Navigating freely-available software tools for metabolomics analysis

[1]  Suzanne M. Paley,et al.  The MetaCyc database of metabolic pathways and enzymes , 2017, Nucleic Acids Res..

[2]  Harald Barsnes,et al.  BioContainers: an open-source and community-driven framework for software standardization , 2017, Bioinform..

[3]  Juho Rousu,et al.  Critical Assessment of Small Molecule Identification 2016: automated methods , 2017, Journal of Cheminformatics.

[4]  Christoph Steinbeck,et al.  Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy , 2016, Metabolomics.

[5]  Steffen Neumann,et al.  Prediction, Detection, and Validation of Isotope Clusters in Mass Spectrometry Data , 2016, Metabolites.

[6]  Lin Shi,et al.  Large-scale untargeted LC-MS metabolomics data correction using between-batch feature alignment and cluster-based within-batch signal intensity drift correction , 2016, Metabolomics.

[7]  Marta Díaz,et al.  eRah: A Computational Tool Integrating Spectral Deconvolution and Alignment with Quantification and Identification of Metabolites in GC/MS-Based Metabolomics. , 2016, Analytical chemistry.

[8]  Douglas B. Kell,et al.  The metabolome 18 years on: a concept comes of age , 2016, Metabolomics.

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

[10]  Juho Rousu,et al.  Fast metabolite identification with Input Output Kernel Regression , 2016, Bioinform..

[11]  John Chilton,et al.  The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update , 2016, Nucleic Acids Res..

[12]  Jasper Engel,et al.  Non-targeted UHPLC-MS metabolomic data processing methods: a comparative investigation of normalisation, missing value imputation, transformation and scaling , 2016, Metabolomics.

[13]  K. Veselkov,et al.  A guide to the identification of metabolites in NMR-based metabonomics/metabolomics experiments , 2016, Computational and structural biotechnology journal.

[14]  Mark R. Viant,et al.  Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data , 2016, GigaScience.

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

[16]  Liang Li,et al.  Sample normalization methods in quantitative metabolomics. , 2016, Journal of chromatography. A.

[17]  B. Misra,et al.  Updates in metabolomics tools and resources: 2014–2015 , 2016, Electrophoresis.

[18]  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..

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

[20]  Shesh N Rai,et al.  Metabolomics data analysis and missing value issues with application to infarcted mouse hearts , 2015, BMC Bioinformatics.

[21]  Ronghong Li,et al.  MyCompoundID MS/MS Search: Metabolite Identification Using a Library of Predicted Fragment-Ion-Spectra of 383,830 Possible Human Metabolites. , 2015, Analytical chemistry.

[22]  Coral Barbas,et al.  Missing value imputation strategies for metabolomics data , 2015, Electrophoresis.

[23]  Tao Huan,et al.  DnsID in MyCompoundID for rapid identification of dansylated amine- and phenol-containing metabolites in LC-MS-based metabolomics. , 2015, Analytical chemistry.

[24]  Emily L. Kang,et al.  Computational and statistical analysis of metabolomics data , 2015, Metabolomics.

[25]  E. Thévenot,et al.  Analysis of the Human Adult Urinary Metabolome Variations with Age, Body Mass Index, and Gender by Implementing a Comprehensive Workflow for Univariate and OPLS Statistical Analyses. , 2015, Journal of proteome research.

[26]  David I. Ellis,et al.  A tutorial review: Metabolomics and partial least squares-discriminant analysis--a marriage of convenience or a shotgun wedding. , 2015, Analytica chimica acta.

[27]  O. Fiehn,et al.  Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics. , 2015, Trends in analytical chemistry : TRAC.

[28]  Masanori Arita,et al.  MS-DIAL: Data Independent MS/MS Deconvolution for Comprehensive Metabolome Analysis , 2015, Nature Methods.

[29]  David S. Wishart,et al.  MetaboAnalyst 3.0—making metabolomics more meaningful , 2015, Nucleic Acids Res..

[30]  Johann A. Gagnon-Bartsch,et al.  Statistical methods for handling unwanted variation in metabolomics data. , 2015, Analytical chemistry.

[31]  Jean-Baptiste Cazier,et al.  mQTL.NMR: an integrated suite for genetic mapping of quantitative variations of (1)H NMR-based metabolic profiles. , 2015, Analytical chemistry.

[32]  S. Gregory,et al.  Comparison of GC-MS and GC×GC-MS in the analysis of human serum samples for biomarker discovery. , 2015, Journal of proteome research.

[33]  Xiang Zhan,et al.  Kernel approaches for differential expression analysis of mass spectrometry-based metabolomics data , 2015, BMC Bioinformatics.

[34]  Arnald Alonso,et al.  Analytical Methods in Untargeted Metabolomics: State of the Art in 2015 , 2015, Front. Bioeng. Biotechnol..

[35]  J. Everett A New Paradigm for Known Metabolite Identification in Metabonomics/Metabolomics: Metabolite Identification Efficiency , 2015, Computational and structural biotechnology journal.

[36]  Atefeh Rafiei,et al.  Comparison of peak-picking workflows for untargeted liquid chromatography/high-resolution mass spectrometry metabolomics data analysis. , 2015, Rapid communications in mass spectrometry : RCM.

[37]  Daniel Jacob,et al.  Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics , 2014, Bioinform..

[38]  David S. Wishart,et al.  Accurate, Fully-Automated NMR Spectral Profiling for Metabolomics , 2014, PloS one.

[39]  A. Emwas,et al.  The strengths and weaknesses of NMR spectroscopy and mass spectrometry with particular focus on metabolomics research. , 2015, Methods in molecular biology.

[40]  Victor Treviño,et al.  GridMass: a fast two-dimensional feature detection method for LC/MS. , 2015, Journal of mass spectrometry : JMS.

[41]  Riyas Vettukattil,et al.  Preprocessing of raw metabonomic data. , 2015, Methods in molecular biology.

[42]  Vinod Scaria,et al.  Insights into structural variations and genome rearrangements in prokaryotic genomes , 2015, Bioinform..

[43]  Michael L. Turner,et al.  The influence of scaling metabolomics data on model classification accuracy , 2015, Metabolomics.

[44]  Yuliya V. Karpievitch,et al.  Metabolomics Data Normalization with EigenMS , 2014, PloS one.

[45]  Weihuan Niu,et al.  Comparative evaluation of eight software programs for alignment of gas chromatography-mass spectrometry chromatograms in metabolomics experiments. , 2014, Journal of chromatography. A.

[46]  Josep Gómez,et al.  Dolphin: a tool for automatic targeted metabolite profiling using 1D and 2D 1H-NMR data , 2014, Analytical and Bioanalytical Chemistry.

[47]  Ralf J. O. Torgrip,et al.  Massifquant: open-source Kalman filter-based XC-MS isotope trace feature detection , 2014, Bioinform..

[48]  J. Coble,et al.  Comparative evaluation of preprocessing freeware on chromatography/mass spectrometry data for signature discovery. , 2014, Journal of chromatography. A.

[49]  G. Weingart,et al.  metaMS: an open-source pipeline for GC-MS-based untargeted metabolomics. , 2014, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[50]  Nathaniel G Mahieu,et al.  Credentialing Features: A Platform to Benchmark and Optimize Untargeted Metabolomic Methods , 2014, Analytical chemistry.

[51]  Simon Tavaré,et al.  Normalization of metabolomics data with applications to correlation maps , 2014, Bioinform..

[52]  William L. Lowe,et al.  Metabomxtr: an R package for mixture-model analysis of non-targeted metabolomics data , 2014, Bioinform..

[53]  Vincent J. Henry,et al.  OMICtools: an informative directory for multi-omic data analysis , 2014, Database J. Biol. Databases Curation.

[54]  Rainer Breitling,et al.  MetAssign: probabilistic annotation of metabolites from LC–MS data using a Bayesian clustering approach , 2014, Bioinform..

[55]  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..

[56]  Piotr S. Gromski,et al.  Influence of Missing Values Substitutes on Multivariate Analysis of Metabolomics Data , 2014, Metabolites.

[57]  Ronghong Li,et al.  PEP search in MyCompoundID: detection and identification of dipeptides and tripeptides using dimethyl labeling and hydrophilic interaction liquid chromatography tandem mass spectrometry. , 2014, Analytical chemistry.

[58]  Alexandre Perera-Lluna,et al.  An R package to analyse LC/MS metabolomic data: MAIT (Metabolite Automatic Identification Toolkit) , 2014, Bioinform..

[59]  Emma L. Schymanski,et al.  Identifying small molecules via high resolution mass spectrometry: communicating confidence. , 2014, Environmental science & technology.

[60]  Xavier Correig,et al.  Focus: a robust workflow for one-dimensional NMR spectral analysis. , 2014, Analytical chemistry.

[61]  Tytus D. Mak,et al.  MetaboLyzer: a novel statistical workflow for analyzing Postprocessed LC-MS metabolomics data. , 2014, Analytical chemistry.

[62]  Emilien L. Jamin,et al.  ProbMetab : an R package for Bayesian probabilistic annotation of LC-MS based metabolomics , 2013 .

[63]  A. Zell,et al.  Metabolites from Liquid Chromatography-Mass Spectrometry Data , 2014 .

[64]  Charmion Cruickshank-Quinn,et al.  MSPrep - Summarization, normalization and diagnostics for processing of mass spectrometry-based metabolomic data , 2014, Bioinform..

[65]  George Varghese,et al.  Using Genome Query Language to uncover genetic variation , 2014, Bioinform..

[66]  Isobel Claire Gormley,et al.  MetSizeR: selecting the optimal sample size for metabolomic studies using an analysis based approach , 2013, BMC Bioinformatics.

[67]  Andreas Zell,et al.  Automated Label-free Quantification of Metabolites from Liquid Chromatography–Mass Spectrometry Data* , 2013, Molecular & Cellular Proteomics.

[68]  Christoph Steinbeck,et al.  The role of reporting standards for metabolite annotation and identification in metabolomic studies , 2013, GigaScience.

[69]  T. Kokubun,et al.  Direct and unbiased information recovery from liquid chromatography-mass spectrometry raw data for phenotype-differentiating metabolites based on screening window coefficient of ion currents. , 2013, Analytical chemistry.

[70]  Alexander Goesmann,et al.  MeltDB 2.0–advances of the metabolomics software system , 2013, Bioinform..

[71]  Emma L. Schymanski,et al.  The Critical Assessment of Small Molecule Identification (CASMI): Challenges Solutions , 2013, Metabolites.

[72]  Lars Ridder,et al.  Automatic chemical structure annotation of an LC-MS(n) based metabolic profile from green tea. , 2013, Analytical chemistry.

[73]  Dimitrios Spiliotopoulos,et al.  muma, An R Package for Metabolomics Univariate and Multivariate Statistical Analysis , 2013 .

[74]  Tao Huan,et al.  MyCompoundID: using an evidence-based metabolome library for metabolite identification. , 2013, Analytical chemistry.

[75]  Aalim M. Weljie,et al.  Computational Tools for the Secondary Analysis of Metabolomics Experiments , 2013, Computational and structural biotechnology journal.

[76]  John L Markley,et al.  Databases and Software for NMR-Based Metabolomics. , 2013, Current Metabolomics.

[77]  Rainer Breitling,et al.  mzMatch–ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data , 2012, Bioinform..

[78]  David S. Wishart,et al.  HMDB 3.0—The Human Metabolome Database in 2013 , 2012, Nucleic Acids Res..

[79]  Christoph Steinbeck,et al.  MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data , 2012, Nucleic Acids Res..

[80]  Bror Jönsson,et al.  TRACMASS—A Lagrangian Trajectory Model , 2013 .

[81]  Emma L. Schymanski,et al.  Automatic recalibration and processing of tandem mass spectra using formula annotation. , 2013, Journal of mass spectrometry : JMS.

[82]  Steffen Neumann,et al.  Nearline acquisition and processing of liquid chromatography-tandem mass spectrometry data , 2012, Metabolomics.

[83]  T. Speed,et al.  Normalizing and integrating metabolomics data. , 2012, Analytical chemistry.

[84]  S. Wijmenga,et al.  NMR and pattern recognition methods in metabolomics: from data acquisition to biomarker discovery: a review. , 2012, Analytica chimica acta.

[85]  Ben Ernest,et al.  MetabR: an R script for linear model analysis of quantitative metabolomic data , 2012, BMC Research Notes.

[86]  Yann Guitton,et al.  MSeasy: unsupervised and untargeted GC-MS data processing , 2012, Bioinform..

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

[88]  Maria De Iorio,et al.  BATMAN - an R package for the automated quantification of metabolites from nuclear magnetic resonance spectra using a Bayesian model , 2012, Bioinform..

[89]  Natalie I. Tasman,et al.  A Cross-platform Toolkit for Mass Spectrometry and Proteomics , 2012, Nature Biotechnology.

[90]  G. Siuzdak,et al.  XCMS Online: a web-based platform to process untargeted metabolomic data. , 2012, Analytical chemistry.

[91]  Santosh Kumar Bharti,et al.  Quantitative 1H NMR spectroscopy , 2012 .

[92]  Rainer Breitling,et al.  IDEOM: an Excel interface for analysis of LC-MS-based metabolomics data , 2012, Bioinform..

[93]  Masaru Tomita,et al.  Bioinformatics Tools for Mass Spectroscopy-Based Metabolomic Data Processing and Analysis , 2012, Current bioinformatics.

[94]  H. Ressom,et al.  LC-MS-based metabolomics. , 2012, Molecular bioSystems.

[95]  S. Neumann,et al.  CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. , 2012, Analytical chemistry.

[96]  Mark Earll,et al.  Open source software for mass spectrometry and metabolomics , 2012 .

[97]  Theodoros N. Arvanitis,et al.  Birmingham Metabolite Library: a publicly accessible database of 1-D 1H and 2-D 1H J-resolved NMR spectra of authentic metabolite standards (BML-NMR) , 2011, Metabolomics.

[98]  Francesco Savorani,et al.  icoshift: An effective tool for the alignment of chromatographic data. , 2011, Journal of chromatography. A.

[99]  Arjen Lommen,et al.  MetAlign 3.0: performance enhancement by efficient use of advances in computer hardware , 2011, Metabolomics.

[100]  Age K. Smilde,et al.  Double-check: validation of diagnostic statistics for PLS-DA models in metabolomics studies , 2011, Metabolomics.

[101]  X. Zhang,et al.  Statistical Analysis of Gas Chromatography Retention Index Database , 2011, 2011 5th International Conference on Bioinformatics and Biomedical Engineering.

[102]  R. Breitling,et al.  PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis. , 2011, Analytical chemistry.

[103]  David S Wishart,et al.  Towards automatic metabolomic profiling of high-resolution one-dimensional proton NMR spectra , 2011, Journal of biomolecular NMR.

[104]  Douglas B. Kell,et al.  Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets , 2011, Bioinform..

[105]  Eric W Deutsch,et al.  Spectra, chromatograms, Metadata: mzML-the standard data format for mass spectrometer output. , 2011, Methods in molecular biology.

[106]  Elizabeth Want,et al.  Processing and analysis of GC/LC-MS-based metabolomics data. , 2011, Methods in molecular biology.

[107]  Knut Reinert,et al.  OpenMS and TOPP: open source software for LC-MS data analysis. , 2011, Methods in molecular biology.

[108]  Isobel Claire Gormley,et al.  Probabilistic principal component analysis for metabolomic data , 2010, BMC Bioinformatics.

[109]  Mark R. Viant,et al.  MI-Pack: Increased confidence of metabolite identification in mass spectra by integrating accurate masses and metabolic pathways , 2010 .

[110]  Joshua D Rabinowitz,et al.  Metabolomic analysis and visualization engine for LC-MS data. , 2010, Analytical chemistry.

[111]  Lennart Martens,et al.  mzML—a Community Standard for Mass Spectrometry Data* , 2010, Molecular & Cellular Proteomics.

[112]  Oliver Hofmann,et al.  ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level , 2010, Bioinform..

[113]  Matej Oresic,et al.  MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data , 2010, BMC Bioinformatics.

[114]  M. Hirai,et al.  MassBank: a public repository for sharing mass spectral data for life sciences. , 2010, Journal of mass spectrometry : JMS.

[115]  Frank T Peters,et al.  Automated mass spectral deconvolution and identification system for GC-MS screening for drugs, poisons, and metabolites in urine. , 2010, Clinical chemistry.

[116]  Kazuo Shinozaki,et al.  Statistical indices for simultaneous large-scale metabolite detections for a single NMR spectrum. , 2010, Analytical chemistry.

[117]  Knut Reinert,et al.  OpenMS and TOPP: Open Source Software for LC-MS Data Analysis , 2010, Proteome Bioinformatics.

[118]  Rafael Brüschweiler,et al.  Web server suite for complex mixture analysis by covariance NMR , 2009, Magnetic resonance in chemistry : MRC.

[119]  J. Markley,et al.  rNMR: open source software for identifying and quantifying metabolites in NMR spectra , 2009, Magnetic resonance in chemistry : MRC.

[120]  Kazuki Saito,et al.  Compensation for systematic cross-contribution improves normalization of mass spectrometry based metabolomics data. , 2009, Analytical chemistry.

[121]  Wanchang Lin,et al.  Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour 'rules' , 2009, BMC Bioinformatics.

[122]  Dietmar Schomburg,et al.  MetaboliteDetector: comprehensive analysis tool for targeted and nontargeted GC/MS based metabolome analysis. , 2009, Analytical chemistry.

[123]  J. Keeler,et al.  Forty years of Magnetic Resonance in Chemistry and fifty years of the Experimental NMR Conference , 2009 .

[124]  Zsuzsanna Lipták,et al.  SIRIUS: decomposing isotope patterns for metabolite identification , 2008, Bioinform..

[125]  David S. Wishart,et al.  MetaboMiner – semi-automated identification of metabolites from 2D NMR spectra of complex biofluids , 2008, BMC Bioinformatics.

[126]  Steffen Neumann,et al.  Highly sensitive feature detection for high resolution LC/MS , 2008, BMC Bioinformatics.

[127]  R. Whittal,et al.  Interferences and contaminants encountered in modern mass spectrometry. , 2008, Analytica chimica acta.

[128]  Steffen Neumann,et al.  Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements , 2008, BMC Bioinformatics.

[129]  Jun Hyoung Lee,et al.  Phenotypic engineering by reprogramming gene transcription using novel artificial transcription factors in Escherichia coli , 2008, Nucleic acids research.

[130]  John L Markley,et al.  Metabolite identification via the Madison Metabolomics Consortium Database , 2008, Nature Biotechnology.

[131]  Age K. Smilde,et al.  UvA-DARE ( Digital Academic Repository ) Assessment of PLSDA cross validation , 2008 .

[132]  Jacco D. van Beek,et al.  matNMR: A flexible toolbox for processing, analyzing and visualizing magnetic resonance data in Matlab® , 2007 .

[133]  Mark P. Styczynski,et al.  Systematic identification of conserved metabolites in GC/MS data for metabolomics and biomarker discovery. , 2007, Analytical chemistry.

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

[135]  J. V. van Beek,et al.  matNMR: a flexible toolbox for processing, analyzing and visualizing magnetic resonance data in Matlab. , 2007, Journal of magnetic resonance.

[136]  Qi Zhao,et al.  HiRes - a tool for comprehensive assessment and interpretation of metabolomic data , 2006, Bioinform..

[137]  Pan Du,et al.  Bioinformatics Original Paper Improved Peak Detection in Mass Spectrum by Incorporating Continuous Wavelet Transform-based Pattern Matching , 2022 .

[138]  E. Marcotte,et al.  Chromatographic alignment of ESI-LC-MS proteomics data sets by ordered bijective interpolated warping. , 2006, Analytical chemistry.

[139]  R. A. van den Berg,et al.  Centering, scaling, and transformations: improving the biological information content of metabolomics data , 2006, BMC Genomics.

[140]  Corey D Broeckling,et al.  MET-IDEA: data extraction tool for mass spectrometry-based metabolomics. , 2006, Analytical chemistry.

[141]  J. Lindon,et al.  Scaling and normalization effects in NMR spectroscopic metabonomic data sets. , 2006, Analytical chemistry.

[142]  R. Abagyan,et al.  XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. , 2006, Analytical chemistry.

[143]  David S. Wishart,et al.  DrugBank: a comprehensive resource for in silico drug discovery and exploration , 2005, Nucleic Acids Res..

[144]  Mark P. Styczynski,et al.  A generic motif discovery algorithm for sequential data. , 2006, Bioinformatics.

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

[146]  D. Gauguier,et al.  Statistical total correlation spectroscopy: an exploratory approach for latent biomarker identification from metabolic 1H NMR data sets. , 2005, Analytical chemistry.

[147]  Chris F. Taylor,et al.  A common open representation of mass spectrometry data and its application to proteomics research , 2004, Nature Biotechnology.

[148]  Susumu Goto,et al.  The KEGG resource for deciphering the genome , 2004, Nucleic Acids Res..

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

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

[151]  Alan S. Stern,et al.  NMR Data Processing , 1996 .

[152]  Russ Rew,et al.  NetCDF: an interface for scientific data access , 1990, IEEE Computer Graphics and Applications.