New software tools, databases, and resources in metabolomics: updates from 2020
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Title
New software tools, databases, and resources in metabolomics: updates from 2020
Authors
Keywords
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Journal
Metabolomics
Volume 17, Issue 5, Pages -
Publisher
Springer Science and Business Media LLC
Online
2021-05-12
DOI
10.1007/s11306-021-01796-1
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Note: Only part of the references are listed.- patRoon: open source software platform for environmental mass spectrometry based non-target screening
- (2021) Rick Helmus et al. Journal of Cheminformatics
- Public LC-Orbitrap Tandem Mass Spectral Library for Metabolite Identification
- (2021) Prasad Phapale et al. JOURNAL OF PROTEOME RESEARCH
- Signature Mapping (SigMa): An efficient approach for processing complex human urine 1H NMR metabolomics data
- (2020) Bekzod Khakimov et al. ANALYTICA CHIMICA ACTA
- Targeted Realignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection
- (2020) Chiung-Ting Wu et al. BIOINFORMATICS
- CROP: correlation-based reduction of feature multiplicities in untargeted metabolomic data
- (2020) Štěpán Kouřil et al. BIOINFORMATICS
- AlpsNMR: an R package for signal processing of fully untargeted NMR-based metabolomics
- (2020) Francisco Madrid-Gambin et al. BIOINFORMATICS
- The Connection and Disconnection Between Microbiome and Metabolome: A Critical Appraisal in Clinical Research
- (2020) Biswapriya B. Misra Biological Research for Nursing
- Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics
- (2020) Kendra J. Adams et al. JOURNAL OF PROTEOME RESEARCH
- High Resolution GC-Orbitrap-MS Metabolomics Using Both Electron Ionization and Chemical Ionization for Analysis of Human Plasma
- (2020) Biswapriya B. Misra et al. JOURNAL OF PROTEOME RESEARCH
- Software tools, databases and resources in metabolomics: updates from 2018 to 2019
- (2020) Keiron O’Shea et al. Metabolomics
- Mass spectrometry searches using MASST
- (2020) Mingxun Wang et al. NATURE BIOTECHNOLOGY
- MESSAR: Automated recommendation of metabolite substructures from tandem mass spectra
- (2020) Youzhong Liu et al. PLoS One
- Spatial metabolomics of in situ host–microbe interactions at the micrometre scale
- (2020) Benedikt Geier et al. Nature Microbiology
- Subcellular Mass Spectrometry Imaging and Absolute Quantitative Analysis across Organelles
- (2020) Aurélien Thomen et al. ACS Nano
- AutoTuner: High Fidelity and Robust Parameter Selection for Metabolomics Data Processing
- (2020) Craig McLean et al. ANALYTICAL CHEMISTRY
- Hydrogen/Deuterium and 16O/18O-Exchange Mass Spectrometry Boosting the Reliability of Compound Identification
- (2020) Yury Kostyukevich et al. ANALYTICAL CHEMISTRY
- Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics
- (2020) Paolo Bonini et al. ANALYTICAL CHEMISTRY
- Comparison of Full-Scan, Data-Dependent, and Data-Independent Acquisition Modes in Liquid Chromatography–Mass Spectrometry Based Untargeted Metabolomics
- (2020) Jian Guo et al. ANALYTICAL CHEMISTRY
- CPVA: a web-based metabolomic tool for chromatographic peak visualization and annotation
- (2020) Hemi Luan et al. BIOINFORMATICS
- MIAMI––a tool for non-targeted detection of metabolic flux changes for mode of action identification
- (2020) Christian-Alexander Dudek et al. BIOINFORMATICS
- Data normalization strategies in metabolomics: Current challenges, approaches, and tools
- (2020) Biswapriya B Misra EUROPEAN JOURNAL OF MASS SPECTROMETRY
- Consecutive Queries to Assess Biological Correlation in NMR Metabolomics: Performance of Comprehensive Search of Multiplets over Typical 1D 1H NMR Database Search
- (2020) Andrés Charris-Molina et al. JOURNAL OF PROTEOME RESEARCH
- lipidr: A Software Tool for Data Mining and Analysis of Lipidomics Datasets
- (2020) Ahmed Mohamed et al. JOURNAL OF PROTEOME RESEARCH
- Current status of retention time prediction in metabolite identification
- (2020) Michael Witting et al. JOURNAL OF SEPARATION SCIENCE
- Reproducible molecular networking of untargeted mass spectrometry data using GNPS
- (2020) Allegra T. Aron et al. Nature Protocols
- NOREVA: enhanced normalization and evaluation of time-course and multi-class metabolomic data
- (2020) Qingxia Yang et al. NUCLEIC ACIDS RESEARCH
- Data‐Independent Acquisition Mass Spectrometry‐Based Proteomics and Software Tools: A Glimpse in 2020
- (2020) Fangfei Zhang et al. PROTEOMICS
- LipidCreator workbench to probe the lipidomic landscape
- (2020) Bing Peng et al. Nature Communications
- Review on natural products databases: where to find data in 2020
- (2020) Maria Sorokina et al. Journal of Cheminformatics
- Hierarchical clustering of MS/MS spectra from the firefly metabolome identifies new lucibufagin compounds
- (2020) Catherine Rawlinson et al. Scientific Reports
- “Notame”: Workflow for Non-Targeted LC–MS Metabolic Profiling
- (2020) Anton Klåvus et al. Metabolites
- Lipid Annotator: Towards Accurate Annotation in Non-Targeted Liquid Chromatography High-Resolution Tandem Mass Spectrometry (LC-HRMS/MS) Lipidomics Using a Rapid and User-Friendly Software
- (2020) Jeremy P. Koelmel et al. Metabolites
- Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources
- (2020) Tara Eicher et al. Metabolites
- Deep Learning Driven GC-MS Library Search and Its Application for Metabolomics
- (2020) Dmitriy D. Matyushin et al. ANALYTICAL CHEMISTRY
- Improved Annotation of Untargeted Metabolomics Data through Buffer Modifications That Shift Adduct Mass and Intensity
- (2020) Wenyun Lu et al. ANALYTICAL CHEMISTRY
- MS-CleanR: A Feature-Filtering Workflow for Untargeted LC–MS Based Metabolomics
- (2020) Ophélie Fraisier-Vannier et al. ANALYTICAL CHEMISTRY
- Phosphorus NMR and Its Application to Metabolomics
- (2020) Fatema Bhinderwala et al. ANALYTICAL CHEMISTRY
- Reference Standardization for Quantification and Harmonization of Large-Scale Metabolomics
- (2020) Ken H. Liu et al. ANALYTICAL CHEMISTRY
- Concepts and Software Package for Efficient Quality Control in Targeted Metabolomics Studies: MeTaQuaC
- (2020) Mathias Kuhring et al. ANALYTICAL CHEMISTRY
- DropMS: Petroleomics Data Treatment Based in Web Server for High-Resolution Mass Spectrometry
- (2020) Thalles R. Rosa et al. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
- RGCxGC toolbox: An R-package for data processing in comprehensive two-dimensional gas chromatography-mass spectrometry
- (2020) Cristian Quiroz-Moreno et al. MICROCHEMICAL JOURNAL
- A lipidome atlas in MS-DIAL 4
- (2020) Hiroshi Tsugawa et al. NATURE BIOTECHNOLOGY
- Development of a plasma pseudotargeted metabolomics method based on ultra-high-performance liquid chromatography–mass spectrometry
- (2020) Fujian Zheng et al. Nature Protocols
- Chemical Derivatization in LC-MS Based Metabolomics Study
- (2020) Shuang Zhao et al. TRAC-TRENDS IN ANALYTICAL CHEMISTRY
- Harmonization of quality metrics and power calculation in multi-omic studies
- (2020) Sonia Tarazona et al. Nature Communications
- Fast and sensitive flow-injection mass spectrometry metabolomics by analyzing sample-specific ion distributions
- (2020) Boris Sarvin et al. Nature Communications
- metPropagate: network-guided propagation of metabolomic information for prioritization of metabolic disease genes
- (2020) Emma J. Graham Linck et al. npj Genomic Medicine
- Machine Learning Applications for Mass Spectrometry-Based Metabolomics
- (2020) Ulf W. Liebal et al. Metabolites
- QSRR Automator: A Tool for Automating Retention Time Prediction in Lipidomics and Metabolomics
- (2020) Bradley C. Naylor et al. Metabolites
- Metabolite AutoPlotter - an application to process and visualise metabolite data in the web browser
- (2020) Matthias Pietzke et al. Cancer & Metabolism
- Multi-omics integration in biomedical research – A metabolomics-centric review
- (2020) Maria A. Wörheide et al. ANALYTICA CHIMICA ACTA
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- (2020) Tom van der Laan et al. ANALYTICAL CHEMISTRY
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- (2020) Vivian Delcourt et al. ANALYTICAL CHEMISTRY
- MRMkit: Automated Data Processing for Large-Scale Targeted Metabolomics Analysis
- (2020) Guoshou Teo et al. ANALYTICAL CHEMISTRY
- Retrieving and Utilizing Hypothetical Neutral Losses from Tandem Mass Spectra for Spectral Similarity Analysis and Unknown Metabolite Annotation
- (2020) Shipei Xing et al. ANALYTICAL CHEMISTRY
- Raman2imzML converts Raman imaging data into the standard mass spectrometry imaging format
- (2020) Stefania Alexandra Iakab et al. BMC BIOINFORMATICS
- A web-based system for creating, viewing, and editing precursor mass spectrometry ground truth data
- (2020) Jessica Henning et al. BMC BIOINFORMATICS
- IP4M: an integrated platform for mass spectrometry-based metabolomics data mining
- (2020) Dandan Liang et al. BMC BIOINFORMATICS
- Deep learning meets metabolomics: a methodological perspective
- (2020) Partho Sen et al. BRIEFINGS IN BIOINFORMATICS
- An Enhanced Isotopic Fine Structure Method for Exact Mass Analysis in Discovery Metabolomics: FIA-CASI-FTMS
- (2020) Christopher J. Thompson et al. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
- Mass Spectrometry Techniques in Emerging Pathogens Studies: COVID-19 Perspectives
- (2020) Iqbal Mahmud et al. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
- MASS SPECTROMETRY TECHNOLOGIES TO ADVANCE CARE FOR CANCER PATIENTS IN CLINICAL AND INTRAOPERATIVE USE
- (2020) Jialing Zhang et al. MASS SPECTROMETRY REVIEWS
- MetaboShiny: interactive analysis and metabolite annotation of mass spectrometry-based metabolomics data
- (2020) Joanna C. Wolthuis et al. Metabolomics
- MetFID: artificial neural network-based compound fingerprint prediction for metabolite annotation
- (2020) Ziling Fan et al. Metabolomics
- MetaClean: a machine learning-based classifier for reduced false positive peak detection in untargeted LC–MS metabolomics data
- (2020) Kelsey Chetnik et al. Metabolomics
- ReDU: a framework to find and reanalyze public mass spectrometry data
- (2020) Alan K. Jarmusch et al. NATURE METHODS
- METLIN MS2 molecular standards database: a broad chemical and biological resource
- (2020) Jingchuan Xue et al. NATURE METHODS
- Ion mobility collision cross-section atlas for known and unknown metabolite annotation in untargeted metabolomics
- (2020) Zhiwei Zhou et al. Nature Communications
- Raman-guided subcellular pharmaco-metabolomics for metastatic melanoma cells
- (2020) Jiajun Du et al. Nature Communications
- Developing Unique Nontarget High-Resolution Mass Spectrometry Signatures to Track Contaminant Sources in Urban Waters
- (2020) Bowen Du et al. Environmental Science & Technology Letters
- A Python-Based Pipeline for Preprocessing LC–MS Data for Untargeted Metabolomics Workflows
- (2020) Gabriel Riquelme et al. Metabolites
- BALSAM—An Interactive Online Platform for Breath Analysis, Visualization and Classification
- (2020) Philipp Weber et al. Metabolites
- A graph density-based strategy for features fusion from different peak extract software to achieve more metabolites in metabolic profiling from high-resolution mass spectrometry
- (2020) Ran Ju et al. ANALYTICA CHIMICA ACTA
- Exploring the Use of Gas Chromatography Coupled to Chemical Ionization Mass Spectrometry (GC-CI-MS) for Stable Isotope Labeling in Metabolomics
- (2020) Jordi Capellades et al. ANALYTICAL CHEMISTRY
- Automatic Annotation and Dereplication of Tandem Mass Spectra of Peptidic Natural Products
- (2020) Emma Ricart et al. ANALYTICAL CHEMISTRY
- SmartPeak Automates Targeted and Quantitative Metabolomics Data Processing
- (2020) Svetlana Kutuzova et al. ANALYTICAL CHEMISTRY
- Metabolite-Investigator: an integrated user-friendly workflow for metabolomics multi-study analysis
- (2020) Carl Beuchel et al. BIOINFORMATICS
- struct: an R/Bioconductor-based framework for standardized metabolomics data analysis and beyond
- (2020) Gavin Rhys Lloyd et al. BIOINFORMATICS
- MFAssignR: Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures
- (2020) Simeon K. Schum et al. ENVIRONMENTAL RESEARCH
- Characterization of Monophasic Solvent-Based Tissue Extractions for the Detection of Polar Metabolites and Lipids Applying Ultrahigh-Performance Liquid Chromatography–Mass Spectrometry Clinical Metabolic Phenotyping Assays
- (2020) Andrew D. Southam et al. JOURNAL OF PROTEOME RESEARCH
- Evaluation of Single Sample Network Inference Methods for Metabolomics-Based Systems Medicine
- (2020) Sanjeevan Jahagirdar et al. JOURNAL OF PROTEOME RESEARCH
- Evaluating and minimizing batch effects in metabolomics
- (2020) Wei Han et al. MASS SPECTROMETRY REVIEWS
- SUMMER, a shiny utility for metabolomics and multiomics exploratory research
- (2020) Ling Huang et al. Metabolomics
- Applying NMR compound identification using NMRfilter to match predicted to experimental data
- (2020) Stefan Kuhn et al. Metabolomics
- Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra
- (2020) Kai Dührkop et al. NATURE BIOTECHNOLOGY
- Chemically informed analyses of metabolomics mass spectrometry data with Qemistree
- (2020) Anupriya Tripathi et al. Nature Chemical Biology
- %polynova_2way: A SAS macro for implementation of mixed models for metabolomics data
- (2020) Rodrigo Manjarin et al. PLoS One
- State of the Field in Multi-Omics Research: From Computational Needs to Data Mining and Sharing
- (2020) Michal Krassowski et al. Frontiers in Genetics
- SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information
- (2019) Kai Dührkop et al. NATURE METHODS
- MetumpX—a metabolomics support package for untargeted mass spectrometry
- (2019) Bilal Wajid et al. BIOINFORMATICS
- Deep annotation of untargeted LC-MS metabolomics data with Binner
- (2019) Maureen Kachman et al. BIOINFORMATICS
- Comparison of Software Tools for Liquid Chromatography–High-Resolution Mass Spectrometry Data Processing in Nontarget Screening of Environmental Samples
- (2019) Lotta L. Hohrenk et al. ANALYTICAL CHEMISTRY
- EpiMetal: an open-source graphical web browser tool for easy statistical analyses in epidemiology and metabolomics
- (2019) Jussi Ekholm et al. INTERNATIONAL JOURNAL OF EPIDEMIOLOGY
- Navigating freely-available software tools for metabolomics analysis
- (2017) Rachel Spicer et al. Metabolomics
- Updates in metabolomics tools and resources: 2014-2015
- (2015) Biswapriya B. Misra et al. ELECTROPHORESIS
- MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis
- (2015) Hiroshi Tsugawa et al. NATURE METHODS
- OMICtools: an informative directory for multi-omic data analysis
- (2014) V. J. Henry et al. Database-The Journal of Biological Databases and Curation
- Highly sensitive feature detection for high resolution LC/MS
- (2008) Ralf Tautenhahn et al. BMC BIOINFORMATICS
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