotgun proteomics , 2016, Nature Protocols.
[55] Sándor Suhai,et al. Fragmentation pathways of protonated peptides. , 2005, Mass spectrometry reviews.
[56] D. Creasy,et al. Unimod: Protein modifications for mass spectrometry , 2004, Proteomics.
[57] Ronald J A Wanders,et al. Proteomic and Biochemical Studies of Lysine Malonylation Suggest Its Malonic Aciduria-associated Regulatory Role in Mitochondrial Function and Fatty Acid Oxidation* , 2015, Molecular & Cellular Proteomics.
[58] Eric W. Deutsch,et al. A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis , 2013, Nature.
[59] Bernhard Kuster,et al. DMSO enhances electrospray response, boosting sensitivity of proteomic experiments , 2013, Nature Methods.
[60] Albert J. R. Heck,et al. Analytical Utility of Mass Spectral Binning in Proteomic Experiments by SPectral Immonium Ion Detection (SPIID)* , 2014, Molecular & Cellular Proteomics.
[61] D. Schriemer,et al. Nonenzymatic biotinylation of histone H2A , 2009, Protein science : a publication of the Protein Society.
[62] Yi Tang,et al. Lysine Propionylation and Butyrylation Are Novel Post-translational Modifications in Histones*S , 2007, Molecular & Cellular Proteomics.
[63] Lennart Martens,et al. MS2PIP: a tool for MS/MS peak intensity prediction , 2013, Bioinform..