Methods of Metabolite Identification Using MS/MS Data

Researchers in bioinformatics and medical science fields have been developing various innovative information systems and software tools using emerging technologies. Metabolite profiling is one of t...

[1]  Lars Ridder,et al.  Substructure-based annotation of high-resolution multistage MS(n) spectral trees. , 2012, Rapid communications in mass spectrometry : RCM.

[2]  Chris Morley,et al.  Open Babel: An open chemical toolbox , 2011, J. Cheminformatics.

[3]  Xin Xiong,et al.  Metabolic reaction network-based recursive metabolite annotation for untargeted metabolomics , 2019, Nature Communications.

[4]  Xiaoqin Zeng,et al.  MIDAS-G: a computational platform for investigating fragmentation rules of tandem mass spectrometry in metabolomics , 2017, Metabolomics.

[5]  Lars Ridder,et al.  Automatic Compound Annotation from Mass Spectrometry Data Using MAGMa. , 2014, Mass spectrometry.

[6]  Eoin Fahy,et al.  Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools , 2015, Nucleic Acids Res..

[7]  O. Fiehn.  Metabolomics – the link between genotypes and phenotypes , 2004, Plant Molecular Biology.

[8]  Thomas Hankemeier,et al.  Microbial metabolomics: toward a platform with full metabolome coverage. , 2007, Analytical biochemistry.

[9]  S. Böcker,et al.  Searching molecular structure databases with tandem mass spectra using CSI:FingerID , 2015, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Kazuki Saito,et al.  Hydrogen Rearrangement Rules: Computational MS/MS Fragmentation and Structure Elucidation Using MS-FINDER Software. , 2016, Analytical chemistry.

[11]  Guangji Wang,et al.  Metabolic Pathway Extension Approach for Metabolomic Biomarker Identification. , 2017, Analytical chemistry.

[12]  J. Idle,et al.  LC-MS-Based Metabolomics in Drug Metabolism , 2007, Drug metabolism reviews.

[13]  Pieter C Dorrestein,et al.  Illuminating the dark matter in metabolomics , 2015, Proceedings of the National Academy of Sciences.

[14]  Hongmei Lu,et al.  Deep MS/MS-Aided Structural-Similarity Scoring for Unknown Metabolite Identification. , 2019, Analytical chemistry.

[15]  Götz Schlotterbeck,et al.  Application of metabonomics in a compound ranking study in early drug development revealing drug-induced excretion of choline into urine. , 2006, Chemical research in toxicology.

[16]  T. Hankemeier,et al.  Microbial metabolomics with gas chromatography/mass spectrometry. , 2006, Analytical chemistry.

[17]  David S. Wishart,et al.  HMDB 4.0: the human metabolome database for 2018 , 2017, Nucleic Acids Res..

[18]  Reinhard Laubenbacher,et al.  Bioinformatics tools for cancer metabolomics , 2011, Metabolomics.

[19]  Adrià Cereto-Massagué,et al.  Molecular fingerprint similarity search in virtual screening. , 2015, Methods.

[20]  T. Veenstra,et al.  Cancer biomarker discovery: Opportunities and pitfalls in analytical methods , 2011, Electrophoresis.

[21]  Wim Soetaert,et al.  Microbial metabolomics: past, present and future methodologies , 2006, Biotechnology Letters.

[22]  Emma L. Schymanski,et al.  MetFrag relaunched: incorporating strategies beyond in silico fragmentation , 2016, Journal of Cheminformatics.

[23]  Juho Rousu,et al.  Metabolite identification and molecular fingerprint prediction through machine learning , 2012, Bioinform..

[24]  Warwick B Dunn,et al.  Current trends and future requirements for the mass spectrometric investigation of microbial, mammalian and plant metabolomes , 2008, Physical biology.

[25]  R. Buják,et al.  Metabolomics in urogenital cancer. , 2011, Bioanalysis.

[26]  Sebastian Böcker,et al.  Computational mass spectrometry for small-molecule fragmentation , 2014 .

[27]  Matthias Müller-Hannemann,et al.  In silico fragmentation for computer assisted identification of metabolite mass spectra , 2010, BMC Bioinformatics.

[28]  David S. Wishart,et al.  CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra , 2014, Nucleic Acids Res..

[29]  Benjamin P Bowen,et al.  Dealing with the unknown: Metabolomics and Metabolite Atlases , 2010, Journal of the American Society for Mass Spectrometry.

[30]  Diether Lambrechts,et al.  Improved metabolite identification with MIDAS and MAGMa through MS/MS spectral dataset-driven parameter optimization , 2016, Metabolomics.

[31]  D. Wishart.  Advances in metabolite identification. , 2011, Bioanalysis.

[32]  Oliver Fiehn,et al.  Advances in structure elucidation of small molecules using mass spectrometry , 2010, Bioanalytical reviews.

[33]  Kyoungmi Kim,et al.  Urine Metabolomics Analysis for Kidney Cancer Detection and Biomarker Discovery*S , 2009, Molecular & Cellular Proteomics.

[34]  Sebastian Böcker,et al.  Fragmentation trees reloaded , 2014, Journal of Cheminformatics.

[35]  S. Tan,et al.  Chiral liquid chromatography-mass spectrometry (LC-MS/MS) method development for the detection of salbutamol in urine samples. , 2016, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[36]  Jun Feng Xiao,et al.  Metabolite identification and quantitation in LC-MS/MS-based metabolomics. , 2012, Trends in analytical chemistry : TRAC.

[37]  R. Friedman,et al.  Mass spectral metabonomics beyond elemental formula: chemical database querying by matching experimental with computational fragmentation spectra. , 2008, Analytical chemistry.

[38]  D. Kell.  Systems biology, metabolic modelling and metabolomics in drug discovery and development. , 2006, Drug discovery today.

[39]  Sebastian Böcker,et al.  Searching molecular structure databases using tandem MS data: are we there yet? , 2017, Current opinion in chemical biology.

[40]  Juho Rousu,et al.  SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information , 2019, Nature Methods.

[41]  Gang Fu,et al.  PubChem Substance and Compound databases , 2015, Nucleic Acids Res..

[42]  Russ Greiner,et al.  Competitive fragmentation modeling of ESI-MS/MS spectra for putative metabolite identification , 2013, Metabolomics.

[43]  Emma L. Schymanski,et al.  Matching structures to mass spectra using fragmentation patterns: are the results as good as they look? , 2009, Analytical chemistry.

[44]  Sebastian Böcker,et al.  Computational mass spectrometry for small molecules , 2013, Journal of Cheminformatics.

[45]  John C. Lindon,et al.  Metabonomics Techniques and Applications to Pharmaceutical Research & Development , 2006, Pharmaceutical Research.

[46]  David I. Ellis,et al.  Metabolomics: Current analytical platforms and methodologies , 2005 .

[47]  R. Abagyan,et al.  METLIN: A Metabolite Mass Spectral Database , 2005, Therapeutic drug monitoring.

[48]  Bernd Markus Lange,et al.  Open-Access Metabolomics Databases for Natural Product Research: Present Capabilities and Future Potential , 2015, Front. Bioeng. Biotechnol..

[49]  António E. N. Ferreira,et al.  Metabolomics for undergraduates: Identification and pathway assignment of mitochondrial metabolites , 2016, Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology.

[50]  R. Lewensohn,et al.  Metabolomics: Moving to the Clinic , 2010, Journal of Neuroimmune Pharmacology.

[51]  E. Want,et al.  Liquid chromatography-mass spectrometry based global metabolite profiling: a review. , 2012, Analytica chimica acta.

[52]  Ralf Tautenhahn,et al.  An accelerated workflow for untargeted metabolomics using the METLIN database , 2012, Nature Biotechnology.

[53]  David W. Russell,et al.  LMSD: LIPID MAPS structure database , 2006, Nucleic Acids Res..

[54]  T. Mak,et al.  Regulation of cancer cell metabolism , 2011, Nature Reviews Cancer.

[55]  Kiyoko F. Aoki-Kinoshita,et al.  From genomics to chemical genomics: new developments in KEGG , 2005, Nucleic Acids Res..

[56]  B. Bowen,et al.  MIDAS: a database-searching algorithm for metabolite identification in metabolomics. , 2014, Analytical chemistry.

[57]  Julio E. Peironcely,et al.  Automated pipeline for de novo metabolite identification using mass-spectrometry-based metabolomics. , 2013, Analytical chemistry.