Updates in metabolomics tools and resources: 2014-2015. (Q38606497)

4 September 2017

Updates in metabolomics tools and resources: 2014-2015. (English)

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4 September 2017

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Justin J J van der Hooft

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Justin J J van der Hooft

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4 September 2017

Biswapriya B Misra

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publication date

14 October 2015

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4 September 2017

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4 September 2017

37

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4 September 2017

86-110

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4 September 2017

1

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Innovation: Metabolomics: the apogee of the omics trilogy

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Biological insights through nontargeted metabolomics.

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Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective

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Analytical methods in untargeted metabolomics: state of the art in 2015.

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High-throughput discovery metabolomics

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Tools for computational processing of LC-MS datasets: a user's perspective.

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Wavelet-based peak detection and a new charge inference procedure for MS/MS implemented in ProteoWizard's msConvert

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XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification

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Improving peak detection in high-resolution LC/MS metabolomics data using preexisting knowledge and machine learning approach

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

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MRMPROBS suite for metabolomics using large-scale MRM assays

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Discriminating precursors of common fragments for large-scale metabolite profiling by triple quadrupole mass spectrometry

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MUSCLE: automated multi-objective evolutionary optimization of targeted LC-MS/MS analysis.

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IsoMS: automated processing of LC-MS data generated by a chemical isotope labeling metabolomics platform

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Quantitative Metabolome Analysis Based on Chromatographic Peak Reconstruction in Chemical Isotope Labeling Liquid Chromatography Mass Spectrometry

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isoMETLIN: a database for isotope-based metabolomics.

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Automated LC-HRMS(/MS) approach for the annotation of fragment ions derived from stable isotope labeling-assisted untargeted metabolomics

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IPO: a tool for automated optimization of XCMS parameters

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

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A data preprocessing strategy for metabolomics to reduce the mask effect in data analysis

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

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

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Metabolite identification through multiple kernel learning on fragmentation trees

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Intensity drift removal in LC/MS metabolomics by common variance compensation.

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Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets

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Fast parametric time warping of peak lists

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Stronger findings for metabolomics through Bayesian modeling of multiple peaks and compound correlations

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PLS/OPLS models in metabolomics: the impact of permutation of dataset rows on the K-fold cross-validation quality parameters

21 January 2018

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Investigating sources of variability in metabolomic data in the EPIC study: the Principal Component Partial R-square (PC-PR2) method

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Metabolomics data normalization with EigenMS.

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RepExplore: addressing technical replicate variance in proteomics and metabolomics data analysis

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Normalyzer: a tool for rapid evaluation of normalization methods for omics data sets

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MSPrep--summarization, normalization and diagnostics for processing of mass spectrometry-based metabolomic data

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MIRA: mutual information-based reporter algorithm for metabolic networks

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

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METLIN: a metabolite mass spectral database

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BioSM: metabolomics tool for identifying endogenous mammalian biochemical structures in chemical structure space

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A molecular structure matching approach to efficient identification of endogenous mammalian biochemical structures

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

21 January 2018

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Method for the Compound Annotation of Conjugates in Nontargeted Metabolomics Using Accurate Mass Spectrometry, Multistage Product Ion Spectra and Compound Database Searching

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GS-align for glycan structure alignment and similarity measurement.

21 January 2018

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Credentialing features: a platform to benchmark and optimize untargeted metabolomic methods

21 January 2018

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HAMMER: automated operation of mass frontier to construct in silico mass spectral fragmentation libraries

21 January 2018

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Ultrafast PubChem searching combined with improved filtering rules for elemental composition analysis.

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Lipid-Pro: a computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms

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Automatic Compound Annotation from Mass Spectrometry Data Using MAGMa

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Substructure-based annotation of high-resolution multistage MS(n) spectral trees.

21 January 2018

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In silico prediction and automatic LC-MS(n) annotation of green tea metabolites in urine

21 January 2018

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

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Metabolome searcher: a high throughput tool for metabolite identification and metabolic pathway mapping directly from mass spectrometry and using genome restriction

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MET-COFEA: a liquid chromatography/mass spectrometry data processing platform for metabolite compound feature extraction and annotation

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MS2Analyzer: A software for small molecule substructure annotations from accurate tandem mass spectra

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MIDAS: a database-searching algorithm for metabolite identification in metabolomics.

21 January 2018

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Quantitative molecular networking to profile marine cyanobacterial metabolomes

21 January 2018

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Mass spectral molecular networking of living microbial colonies

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Molecular networking as a dereplication strategy

21 January 2018

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mzGroupAnalyzer--predicting pathways and novel chemical structures from untargeted high-throughput metabolomics data

21 January 2018

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

21 January 2018

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RAMClust: a novel feature clustering method enables spectral-matching-based annotation for metabolomics data

21 January 2018

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Relative mass defect filtering of mass spectra: a path to discovery of plant specialized metabolites.

21 January 2018

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21 January 2018

Pathways with PathWhiz

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Metabolic pathway predictions for metabolomics: a molecular structure matching approach

21 January 2018

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Integrated enrichment analysis and pathway-centered visualization of metabolomics, proteomics, transcriptomics, and genomics data by using the InCroMAP software

21 January 2018

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iPEAP: integrating multiple omics and genetic data for pathway enrichment analysis.

21 January 2018

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Pathomx: an interactive workflow-based tool for the analysis of metabolomic data

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KEGG for integration and interpretation of large-scale molecular data sets

21 January 2018

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PubChem3D: a new resource for scientists

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MetaMapR: pathway independent metabolomic network analysis incorporating unknowns

21 January 2018

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Systemic alterations in the metabolome of diabetic NOD mice delineate increased oxidative stress accompanied by reduced inflammation and hypertriglyceremia

21 January 2018

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Metabolomic markers of altered nucleotide metabolism in early stage adenocarcinoma

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Diabetes Associated Metabolomic Perturbations in NOD Mice

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The guard cell metabolome: functions in stomatal movement and global food security

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MetabNet: An R Package for Metabolic Association Analysis of High-Resolution Metabolomics Data.

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Integrated network analysis and effective tools in plant systems biology.

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KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape.

21 January 2018

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Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach.

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MetaNET--a web-accessible interactive platform for biological metabolic network analysis

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FunRich: An open access standalone functional enrichment and interaction network analysis tool

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Network portal: a database for storage, analysis and visualization of biological networks.

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Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments

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Efficient searching and annotation of metabolic networks using chemical similarity

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BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology

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High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

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Selective paired ion contrast analysis: a novel algorithm for analyzing postprocessed LC-MS metabolomics data possessing high experimental noise

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KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems

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IIS--Integrated Interactome System: a web-based platform for the annotation, analysis and visualization of protein-metabolite-gene-drug interactions by integrating a variety of data sources and tools

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Efficient visualization of high-throughput targeted proteomics experiments: TAPIR.

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Assessing multivariate gene-metabolome associations with rare variants using Bayesian reduced rank regression

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PubChem: Integrated Platform of Small Molecules and Biological Activities

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ChemSpider: An Online Chemical Information Resource

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Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database

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TMDB: a literature-curated database for small molecular compounds found from tea.

21 January 2018

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BioPhytMol: a drug discovery community resource on anti-mycobacterial phytomolecules and plant extracts

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mVOC: a database of microbial volatiles

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PhenoMeter: A Metabolome Database Search Tool Using Statistical Similarity Matching of Metabolic Phenotypes for High-Confidence Detection of Functional Links

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T3DB: the toxic exposome database

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Direct infusion mass spectrometry metabolomics dataset: a benchmark for data processing and quality control

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The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?".

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linkedISA: semantic representation of ISA-Tab experimental metadata

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The Metabolomics Standards Initiative

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Quality control for plant metabolomics: reporting MSI-compliant studies

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

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Metabolonote: a wiki-based database for managing hierarchical metadata of metabolome analyses

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

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MetaDB a Data Processing Workflow in Untargeted MS-Based Metabolomics Experiments.

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ProteoWizard: open source software for rapid proteomics tools development

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The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience

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jmzTab: a java interface to the mzTab data standard

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pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library

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PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more

21 January 2018

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SpeckTackle: JavaScript charts for spectroscopy

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BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data

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EXIMS: an improved data analysis pipeline based on a new peak picking method for EXploring Imaging Mass Spectrometry data

21 January 2018

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Maui-VIA: A User-Friendly Software for Visual Identification, Alignment, Correction, and Quantification of Gas Chromatography-Mass Spectrometry Data.

21 January 2018

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CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets

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Identifying and quantifying metabolites by scoring peaks of GC-MS data

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BiPACE 2D--graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry

21 January 2018

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Pattern Recognition-Based Approach for Identifying Metabolites in Nuclear Magnetic Resonance-Based Metabolomics.

21 January 2018

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Focus: a robust workflow for one-dimensional NMR spectral analysis

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Bayesian deconvolution and quantification of metabolites in complex 1D NMR spectra using BATMAN.

21 January 2018

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Normalization of metabolomics data with applications to correlation maps

21 January 2018

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Accurate, fully-automated NMR spectral profiling for metabolomics

21 January 2018

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Building blocks for automated elucidation of metabolites: natural product-likeness for candidate ranking

21 January 2018

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Unified and isomer-specific NMR metabolomics database for the accurate analysis of (13)C-(1)H HSQC spectra

21 January 2018

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Customized metabolomics database for the analysis of NMR ¹H-¹H TOCSY and ¹³C-¹H HSQC-TOCSY spectra of complex mixtures

21 January 2018

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MVAPACK: a complete data handling package for NMR metabolomics

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NMR/MS Translator for the Enhanced Simultaneous Analysis of Metabolomics Mixtures by NMR Spectroscopy and Mass Spectrometry: Application to Human Urine.

21 January 2018

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(13)C NMR Metabolomics: INADEQUATE Network Analysis.

21 January 2018

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MetaboAnalyst 3.0--making metabolomics more meaningful

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Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses

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Autonomous metabolomics for rapid metabolite identification in global profiling

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Mass++: A Visualization and Analysis Tool for Mass Spectrometry

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MASSyPup--an 'out of the box' solution for the analysis of mass spectrometry data

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MetaboLyzer: a novel statistical workflow for analyzing Postprocessed LC-MS metabolomics data

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Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics

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Haystack, a web-based tool for metabolomics research

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ALLocator: an interactive web platform for the analysis of metabolomic LC-ESI-MS datasets, enabling semi-automated, user-revised compound annotation and mass isotopomer ratio analysis

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Metabolomic Characterization of Knockout Mutants in Arabidopsis: Development of a Metabolite Profiling Database for Knockout Mutants in Arabidopsis.

21 January 2018

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MassCascade: Visual Programming for LC-MS Data Processing in Metabolomics

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A comparison of common programming languages used in bioinformatics.

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imDEV: a graphical user interface to R multivariate analysis tools in Microsoft Excel

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Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics

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"Retention projection" enables reliable use of shared gas chromatographic retention data across laboratories, instruments, and methods

21 January 2018

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Metabolite identification: are you sure? And how do your peers gauge your confidence?

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FELPS.201500417

CeCaFDB: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13C-fluxomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FELPS.201500417

MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FELPS.201500417

tEFMA: computing thermodynamically feasible elementary flux modes in metabolic networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FELPS.201500417

Visual workflows for 13C-metabolic flux analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FELPS.201500417

Metabolomics of aquatic organisms: the new omics on the block

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FELPS.201500417

GPMS: A Genetic Programming Based Approach to Multiple Alignment of Liquid Chromatography-Mass Spectrometry Data

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FELPS.201500417

7 January 2021

Metabolite profiling in LC–DAD using multivariate curve resolution: the alsace package for R

1 reference

https://api.crossref.org/works/10.1002%2FELPS.201500417

7 January 2021

Tear proteomic profile in three distinct ocular surface diseases: keratoconus, pterygium, and dry eye related to graft-versus-host disease

1 reference

https://api.crossref.org/works/10.1002%2FELPS.201500417

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1002%2FELPS.201500417

7 January 2021

Clustering of 3D-Structure Similarity Based Network of Secondary Metabolites Reveals Their Relationships with Biological Activities.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.201500417

7 January 2021

The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again

1 reference

https://api.crossref.org/works/10.1002%2FELPS.201500417

7 January 2021

QTREDS: a Ruby on Rails-based platform for omics laboratories

1 reference

https://api.crossref.org/works/10.1002%2FELPS.201500417

7 January 2021

Compound identification in gas chromatography/mass spectrometry-based metabolomics by blind source separation

1 reference

https://api.crossref.org/works/10.1002%2FELPS.201500417

7 January 2021

The SBW-MATLAB interface

1 reference

https://api.crossref.org/works/10.1002%2FELPS.201500417

7 January 2021

Proposed quantitative and alphanumeric metabolite identification metrics

1 reference

https://api.crossref.org/works/10.1002%2FELPS.201500417

7 January 2021

Identifiers

DOI

10.1002/ELPS.201500417

1 reference

4 September 2017

1 reference

PubMed ID

26464019