Navigating freely-available software tools for metabolomics analysis

eRah: A Computational Tool Integrating Spectral Deconvolution and Alignment with Quantification and Identification of Metabolites in GC/MS-Based Metabolomics

(2016) Xavier Domingo-Almenara et al.   ANALYTICAL CHEMISTRY

Hydrogen Rearrangement Rules: Computational MS/MS Fragmentation and Structure Elucidation Using MS-FINDER Software

(2016) Hiroshi Tsugawa et al.   ANALYTICAL CHEMISTRY

Fast metabolite identification with Input Output Kernel Regression

(2016) Céline Brouard et al.   BIOINFORMATICS

Sample normalization methods in quantitative metabolomics

(2016) Yiman Wu et al.   JOURNAL OF CHROMATOGRAPHY A

The metabolome 18 years on: a concept comes of age

(2016) Douglas B. Kell et al.   Metabolomics

Large-scale untargeted LC-MS metabolomics data correction using between-batch feature alignment and cluster-based within-batch signal intensity drift correction

(2016) Carl Brunius et al.   Metabolomics

Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy

(2016) Ralf J. M. Weber et al.   Metabolomics

Non-targeted UHPLC-MS metabolomic data processing methods: a comparative investigation of normalisation, missing value imputation, transformation and scaling

(2016) Riccardo Di Guida et al.   Metabolomics

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

MetFrag relaunched: incorporating strategies beyond in silico fragmentation

(2016) Christoph Ruttkies et al.   Journal of Cheminformatics

Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data

(2016) Robert L. Davidson et al.   GigaScience

A guide to the identification of metabolites in NMR-based metabonomics/metabolomics experiments

(2016) Anthony C. Dona et al.   Computational and Structural Biotechnology Journal

A tutorial review: Metabolomics and partial least squares-discriminant analysis – a marriage of convenience or a shotgun wedding

(2015) Piotr S. Gromski et al.   ANALYTICA CHIMICA ACTA

MyCompoundID MS/MS Search: Metabolite Identification Using a Library of Predicted Fragment-Ion-Spectra of 383,830 Possible Human Metabolites

(2015) Tao Huan et al.   ANALYTICAL CHEMISTRY

mQTL.NMR: An Integrated Suite for Genetic Mapping of Quantitative Variations of 1H NMR-Based Metabolic Profiles

(2015) Lyamine Hedjazi et al.   ANALYTICAL CHEMISTRY

Statistical Methods for Handling Unwanted Variation in Metabolomics Data

(2015) Alysha M. De Livera et al.   ANALYTICAL CHEMISTRY

DnsID in MyCompoundID for Rapid Identification of Dansylated Amine- and Phenol-Containing Metabolites in LC–MS-Based Metabolomics

(2015) Tao Huan et al.   ANALYTICAL CHEMISTRY

Metabolomics data analysis and missing value issues with application to infarcted mouse hearts

(2015) Jasmit S Shah et al.   BMC BIOINFORMATICS

Kernel approaches for differential expression analysis of mass spectrometry-based metabolomics data

(2015) Xiang Zhan et al.   BMC BIOINFORMATICS

Missing value imputation strategies for metabolomics data

(2015) Emily Grace Armitage et al.   ELECTROPHORESIS

Updates in metabolomics tools and resources: 2014-2015

(2015) Biswapriya B. Misra et al.   ELECTROPHORESIS

GridMass: a fast two-dimensional feature detection method for LC/MS

(2015) Victor Treviño et al.   JOURNAL OF MASS SPECTROMETRY

Comparison of GC-MS and GC×GC-MS in the Analysis of Human Serum Samples for Biomarker Discovery

(2015) Jason H. Winnike et al.   JOURNAL OF PROTEOME RESEARCH

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) Etienne A. Thévenot et al.   JOURNAL OF PROTEOME RESEARCH

Computational and statistical analysis of metabolomics data

(2015) Sheng Ren et al.   Metabolomics

MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis

(2015) Hiroshi Tsugawa et al.   NATURE METHODS

MetaboAnalyst 3.0—making metabolomics more meaningful

(2015) Jianguo Xia et al.   NUCLEIC ACIDS RESEARCH

Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools

(2015) Manish Sud et al.   NUCLEIC ACIDS RESEARCH

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2015) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics

(2015) Arpana Vaniya et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

A New Paradigm for Known Metabolite Identification in Metabonomics/Metabolomics: Metabolite Identification Efficiency

(2015) Jeremy R. Everett   Computational and Structural Biotechnology Journal

Accurate, Fully-Automated NMR Spectral Profiling for Metabolomics

(2015) Siamak Ravanbakhsh et al.   PLoS One

Dolphin: a tool for automatic targeted metabolite profiling using 1D and 2D 1H-NMR data

(2014) Josep Gómez et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

PEP Search in MyCompoundID: Detection and Identification of Dipeptides and Tripeptides Using Dimethyl Labeling and Hydrophilic Interaction Liquid Chromatography Tandem Mass Spectrometry

(2014) Yanan Tang et al.   ANALYTICAL CHEMISTRY

Credentialing Features: A Platform to Benchmark and Optimize Untargeted Metabolomic Methods

(2014) Nathaniel Guy Mahieu et al.   ANALYTICAL CHEMISTRY

Metabomxtr: an R package for mixture-model analysis of non-targeted metabolomics data

(2014) Michael Nodzenski et al.   BIOINFORMATICS

ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics

(2014) Ricardo R. Silva et al.   BIOINFORMATICS

MetAssign: probabilistic annotation of metabolites from LC–MS data using a Bayesian clustering approach

(2014) Rónán Daly et al.   BIOINFORMATICS

Massifquant: open-source Kalman filter-based XC-MS isotope trace feature detection

(2014) Christopher J. Conley et al.   BIOINFORMATICS

Normalization of metabolomics data with applications to correlation maps

(2014) Alexandra Jauhiainen et al.   BIOINFORMATICS

An R package to analyse LC/MS metabolomic data: MAIT (Metabolite Automatic Identification Toolkit)

(2014) Francesc Fernández-Albert et al.   BIOINFORMATICS

Identifying Small Molecules via High Resolution Mass Spectrometry: Communicating Confidence

(2014) Emma L. Schymanski et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Comparative evaluation of preprocessing freeware on chromatography/mass spectrometry data for signature discovery

(2014) Jamie B. Coble et al.   JOURNAL OF CHROMATOGRAPHY A

Comparative evaluation of eight software programs for alignment of gas chromatography–mass spectrometry chromatograms in metabolomics experiments

(2014) Weihuan Niu et al.   JOURNAL OF CHROMATOGRAPHY A

metaMS: An open-source pipeline for GC–MS-based untargeted metabolomics

(2014) Ron Wehrens et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

The influence of scaling metabolomics data on model classification accuracy

(2014) Piotr S. Gromski et al.   Metabolomics

CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra

(2014) Felicity Allen et al.   NUCLEIC ACIDS RESEARCH

Metabolomics Data Normalization with EigenMS

(2014) Yuliya V. Karpievitch et al.   PLoS One

Comparison of peak-picking workflows for untargeted liquid chromatography/high-resolution mass spectrometry metabolomics data analysis

(2014) Atefeh Rafiei et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

OMICtools: an informative directory for multi-omic data analysis

(2014) V. J. Henry et al.   Database-The Journal of Biological Databases and Curation

Focus: A Robust Workflow for One-Dimensional NMR Spectral Analysis

(2013) Arnald Alonso et al.   ANALYTICAL CHEMISTRY

MetaboLyzer: A Novel Statistical Workflow for Analyzing Postprocessed LC–MS Metabolomics Data

(2013) Tytus D. Mak et al.   ANALYTICAL CHEMISTRY

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) Tetsuo Kokubun et al.   ANALYTICAL CHEMISTRY

MyCompoundID: Using an Evidence-Based Metabolome Library for Metabolite Identification

(2013) Liang Li et al.   ANALYTICAL CHEMISTRY

Automatic Chemical Structure Annotation of an LC–MSn Based Metabolic Profile from Green Tea

(2013) Lars Ridder et al.   ANALYTICAL CHEMISTRY

MeltDB 2.0-advances of the metabolomics software system

(2013) N. Kessler et al.   BIOINFORMATICS

MSPrep—Summarization, normalization and diagnostics for processing of mass spectrometry–based metabolomic data

(2013) Grant Hughes et al.   BIOINFORMATICS

MetSizeR: selecting the optimal sample size for metabolomic studies using an analysis based approach

(2013) Gift Nyamundanda et al.   BMC BIOINFORMATICS

Automatic recalibration and processing of tandem mass spectra using formula annotation

(2013) Michael A. Stravs et al.   JOURNAL OF MASS SPECTROMETRY

Automated Label-free Quantification of Metabolites from Liquid Chromatography–Mass Spectrometry Data

(2013) Erhan Kenar et al.   MOLECULAR & CELLULAR PROTEOMICS

The role of reporting standards for metabolite annotation and identification in metabolomic studies

(2013) Reza M Salek et al.   GigaScience

COMPUTATIONAL TOOLS FOR THE SECONDARY ANALYSIS OF METABOLOMICS EXPERIMENTS

(2013) Sean C. Booth et al.   Computational and Structural Biotechnology Journal

NMR and pattern recognition methods in metabolomics: From data acquisition to biomarker discovery: A review

(2012) Agnieszka Smolinska et al.   ANALYTICA CHIMICA ACTA

XCMS Online: A Web-Based Platform to Process Untargeted Metabolomic Data

(2012) Ralf Tautenhahn et al.   ANALYTICAL CHEMISTRY

Normalizing and Integrating Metabolomics Data

(2012) Alysha M. De Livera et al.   ANALYTICAL CHEMISTRY

Metabolite identification and molecular fingerprint prediction through machine learning

(2012) M. Heinonen et al.   BIOINFORMATICS

mzMatch–ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data

(2012) Achuthanunni Chokkathukalam et al.   BIOINFORMATICS

BATMAN--an R package for the automated quantification of metabolites from nuclear magnetic resonance spectra using a Bayesian model

(2012) J. Hao et al.   BIOINFORMATICS

IDEOM: an Excel interface for analysis of LC–MS-based metabolomics data

(2012) Darren J. Creek et al.   BIOINFORMATICS

MSeasy: unsupervised and untargeted GC-MS data processing

(2012) Florence Nicolè et al.   BIOINFORMATICS

Bioinformatics Tools for Mass Spectroscopy-Based Metabolomic Data Processing and Analysis

(2012) Masahiro Sugimoto et al.   Current Bioinformatics

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data

(2012) Kenneth Haug et al.   NUCLEIC ACIDS RESEARCH

HMDB 3.0—The Human Metabolome Database in 2013

(2012) David S. Wishart et al.   NUCLEIC ACIDS RESEARCH

Quantitative 1H NMR spectroscopy

(2012) Santosh Kumar Bharti et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

PeakML/mzMatch: A File Format, Java Library, R Library, and Tool-Chain for Mass Spectrometry Data Analysis

(2011) Richard A. Scheltema et al.   ANALYTICAL CHEMISTRY

CAMERA: An Integrated Strategy for Compound Spectra Extraction and Annotation of Liquid Chromatography/Mass Spectrometry Data Sets

(2011) Carsten Kuhl et al.   ANALYTICAL CHEMISTRY

Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets

(2011) M. Brown et al.   BIOINFORMATICS

Probabilistic principal component analysis for metabolomic data

(2011) Gift Nyamundanda et al.   BMC BIOINFORMATICS

Towards automatic metabolomic profiling of high-resolution one-dimensional proton NMR spectra

(2011) Pascal Mercier et al.   JOURNAL OF BIOMOLECULAR NMR

icoshift: An effective tool for the alignment of chromatographic data

(2011) Giorgio Tomasi et al.   JOURNAL OF CHROMATOGRAPHY A

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) Christian Ludwig et al.   Metabolomics

Double-check: validation of diagnostic statistics for PLS-DA models in metabolomics studies

(2011) Ewa Szymańska et al.   Metabolomics

MetAlign 3.0: performance enhancement by efficient use of advances in computer hardware

(2011) Arjen Lommen et al.   Metabolomics

LC-MS-based metabolomics

(2011) Bin Zhou et al.   Molecular BioSystems

Metabolomic Analysis and Visualization Engine for LC−MS Data

(2010) Eugene Melamud et al.   ANALYTICAL CHEMISTRY

Statistical Indices for Simultaneous Large-Scale Metabolite Detections for a Single NMR Spectrum

(2010) Eisuke Chikayama et al.   ANALYTICAL CHEMISTRY

ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level

(2010) P. Rocca-Serra et al.   BIOINFORMATICS

MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

(2010) Tomáš Pluskal et al.   BMC BIOINFORMATICS

MI-Pack: Increased confidence of metabolite identification in mass spectra by integrating accurate masses and metabolic pathways

(2010) Ralf J.M. Weber et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Automated Mass Spectral Deconvolution and Identification System for GC-MS Screening for Drugs, Poisons, and Metabolites in Urine

(2010) M. R. Meyer et al.   CLINICAL CHEMISTRY

MassBank: a public repository for sharing mass spectral data for life sciences

(2010) Hisayuki Horai et al.   JOURNAL OF MASS SPECTROMETRY

mzML—a Community Standard for Mass Spectrometry Data

(2010) Lennart Martens et al.   MOLECULAR & CELLULAR PROTEOMICS

Compensation for Systematic Cross-Contribution Improves Normalization of Mass Spectrometry Based Metabolomics Data

(2009) Henning Redestig et al.   ANALYTICAL CHEMISTRY

MetaboliteDetector: Comprehensive Analysis Tool for Targeted and Nontargeted GC/MS Based Metabolome Analysis

(2009) Karsten Hiller et al.   ANALYTICAL CHEMISTRY

Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour 'rules'

(2009) John Draper et al.   BMC BIOINFORMATICS

rNMR: open source software for identifying and quantifying metabolites in NMR spectra

(2009) Ian A. Lewis et al.   MAGNETIC RESONANCE IN CHEMISTRY

Interferences and contaminants encountered in modern mass spectrometry

(2008) Bernd O. Keller et al.   ANALYTICA CHIMICA ACTA

SIRIUS: decomposing isotope patterns for metabolite identification†

(2008) Sebastian Böcker et al.   BIOINFORMATICS

Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements

(2008) Eva Lange et al.   BMC BIOINFORMATICS

MetaboMiner – semi-automated identification of metabolites from 2D NMR spectra of complex biofluids

(2008) Jianguo Xia et al.   BMC BIOINFORMATICS

Highly sensitive feature detection for high resolution LC/MS

(2008) Ralf Tautenhahn et al.   BMC BIOINFORMATICS

Assessment of PLSDA cross validation

(2008) Johan A. Westerhuis et al.   Metabolomics

Metabolite identification via the Madison Metabolomics Consortium Database

(2008) Qiu Cui et al.   NATURE BIOTECHNOLOGY