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Trends in Computational Metabolomics (2021–2025) DOI

Awesome A curated list of computational tools, databases, and software for metabolomics research published between 2021-2025.

Citation

Domingo-Fernández, D., Healy, D., Kind, T., Allen, A., Colluru, V., and Misra, B. (2025). Trends in computational metabolomics in the last five years (2021–2025). chemRxiv. https://doi.org/10.26434/chemrxiv-2025-f6lvq

Methodology

We compiled this comprehensive list of computational tools and databases through a systematic approach. We began with manual curation of published metabolomics resources starting in 2021, building upon our prior review efforts (Misra, 2021; Misra and van der Hooft, 2015). To ensure complete coverage and minimize gaps, we subsequently employed three complementary strategies:

  1. Computational screening: Used AI-assisted tools and Google Scholar to identify emerging metabolomics software and databases across the 2021–2025 period
  2. Literature review: Systematically examined citations and references in recent comprehensive metabolomics reviews for each functional category
  3. Field experts: Reviewed our compilation with domain experts across different metabolomics subdisciplines

Collaborating

Please make a PR editing the list to add new tools.

📚 Table of Contents

🏷️ Annotation

🧪 Class | Property Prediction

🔍 De Novo Generation

  • DiffMS - Diffusion-based de novo structure generation from MS/MS spectra
  • MASSISTANT - De novo molecular structure prediction from EI-MS spectra via SELFIES encoding
  • MS-BART - Unified encoder-decoder model for de novo structure elucidation from mass spectra
  • MS2Mol - MS/MS to molecule prediction
  • MSGo - Generates molecular structures directly from mass spectra for exposomics
  • MSNovelist - De novo structure elucidation
  • Mass2SMILES - Mass to SMILES conversion
  • MassGenie - De novo molecular structure prediction from mass spectra using transformers
  • OMG - Optimal molecule generation
  • SEISMiQ - Structure elucidation
  • Spec2Mol - Spectrum to molecule
  • TeFT - Transformer for fragmentation

🧠 Learned Spectrum Representations

  • ChemEmbed - Metabolite identification using enhanced MS/MS data and multidimensional molecular embeddings
  • CLERMS - Contrastive learning-based embeddings for tandem mass spectra
  • DeepMASS - Compound annotation via semantic similarity of mass spectral language
  • DreaMS - Self-supervised transformer pre-trained on millions of unannotated MS/MS spectra
  • LSM1-MS2 - Self-supervised foundation model for tandem mass spectrometry
  • MS2DeepScore - Deep learning similarity scoring
  • MS2DeepScore 2.0 - Updated deep learning similarity
  • MSBERT - BERT for mass spectrometry
  • NaFM - Pre-trained foundation model for small-molecule natural products
  • Spec2Vec - Word2Vec for spectra
  • SpecEmbedding - Spectrum embedding

🏎️ Molecular Formula Prediction

  • CRB-FCC - Fragmental chain characterization
  • FIDDLE - Formula identification
  • FSA - Formula subset analysis
  • IDSL.UFA - United formula annotation
  • MIST-CF - Chemical formula prediction
  • RASSP - Rapid approximate subset-based EI-MS spectra prediction
  • BUDDY - Formula prediction and annotation

📚 Molecular Library Retrieval

  • CMSSP - Cross-modal spectrum-structure prediction
  • COSMIC - Confidence scoring for structure annotation
  • CSU-MS2 - MS/MS library search
  • IDSL_MINT - Metabolite identification
  • JESTR - Joint embedding for structure retrieval
  • LC-MS2Struct - LC-MS/MS structure annotation
  • MIST - Mass spectrum identification
  • MVP - Metabolite virtual profiling
  • VInSMoC - Variable interpretation of spectrum-molecule couples

🕸️ Molecular Networking

  • 3D-MPEA - Graph attention model for multidimensional omics annotation
  • BAM - Biotransformation-based annotation method
  • ChemWalker - Annotation propagation via random walks
  • ConCISE - Consensus annotation propagation fusing molecular networking and in silico predictions
  • E-SGMN - Enhanced structure-guided molecular networking
  • IIMN - Ion identity molecular networking
  • IMN4NPD - Integrated molecular networking for natural products
  • MCN - Optimizes per-metabolite connectivity for molecular networking
  • MMSA - Interactive visualization of fragmentation patterns across molecular families
  • ModiFinder - Modification site localization
  • MolNotator - Reduces molecular network redundancy by grouping ion species into neutral molecules
  • MS-Net - Multi-similarity network-based metabolite annotation
  • SGMNS - Structure-guided molecular network strategy
  • SIMILE - Spectral alignment with statistical significance

Others

  • AnnoMe - MS/MS spectra classification
  • AnnoSM - Substituent mode annotation
  • BioTransformer4.0 - Biotransformation prediction
  • IDSL.CSA - Composite spectra analysis
  • Inventa - Structural novelty discovery
  • ipaPy2 - Integrated probabilistic annotation
  • MADGEN - Scaffold-based de novo molecular generation from MS/MS spectra
  • MCheM - Multiplexed post-column derivatization for improved metabolite annotation
  • MetaboAnnotatoR - Automated annotation of all-ion fragmentation LC-MS data
  • MMST - Predicts chemical structures from multimodal spectroscopic data
  • MS2DECIDE - Decision theory for annotation
  • mWISE - Context-based annotation of LC-MS features through diffusion in graphs
  • NetID - Network-based identification
  • OrbiFragsNets - Orbitrap fragmentation networks

🔍 Spectral Similarity Retrieval

⚗️ Spectrum Prediction

  • 3DMolMS - 3D molecular MS prediction
  • CFM-ID 4.0 - Competitive fragmentation modeling
  • CIDMD - Collision-induced dissociation via molecular dynamics
  • DeepCDM - Deep learning prediction of MS/MS spectra for chemically derived molecules
  • ESP - Ensemble spectral prediction model for metabolite annotation
  • FIORA - Fragmentation prediction
  • fragnnet - Fragmentation neural network
  • GrAFF-MS - Graph attention for fragmentation
  • HDSE-MS - MS/MS spectrum prediction via hierarchical distance structural encoding
  • ICEBERG - Geometric deep learning model for CID mass spectrum simulation
  • MARASON - Mass spectrum prediction
  • MassFormer - Transformer for mass spectra
  • MassKG - Knowledge-based fragmentation and deep learning for natural product MS annotation
  • MS2Compound - Generates custom predicted spectra databases for metabolite identification
  • ms-pred - Prefix-tree decoding for predicting mass spectra from molecules
  • NPS-MS - Deep learning MS/MS prediction for novel psychoactive substance identification
  • PPGB-MS2 - MS/MS prediction using precursor-product ion pair graph bag embeddings
  • QC-GN2oMS2 - Quantum chemistry MS prediction
  • SingleFrag - Single fragmentation prediction

🧰 Workflow Tools

🧪 Benchmark/Dataset

  • MassSpecGym - Benchmark for MS/MS molecule discovery and identification tasks
  • MetaBench - Benchmark for evaluating LLM capabilities in metabolomics

🧬 Biosynthetic Gene Clusters

💧 CE-MS

⚡ DIMS

🗃️ Database

  • AMDB - Quantitative animal metabolite database with statistical analysis tools
  • BinDiscover database - Standardized GC-MS metabolomics data from 156,000+ samples across 2,000 studies
  • CCDB - Chemical correlation database cataloguing inter-chemical correlations in metabolomics
  • COCONUT - Natural products database
  • DNA adduct database - LC-HRMS database and bioinformatics tool for DNA adductomics screening
  • EnzyMine - Knowledge base linking enzymatic reaction features with enzyme sequences
  • foodMASST - MS/MS search tool against a food and beverage metabolomics reference database
  • FragHub - Standardized, merged open mass spectral libraries for metabolite annotation
  • GNPS Dashboard - GNPS data visualization
  • HMDB 5.0 - Human metabolome database
  • HREI-MSDB - High-resolution EI-MS database
  • Human Hair Atlas - Hair metabolome atlas
  • LEAFBot - MS/MS spectral library of 300+ botanical natural product standards
  • MarkerDB 2.0 - Biomarker database
  • MassBase - Multi-platform MS depository of metabolites detected across organisms
  • MassSpecBlocks - Database of nonribosomal peptide and polyketide building blocks for MS
  • MCID database - LC-MS metabolite identification using mass search with ppm-level accuracy
  • MedMeta - Integrative database connecting medicinal secondary metabolites and biosynthetic pathways
  • MetaboLights - Metabolomics data repository
  • Metabolome atlas of the aging mouse brain - Mouse brain metabolome
  • MetalinksDB - Prior knowledge resource for metabolite-mediated intercellular signaling
  • MetaNetX 2025 update - Reconciliation and integration of metabolic data across biochemical databases
  • MetHoS - Automated web platform for large-scale multi-experiment metabolomics processing
  • METLIN-CCS - METLIN with CCS values
  • microbeMASST - MS/MS search tool linking spectra to microbial producers taxonomically
  • MiMeDB - Microbiome metabolome database
  • MiMeDB 2.0 - Updated microbiome metabolome database
  • MSCAT - Catalog and guidance tool for metabolomics software selection
  • MSnLib - Open multi-stage fragmentation (MSn) spectral library for ML
  • Natural Products Atlas 2.0 - Natural products database
  • NGlycDB - N-glycan annotation and visualization for mass spectrometry imaging
  • NIST23 - NIST mass spectral library
  • NMRlipids Databank - Quality-evaluated MD simulation database for lipid membranes
  • NPMine - Text-mining tool extracting natural product structures from literature
  • PharmMet DB - In vitro human liver S9-generated drug metabolite reference library
  • plantMASST - MS/MS search tool for plant metabolites across 2,793 species
  • Pyrfume - Unified framework aggregating stimulus-linked olfactory datasets
  • RepoRT - Community-curated retention time repository
  • Spectraverse - Preprocessed, quality-filtered, merged public MS/MS spectral library
  • TOMATOMET - Tomato metabolome

💊 Drug Discovery

  • BitBIRCH-Lean - Memory-efficient clustering of billion-scale drug-like molecular libraries
  • ChromaQuant - Identifies drug-perturbed protein complexes via co-fractionation MS
  • DMetFinder - Drug metabolite finder
  • Limelight - Web-based visualization and analysis of drug-protein adduct MS data
  • SynFrag - Evaluates synthetic accessibility of AI-designed drug molecules

🌱 Exposomics

  • CMDN - Untargeted metabolomics network for high-throughput xenobiotic metabolite annotation
  • EISA-EXPOSOME - Enhanced in-source fragmentation annotation for sensitive chemical identification
  • ExposomeX - Integrated platform for standardized exposome-wide data analysis
  • FeatureHunter - Software for nucleic acid adduct detection from HR-MS/MS data
  • FluoroMatch IM - PFAS identification integrating ion mobility with nontargeted MS
  • HalogenFinder - ML-based workflow for chlorine/bromine disinfection byproduct identification
  • HExpMetDB - Human exposome metabolite database
  • MDRB - MS-based identification of in vivo traditional Chinese medicine components
  • MetabFlow - Database for metabolism of exogenous natural products in vivo and in vitro
  • MSThunder - Nontargeted analysis framework for rapid unknown organic pollutant identification

🌀 FT-ICR MS

  • MetaboDirect - Automated pipeline for FT-ICR MS organic matter characterization
  • MoleTrans - Browser-based tool for FT-ICR MS dissolved organic matter formula analysis

🗂️ Formats

  • Aird - Computation-oriented MS format with high compression and fast decoding
  • AlphaTims - Python package for efficient indexing, access, and visualization of LC-TIMS-MS data
  • CloMet - Converts raw metabolomics data from public repositories into formats for analysis platforms
  • Dear-OMG - Unified compressed storage format for proteomics, genomics, and metabolomics metadata
  • mspack - Lossless and lossy MS data compression exploiting cross-scan redundancy in mzML/mzXML files
  • mwtab Python Library for RESTful Access - Python library for accessing and validating Metabolomics Workbench data via REST API
  • MZA - HDF5-based storage and access tool for multidimensional MS data including ion mobility
  • mzapy - Python package for extraction and processing of MS data in MZA format
  • mzPeak - Community data format designed for high-throughput multidimensional MS workflows
  • pyOpenMS-viz - OpenMS visualization
  • rawrr R - Raw file reading in R
  • SpectriPy - R package enabling translation between R and Python mass spectrometry data structures
  • TIMSCONVERT - Converts Bruker timsTOF raw data to open mzML and imzML formats

🔥 GC-MS

  • ADAP-KDB - Spectral knowledgebase for tracking and prioritizing unknown GC-MS spectra
  • CRISP - GCxGC data processing
  • eROI - Equidistant region-of-interest strategy for deconvolving co-eluted peaks in GC-Orbitrap HRMS
  • gc-ims-tools - Open-source Python package for customizable GC-IMS data handling and analysis
  • GcDUO - Open-source R software for GC×GC-MS data processing using PARAFAC/PARAFAC2 deconvolution
  • GCMS-ID - GC-MS identification
  • isoSCAN - R tool for automated isotopologue quantification in GC-chemical-ionization-MS flux experiments
  • MACE - Open-access EI-MS spectral database of natural products for chemical ecology
  • MetaboPAC - Infers absolute concentrations from GC-MS relative abundances using kinetic models
  • mzrtsim - R package for simulating GC/LC full-scan raw data in mzML for software benchmarking
  • RIpred - Retention index prediction
  • SERDA - Denoising autoencoder for normalizing systematic signal drift in large-scale GC-MS studies
  • SpecTUS - Deep learning model for de novo molecular structure annotation from GC-EI-MS spectra
  • uafR - R package automating GC-MS data retrieval, compound identification, and similarity matching
  • UniqPy - Thermodynamic model for quantifying short-chain fatty acids from headspace GC-MS

🔋 Holistic/Standalone Tools

  • FluoroMatch 2.0 - PFAS workflow
  • GNPS2 - Global natural products social networking
  • MAVEN2 - Open-source LC-MS/MS metabolomics and lipidomics analysis software
  • MAW - Metabolomics analysis workflow
  • MassCube - Python framework for LC-MS peak detection, annotation, and quality control
  • MeRgeION - Transforms LC-MS/MS data into information-rich spectral databases
  • MetaboReport - Interactive web app for metabolomics analysis and reporting
  • MetaboScape 2025 - Proprietary Bruker software for metabolomics with automated annotation and ion mobility integration
  • Metabox 2.0 - Metabolomics toolbox
  • MetEx - Web app for exploring microbial secondary metabolome datasets
  • PlantMetSuite - Web-based platform for plant-specific metabolomics analysis and multi-omics integration
  • Workflow4Metabolomics - Galaxy workflows

🌈 IR

  • Chemprop-IR - ML package for predicting infrared spectra from molecular structures
  • Graphormer-IR - IR prediction with Graphormer
  • Spectro - Multi-modal approach combining IR and NMR data for molecular structure elucidation

🖼️ Imaging MS

  • 13C-SpaceM - 13C spatial metabolomics
  • Aird-MSI - Optimized Aird compression for MSI data achieving 70% storage reduction over imzML
  • Cardinal v3 - MSI analysis in R
  • DeepION - Deep learning ion image representation for mass spectrometry imaging
  • deepPseudoMSI - Deep learning pseudo MSI
  • DIMPLE - Pipeline for clustering metabolite enrichment patterns along developmental gradients in DESI-MSI
  • HT SpaceM - High-throughput single-cell metabolomics combining MALDI imaging MS with batch processing
  • i2i - Processes mass spectrometry imaging data into ion images
  • imzML Writer - Python tool converting continuously acquired MSI data into pixel-aligned imzML files
  • LipidQMap - Open-source platform for omics-scale quantitative lipidomics in MSI
  • M2aia - Interactive tool for 3D reconstruction, visualization, and analysis of MSI datasets
  • macroMS - Web-based suite for image-guided MS of macroscopic samples like microbial colonies
  • mass2adduct - Annotates adducts and background ions in MSI data
  • massNet - Deep learning model for classifying MSI data directly from raw spectra
  • MassVision - MSI platform integrating visualization, segmentation, AI training, and statistical analysis
  • Met-ID - GUI software for metabolite identification from MALDI-MSI using MS1/MS2
  • METASPACE-ML - ML-based metabolite annotation for MSI with improved low-intensity detection
  • MetaVision3D - Computer-vision pipeline transforming serial 2D MALDI-MSI into 3D spatial metabolome models
  • MSI-Explorer - Napari plugin for interactive MSI data processing, spectral analysis, and annotation
  • MSIannotator - Organ-specific, database-driven automated metabolite annotation for MSI
  • MSIGen - Python package for visualizing line-wise MSI data across MS1, MS2, MRM, and IMS modes
  • MSight - Automated integration of MSI with histological stains and LC-MS/MS peptide IDs
  • MSIpixel - Automated pipeline for compound annotation and quantitation in DDA MSI
  • msiFlow - End-to-end software for reproducible multimodal MALDI MSI and microscopy analysis
  • MSroi - Software for compressing and preprocessing MS data from direct infusion, LC-MS, or imaging
  • Multi‑MSI Processor - Software for batch MSI data analysis, biomarker discovery, and spatial workflows
  • Pew2 - Open-source LA-ICP-MS image processing software
  • rMSIannotation - Algorithm for annotating carbon isotopes and adducts in MSI without compound libraries
  • S2IsoMEr - R package propagating isomeric/isobaric ambiguities into enrichment analysis for spatial metabolomics
  • SagMSI - Unsupervised graph convolution network for spatial segmentation of MSI tissue data
  • SmartGate - AI tool for iterative peak selection and spatial tissue segmentation in imaging MS
  • SONAR-MSI - Workflow integrating synchronized ion acquisition with pseudo-MSI and deep learning
  • SpaceM - In situ single-cell metabolomics via microscopy and MALDI imaging MS
  • SpatialMETA - Variational autoencoder for cross-modal integration of spatial transcriptomics and metabolomics
  • SSN - Tandem MS imaging annotation using spatial correlations among product ions
  • subMALDI - Open-framework R package for organizing, preprocessing, and normalizing MS spectral data

🌬️ Ion Mobility MS

  • AllCCS2 - CCS prediction database
  • AutoCCS - Automated CCS calculation
  • AutonoMS - Integrates analytical equipment into automated laboratory workflows
  • CCS Predictor 2.0 - Open-source SVR models to predict CCS values and filter false positives
  • CCSfind - Tool for building CCS databases from experimental LC-IM-MS measurements
  • GCIMS - R package for untargeted GC-IMS data processing including denoising, alignment, and clustering
  • HyperCCS - CCS prediction framework powered by chemical large language models
  • Met4DX - LC-IM-MS/MS data processing for 4D metabolomics
  • MobiLipid - CCS quality control for IM-MS lipidomics using ¹³C-labeled lipid standards
  • MOCCal - Automated multiomics CCS calibration for traveling wave ion mobility
  • Mol2CCS - GNN-based CCS prediction benchmarking with molecular fingerprints and confidence models
  • OpenTIMS, TimsPy, and TimsR - TIMS data tools
  • PACCS - Voxel-projected area and GNN-based CCS prediction for diverse molecules
  • PNNL PreProcessor - Converts LC-IM-MS data to LC-MS format for existing analysis software
  • POMICS - ML-assisted ab initio CCS computation using DFT and conformational modeling
  • PubChemLite plus CCS - Curated chemical collection for exposomics with predicted CCS values from PubChem
  • SigmaCCS - GNN-based CCS prediction from 3D conformers with 282M-value in-silico database
  • Snakemake CCS - Automated ab initio CCS prediction from SMILES using QM on HPC via Snakemake
  • SSN-CCSPIF - Structural similarity networking with CCS prediction interval filtering for IM-MS

🧮 Isotopic

  • Aerith - Visualization of isotopic patterns in stable isotope probing MS data
  • CIL-ExPMRM - Ultrasensitive chemical isotope labeling pseudo-MRM platform for exposomic suspect screening
  • FAMetA - Estimates fatty acid import, de novo lipogenesis, elongation, and desaturation from ¹³C profiles
  • IsoPairFinder - Identifies pathway intermediates from paired ¹²C/¹³C metabolomics data
  • isopair - Suite of tools for LC-MS peak picking using isotopologue pairs
  • Isoreader - R package to read stable isotope ratio MS data from common instrument formats
  • IsoSolve - Integrative framework consolidating MS and NMR isotopic measurements
  • khipu - Annotates adducts, fragments, and isotopes to infer neutral mass in untargeted metabolomics
  • Khipu-web - Web app for annotating isotope-labeled metabolites in stable isotope tracing
  • SIMPEL - R package for automated isotopologue mining from HRMS data for metabolic flux analysis

🔭 Large Scale

  • LargeMetabo - R package integrating multiple experiments for biomarker identification at scale
  • peakPantheR - Peak integration at scale

🧬 Lipidomics

  • ADViSELipidomics - Shiny app for preprocessing, analyzing, and visualizing lipidomics data with batch correction
  • BATL - Bayesian naïve Bayes classifier annotating targeted lipidomics peaks using RT and intensity features
  • DBLiPro - Webserver for human lipid metabolism knowledge base and integrative lipidomic analysis
  • DIATAGe - R package for triacylglycerol identification in DIA-based lipidomics using target-decoy scoring
  • Doxlipid - In silico MS/MS library for annotation of 32 subclasses of oxidized lipids
  • LINEX2 - Lipid network analysis framework inferring enzymatic activity from lipidomics via graph algorithms
  • LipiDetective - Deep learning transformer for molecular lipid species identification from tandem MS
  • LipiDex 2 - Lipidomics processing with MSn tree-based fragmentation, spectral matching, and automated QC
  • LipiDisease - Literature-mining web server associating lipid sets with diseases via PubMed analysis
  • Lipid Spectrum Generator - Open-source in silico spectral library generator for lipid identification in LC-MS/MS
  • Lipid Wizard - Lipid assignment and isotopic peak stripping in 2D-LC-MS using ECN-based RT prediction
  • Lipid4Danalyzer - Lipid identification via 4D alignment of RT, MS1, MS/MS, and CCS
  • LipidA-IDER - Automated lipid A structure annotation from HR-MS/MS for Gram-negative bacteria
  • LipidCruncher - Open-source web platform for processing, visualizing, and analyzing lipidomic data
  • Lipidepifind - Identifies structurally modified lipid epi-metabolites using metabolic network expansion
  • LipidFinder 2.0 - Lipidomics pipeline with artefact filtering, in-source fragment removal, and FDR assessment
  • LipidIN - Platform-independent lipid annotation framework with 168.5M fragmentation library
  • LipidOne 2.0 - Web tool analyzing lipidomic data at class, species, and building block levels
  • LipidOracle - Infers lipid double bond and sn-positions from electron-induced dissociation MS
  • LipidOz - Automated determination of lipid C=C double bond positions from OzID IMS-MS data
  • LipidQuant 1.0 - Automated lipidomic quantitation using lipid class separation with high-resolution MS
  • LipidQuant 2.1 - MATLAB software for high-throughput lipid identification and quantification
  • LipidSig - Web server for lipidomic profiling, differential expression, correlation, and network analysis
  • LipidSig 2.0 - Auto-identifies lipid species and assigns 29 characteristics for integrated lipidomic analysis
  • LipidSigR - R package companion to LipidSig for customizable lipidomics analysis and visualization
  • LipidSpace - Tool comparing lipidomes using graph-based structural similarity models and ML analysis
  • LipidSuite - End-to-end web server for differential lipidomics preprocessing and enrichment analysis
  • LIPID MAPS - Community-standard lipid classification system with databases, pathways, and bioinformatics
  • LipoCLEAN - ML filter improving untargeted lipid ID confidence by rescoring with isotope and chromatographic metrics
  • LORA - Web app for lipid over-representation analysis based on structural hierarchy
  • LPPtiger2 - Cross-platform software for predicting and identifying oxidized complex lipids
  • MS2Lipid - ML model predicting 97 lipid subclasses from MS/MS spectra with 97.4% accuracy
  • MS-RIDD - C=C position-resolved untargeted lipidomics combining oxygen attachment dissociation with computational MS
  • Neurolipid Atlas - Lipidomics data commons for neurodegenerative diseases using iPSC-derived cell data
  • RefLAS - Curated LC-MS lipidomics database based on NIST SRM 1950 human plasma
  • RPLC-IMS-CID-MS Lipid Database - Multidimensional database with RT, CCS, and m/z for 877 lipids across 24 classes
  • RTStaR - Retention time standardization and registration for nLC-nESI-MS/MS lipidomics
  • SimLipid - Software for large-scale LC-MS untargeted lipidomics profiling with customizable library

🕸️ Metabolic Networks

  • DNEA - Differential network enrichment
  • FNICM - Framework for identifying disease-associated core metabolites via perturbed metabolic subnetworks
  • KGMN - Multi-layer network for annotating unknown metabolites using metabolic reactions and MS/MS similarity
  • Kiphynet - Web app simulating metabolic transport and reactions in multi-scale microvascular models
  • M2R - Python add-on to cobrapy for integrating gut microbiota metabolism into human metabolic models
  • MetaboliticsDB - Database of metabolomics analyses with network-based flux analysis and AI disease association
  • MetNet - Automated metabolic network reconstruction and comparison
  • MicroMap - Curated visualization of metabolism across 257,000+ microbial genome-scale metabolic reconstructions
  • MInfer - Derives metabolic interaction networks via Jacobian analysis
  • MINNO - Web tool for refining metabolic networks using empirical metabolomics data in nonmodel organisms
  • NetAurHPD - Framework using graph auralization to predict metabolic pathways from correlation networks
  • Recon8D - ML-based metabolic regulome network from eight omics layers across ~1,000 cancer cell lines
  • Thermo-Flux - Semi-automated Python package adding thermodynamic constraints to genome-scale metabolic models

🗃️ Metadata

  • MatrixLM - Julia package for matrix linear models linking metabolite composition to sample traits
  • MetaXtract - Tool extracting LC-MS acquisition metadata from Thermo Fisher raw files
  • PeakForest - Open-source infrastructure for managing and sharing NMR and MS spectral data
  • SMetaS - Tool for automatically standardizing metabolomics sample metadata using ontology vocabularies

🔀 Multifunctional

  • DEIMoS - Data extraction for ion mobility
  • eMZed 3 - Interactive analysis
  • FERMO - Feature-based molecular networking
  • iMAP - Web server for metabolomics data analysis with feature selection, network analysis, and visualization
  • maplet - R package for reproducible metabolomics statistical pipelines
  • Mass-Suite - Python package for HRMS-based non-targeted analysis for water quality and environmental applications
  • matchms - Python library for mass spectral data curation and similarity scoring
  • MargheRita - R package for LC-MS/MS SWATH metabolomics data analysis and metabolite identification
  • MetaboAnalyst 5.0 - Web platform for LC-HRMS processing, statistical analysis, and functional interpretation
  • MetaboAnalyst 6.0 - Unified platform adding MS2 annotation, exposomics support, and dose-response analysis
  • MetaboAnalystR 4.0 - R package providing a unified LC-MS workflow from raw spectra to compound identification
  • MetaboLink - Web app for LC-MS metabolomics post-processing including correction, filtration, and normalization
  • MetDNA3 - Two-layer interactive networking for metabolite annotation
  • MetMiner, MDAtoolkits - User-friendly pipeline for large-scale plant metabolomics data analysis
  • MetaProViz - R package for metabolomics functional analysis and visualization with curated prior knowledge
  • mpactR - R package automating LC-MS/MS data pre-processing for microbiological samples
  • MS-DIAL 5 - Software for multimodal MS data mining with lipidome structural elucidation and imaging
  • MSOne - AI-powered web-based end-to-end LC-MS analysis suite
  • MZmine 3 - Scalable MS data analysis platform supporting LC/GC-MS, ion mobility, and MS imaging
  • NP3 MS Workflow - Open-source LC-MS/MS workflow for ranking bioactive natural products from complex mixtures
  • OpenMS 3 - Open-source framework of MS algorithms enabling reproducible large-scale data analysis
  • OpenMS WebApps - Framework for building user-friendly MS web applications using Streamlit and OpenMS
  • patRoon 2 - R-based non-target analysis platform with automated transformation product screening for HRMS
  • PMart - Web tool for reproducible QC, statistical analysis, and visualization of multi-omics data
  • POMAShiny - Web-based tool for statistical analysis and visualization of metabolomics and proteomics data
  • Punc'data - JavaScript tool for molecular formula assignment and visualization of ultrahigh-resolution MS data
  • Rodin - Python app for streamlined metabolomics preprocessing, statistics, and pathway analysis
  • SLAW - Scalable, self-optimizing workflow for large-scale untargeted LC-MS metabolomics
  • TidyMass - R-based ecosystem for reproducible and traceable LC-MS untargeted metabolomics analysis
  • TidyMass2 - Enhanced LC-MS framework adding metabolite origin inference and functional module analysis
  • TraceMetrix - Web platform providing interactive traceability across the full metabolomics pipeline
  • UmetaFlow - Snakemake workflow for untargeted metabolomics with preprocessing, annotation, and networking
  • XCMS-METLIN - Integrates XCMS data processing with METLIN's 935,000+ experimental MS/MS spectra

🔗 Multiomics

  • AgeAnnoMO - Multi-omics knowledgebase annotating aging-related genes, proteins, and metabolites across 50 species
  • BATMAN‑TCM 2.0 - Database of ~2.3 million TCM ingredient–target protein interactions for pharmacology
  • BnIR - Multi-omics database for rapeseed integrating genomics, transcriptomics, and metabolomics
  • haCCA - Workflow integrating spatial transcriptomics and MALDI-MSI metabolomics via correlated features
  • HoloFoodR - R/Bioconductor package for accessing and integrating holo-omics data from HoloFood
  • INTEGRATE - Pipeline integrating metabolomics and transcriptomics to characterize metabolic regulation
  • iSODA - Web app for interactive single- and multi-omics data analysis with visualization
  • iTraNet - Web app for visualizing trans-omics networks spanning regulatory and metabolic layers
  • jMorp - Japanese multi-omics reference panel providing metabolome, genome, and metagenome data
  • MetaNet - High-performance R package for constructing and analyzing biological networks from multi-omics
  • MiMeNet - Neural network for predicting metabolite abundances from microbiome composition
  • MODMS - Multi-omics database for alfalfa integrating genomes, transcriptomes, and metabolomics
  • MPOD - Integrated multi-omics database and analysis platform for medicinal plants
  • MultiOmicsIntegrator - Nextflow pipeline for integrated analysis of RNA-seq, proteomics, and metabolomics
  • OmicsAnalyst - Web platform for multi-omics integration via correlation networks and dimension reduction
  • Omics Dashboard - Interactive tool for exploring metabolomics and multi-omics data by cellular system hierarchies
  • OmicsNet 2.0 - Web tool for building multi-omics networks with 3D layouts and microbiome support
  • Paired Omics - Community platform documenting links between metabolome and genome data for natural products
  • SOmicsFusion - Toolbox for coregistering spatial metabolomics with biomedical imaging modalities like MRI
  • SVAtlas - Database integrating single extracellular vesicle multi-omics data across 31 diseases
  • TurbOmics - Web platform for multi-omics integration of metabolomics, proteomics, and transcriptomics
  • TurboPutative - Web server for reducing and prioritizing putative annotations in untargeted LC-MS

🔬 NMR

  • A-SIMA/A-MAP - Toolkit for NMR metabolite identification and multivariate analysis in the POKY suite
  • AQuA - Fast automated quantification of metabolites from 1D ¹H NMR spectra
  • ASICS - Joint automatic identification and quantification of metabolites across ¹H NMR spectral sets
  • Bucket Fuser - Regularized regression for extracting metabolite signals from 1D ¹H NMR spectra
  • CASMDB - Integrated simulated metabolite reference database for 1D ¹H NMR metabolomics
  • COLMAR1d - Web server for automated quantitative 1D NMR metabolomics at arbitrary field strengths
  • COLMARppm - Web server for rapid prediction of ¹H and ¹³C NMR chemical shifts
  • COLMARvista - Open-source JavaScript tool for processing and visualizing 2D and pseudo-3D NMR spectra
  • CReSS - Cross-modal retrieval matching ¹³C NMR spectra to molecular structures
  • DeepSAT - Deep learning for molecular structure elucidation from NMR spectra
  • FlavorFormer - Deep learning model for identifying compounds in flavor mixtures from ¹H NMR spectra
  • InRA - Automated interval-based tool for untargeted ¹H NMR multivariate fingerprinting
  • LAMAIS - Automated qualitative analysis of 1D ¹H NMR mixtures
  • MADByTE - NMR platform using 2D spectra to create chemical similarity networks for natural products
  • Magnetstein - Web application for quantitative NMR mixture analysis using Wasserstein distance
  • MagMet - Web server for automated NMR processing and quantification of serum/plasma metabolites
  • MagMet-F - Automated NMR identification and quantification of metabolites in human fecal extracts
  • mcfNMR - Network flow method for compound identification in NMR mixture spectra without peak-picking
  • MetaboLabPy - Open-source Python package for 1D/2D NMR spectra processing
  • MetAssimulo 2.0 - Web app for simulating realistic 1D and 2D metabolomic ¹H NMR spectra
  • MixONat - Software for ¹³C NMR-based dereplication of natural products in mixtures
  • MultiNMRFit - Open-source tool for high-throughput fitting and parameter extraction from 1D NMR spectra
  • NAPROC-13 - Database of ¹³C NMR spectroscopic data for over 25,000 natural products
  • NMR2Struct - ML framework for predicting molecular structures from 1D NMR spectra
  • NMRformer - Transformer-based deep learning for NMR peak assignment and metabolite identification
  • NMRFx - Software for NMR data processing, visualization, peak assignment, and structure calculation
  • NMRhub - Integrated ecosystem spanning the complete NMR data lifecycle from acquisition to deposition
  • NMRInversions.jl - Julia package for time-domain NMR data processing, inversions, and visualization
  • NMRium - Web-based platform for processing, interpreting, and teaching 1D and 2D NMR spectra
  • NMR molecular networking - Framework adapting molecular networking to HSQC NMR spectra for structure annotation
  • NMRphasing - R package for automated NMR phase error correction using nonlinear shrinkage
  • NMRQNet - Deep learning for automatic NMR identification and quantification of plasma metabolites
  • nmRanalysis - Web application for semi-automated NMR metabolite profiling with ML-driven identification
  • NP-MRD - Comprehensive database of NMR spectra and data for ~282,000 natural products
  • PRIMA-Panel - R Shiny tool for assessing preanalytical variation impact on NMR metabolomics data
  • PROSPRE - Deep learning tool for accurate ¹H NMR chemical shift prediction across solvents
  • Protomix - Python package for preprocessing 1D ¹H-NMR metabolomics data with visualization
  • pSCNN - Pseudo-Siamese CNN for compound identification in NMR mixture spectra
  • PyINETA - Python platform integrating INADEQUATE and ¹³C-JRES NMR for metabolite annotation
  • ROIAL-NMR - Python tool for identifying metabolites from proton NMR regions-of-interest using HMDB
  • SAND - Automated NMR spectral decomposition for metabolomics
  • SMolESY - Automated algorithm for metabolite assignment and quantification in blood ¹H NMR spectra
  • ukbnmr - R package for quality control and technical variation removal in UK Biobank NMR data

🌱 Organism Specific

  • Aspergillus Metabolome Database - Database for m/z-based metabolite annotation in MS studies of Aspergillus
  • FoodAtlas - Knowledge graph of food-chemical relationships extracted from literature using LLMs
  • GMDP Database - Web app for exploring metabolomics data from patients with inborn errors of metabolism
  • gutMGene v2.0 - Database of associations among gut microbes, their metabolites, and host genes
  • gutSMASH - Tool for systematic profiling of primary metabolic pathways in gut microbiome genomes
  • GutUDB - Comprehensive multiomics database for analysis and visualization of intestinal diseases
  • HORDB - Database of peptide hormones with activity, structure, and pharmaceutical information
  • IDBac - MALDI-TOF MS platform for microbial strain prioritization based on phylogeny and metabolites
  • LiqBioer - Curated database of cancer biomarkers in body fluids from liquid biopsy studies
  • MDSi - Multi-omics database for foxtail millet integrating genomics, transcriptomics, and metabolomics
  • MetaDb - Database of plant metabolites and their regulation, emphasizing medicinal plants
  • MetaboSeek - Open-source platform for untargeted comparative LC-MS metabolomics and feature annotation
  • MiMIR - R Shiny app for projecting pre-trained risk models onto Nightingale NMR metabolomics data
  • mVOC 4.0 - Database of ~3,500 microbial volatile organic compounds with MS matching
  • MyxoDB - Database of myxobacterial natural products for NMR-based dereplication
  • Omics Untargeted Key Script - R-based scripts for comprehensive untargeted LC-MS metabolomics data processing
  • OrchidMD - Multi-omics database for orchids integrating five omics layers across 213 species
  • PaIRKAT - Kernel regression method incorporating pathway topology for metabolomics association testing
  • PeanutOmics - Multi-omics platform integrating transcriptomic, proteomic, and metabolomic data for peanut
  • PSC-db - Database of plant secondary compounds with 3D structures and bioactivity data
  • SalivaDB - Comprehensive database of salivary biomarkers in humans for diagnostic research
  • SmilODB - Multi-omics database for Salvia miltiorrhiza integrating genomic and metabolomic data
  • StreptomeDB 4.0 - Database of >8,500 streptomycete natural products with spectral and interaction data
  • The Molecular Human - Multiomics network integrating 18 platforms across biofluids to portray molecular phenotypes

🛤️ Pathway, Enrichment and Ontology Tools

  • ChemFOnt - Hierarchical ontology describing functions and actions of over 341,000 biologically important chemicals
  • EnrichMET - Web tool for pathway enrichment analysis of metabolomics data with multiple databases
  • GINv2.0 - Knowledge base integrating signaling and metabolic networks for pathway analysis
  • IDSL.GOA - Gene ontology enrichment analysis extending biological interpretation beyond pathway-level metabolomics
  • iMSEA - Metabolite set enrichment analysis for deciphering drug interaction mechanisms via metabolomics
  • Lilikoi V2.0 - Personalized pathway-based method for disease classification using metabolomics data
  • massDatabase - R package integrating compound and pathway databases for metabolite annotation and enrichment
  • MBROLE3 - Web server for enrichment analysis of metabolite sets using annotations from multiple databases
  • metGWAS 1.0 - Tool integrating GWAS summary statistics with metabolomics to identify disease-linked pathways
  • metLinkR - R tool for cross-linking metabolite identifiers across spectral, structural, and pathway databases
  • MetChem - R package for chemical-structure-based analysis and interpretation of metabolomic profiling data
  • MIMOSA2 - Tool linking microbial community composition to metabolite variation in paired studies
  • MiNEApy - Python tool for metabolic network enrichment analysis using elementary flux modes
  • MS2MP - Deep learning framework predicting KEGG pathways directly from MS/MS spectra
  • ORA - Best-practice guidelines and benchmarking for over-representation pathway analysis in metabolomics
  • PALS - Tool for scoring pathway-level activity changes from grouped metabolite intensities
  • PaintOmics 4 - Web server for integrative multi-omics visualization on KEGG, Reactome, and MapMan pathways
  • PathBank 2.0 - Comprehensive pathway database providing detailed metabolite and protein pathway maps
  • SBGNview - R package for omics data visualization on pathway maps using standard SBGN format
  • secCellFie - Extension of CellFie quantifying secretory pathway metabolic activity from transcriptomics
  • Viime-Path - Tool for visualizing and integrating enrichment results of altered metabolic pathways
  • WebGestalt - Web platform for integrated enrichment analysis across genomics, proteomics, and metabolomics
  • Xconnector - Tool for connecting and bridging diverse metabolomics databases and their identifiers

🔎 Patterns

⚙️ Pre-processing

✅ Quality Control

  • ALISTER - Pre-analytical quality guidance tool for assessing sample handling in lipidomics/metabolomics
  • CordBat - Batch effect correction for large-scale metabolomics spanning extended collection periods
  • Dbnorm - R package for batch effect normalization in MS-based metabolomics across multiple batches
  • hRUV - Hierarchical method for removing unwanted variation in large-scale LC-MS metabolomics
  • iDIA-QC - Quality control tool using DIA-based consensus metrics to monitor LC-MS/MS performance
  • InjectionDesign - Automated plate design for sample injection order with batch balancing and randomization
  • MAFFIN - Post-acquisition normalization removing sample amount variation in comparative metabolomics
  • marr - Maximum rank reproducibility
  • MassQLab - Automated system suitability testing for mass spectrometry quality control
  • MatrixQCvis - Shiny app for interactive quality assessment and exploratory analysis of omics data
  • MetaMOPE - Web tool for automated mobile phase optimization in HILIC LC-MS metabolomics
  • MetaPro - Software for semi-targeted LC-MS with optimized quantification and spectral curation
  • MSNORM - R tool for evaluating and applying normalization methods to reduce systematic MS variability
  • Msquality - MS quality metrics
  • MultiBaC - Batch effect correction for multi-omic datasets combining data from different batches
  • mzQuality - Quality assurance tool for detecting experimental variation in MS-based metabolomics
  • OSCA Finder - Pipeline for osmolality-based calibration and deep learning-aided urine metabolomics
  • Paramounter - Tool for optimizing LC-MS data processing parameters in untargeted metabolomics
  • PeakQC - Automated quality control for monitoring peak integrity across large MS-based cohorts
  • QC4Metabolomics - QC for metabolomics
  • QComics - Standardized quality control protocol for ensuring reproducibility of metabolomics data
  • QuantyFey - QC-based signal drift correction in quantitative LC-MS analysis without internal standards
  • RALPS - Adversarial deep learning for inter-batch correction in untargeted MS metabolomics
  • Rapid QC-MS - Rapid quality control
  • RawBeans - Tool for monitoring LC-MS system performance via raw data quality control
  • RawHummus - Tool for inspecting raw LC-MS data quality including sensitivity drift and RT shifts
  • Shinyscreen - R/Shiny app for exploration, visualization, and quality assessment of HR-MS raw data
  • WaveICA 2.0 - Wavelet-based ICA method for batch effect removal in untargeted metabolomics

⏱️ RT (Retention Time)

  • ABCoRT - Atom-bond co-learning framework for LC retention time prediction aiding metabolite identification
  • AsRTNet - Multimodal feature fusion model predicting retention times of arsenic compounds
  • CMM-RT - ML regressors trained on 80,000 retention times for cross-method metabolite annotation
  • DeepGCN-RT - Deep graph convolutional network for accurate LC-MS retention time prediction
  • DeepRTAlign - Deep learning method for RT alignment in large-cohort LC-MS studies
  • GNN-RT - Graph neural network predicting LC retention times directly from molecular structures
  • Graphormer-RT - Graphormer model enabling RT prediction and comparison across different LC methods
  • QGeoGNN - ML framework predicting chiral molecule retention times to facilitate enantioseparation
  • ReTimeML - ML tool automating ceramide and sphingomyelin identification using LC-MS/MS retention times
  • retention_time_gnn - Transfer learning GNN predicting retention times for target chromatographic systems
  • RI-based-CPSC - Retention index-based peak shift correction for peak alignment in untargeted metabolomics
  • ROASMI - Model for reliable retention order prediction to aid small molecule identification
  • RT-Ensemble Pred - Ensemble method predicting retention times across different chromatographic methods
  • RT-Pred - ML tool predicting HPLC retention times from molecular structures
  • RT-Transformer - Transformer model for scalable retention time prediction across diverse chromatographic conditions

🦠 Single Cell Metabolomics

  • MetaPhenotype - Meta-learning framework for single-cell MS phenotype classification with limited samples
  • MMEASE - Comprehensive workflow for single-cell metabolomics data analysis
  • scFUMES - Algorithm integrating single-cell transcriptomics to identify cell-type-specific metabolic regulators
  • SCMeTA - Modular Python library for standardized single-cell metabolomics data processing

🗺️ Spatial Metabolomics

  • scSpaMet - Framework for joint protein-metabolite profiling of single cells in tissues
  • SMART - Open-source platform for precise molecular formula assignment in MSI
  • SMAnalyst - Integrated web platform for QC, preprocessing, identification, and analysis of spatial metabolomics
  • SMQVP - GUI software for spatial metabolomics data quality visualization, control, and preprocessing
  • SpaMTP - End-to-end analysis software linking spatial metabolomics with other spatial-omics modalities

🧩 Specialized

  • Amanida - R package for metabolomics meta-analysis combining p-values and fold-changes weighted by study size
  • arcMS - R package for collecting MSE data from Waters UNIFI and storing in Apache Parquet format
  • ATLASx - Biochemical reaction atlas linking known metabolism to predicted enzymatic reactions
  • BAGO - Bayesian optimization for autonomous LC gradient optimization using limited data
  • BioPKS Pipeline, RetroTide - Automated retrobiosynthesis tool integrating polyketide synthases for pathway design
  • BioTransformer 3.0 - Biotransformation prediction
  • BitterMasS - ML model predicting bitter compounds from tandem mass spectrometry data
  • BreathXplorer - Python package for processing real-time HRMS-based exhaled breath metabolomics data
  • CCWeights - R package for automated calibration curve weighting factor selection for LC-MS quantification
  • ChemEcho - Tool translating fragmentation pattern knowledge into human-readable rules via MassQL queries
  • ChemSpectra - Web-based software for visualizing and analyzing IR, MS, and NMR spectroscopic data
  • COMMIT - Gap-filling approach for microbial community metabolic models considering metabolite permeability
  • COVRECON - ML framework identifying metabolite biomarkers of fitness from metabolomics cohort data
  • DarkNPS - Deep learning tool for identifying emerging new psychoactive substances from MS data
  • DeepMet - Large language model approach for interpreting and discovering novel mammalian metabolites
  • Easy-Amanida - Shiny app simplifying metabolomics meta-analysis using reported p-values and fold-changes
  • ECDFormer - Transformer model for accurate electronic circular dichroism spectrum prediction
  • FORUM - Knowledge graph linking chemicals and biomedical concepts for metabolic signature interpretation
  • GlyKAn AZ - Open-source GUI for automated glycan structure identification from LC-MS/MS data
  • homologueDiscoverer - R package for detecting homologous polymer series in untargeted metabolomics data
  • IonFlow - Galaxy/R tool for ionomics data analysis using multivariate statistics and network analysis
  • M2S - Tool for aligning and matching untargeted LC-MS features across separate datasets
  • Maldi Transformer - Transformer neural network architecture for MALDI-TOF MS data analysis
  • MassQL - Query language for directly querying raw mass spectrometry data with user-defined filters
  • MEISTER - Integrative MS framework enabling brain-wide 3D biochemical mapping with single-cell resolution
  • MetaboliteChat - Multimodal LLM integrating molecular-graph and image reasoning for metabolite analysis
  • MetaboLM - Transformer language model pre-trained on plasma metabolomics for chronic disease prediction
  • Metaboverse - Tool for contextualized exploration of metabolic network data and hypothesis generation
  • MetCohort - Large-scale LC-HRMS metabolomics raw data alignment, feature detection, and quantification
  • MetDIT - Deep CNN framework transforming 1D metabolomics data into 2D images for clinical analysis
  • mGWAS-Explorer 2.0 - Platform for causal analysis between metabolites and phenotypes in metabolomics GWAS
  • MINE 2.0 - In silico metabolic network expansion database for annotating unknown metabolomics peaks
  • MODAPro - Deep learning framework integrating variational graph autoencoders for multi-omics integration
  • MolSpectLLM - Foundation model integrating SMILES, experimental spectra, and 3D structure for molecular analysis
  • MSConnect - Integrated data management platform enabling traceable multi-software MS analysis workflows
  • MSident - GUI tool automating metabolite identification from ROIMCR chemometric analysis
  • MS-RT - Benchmark for evaluating MS/MS spectral clustering algorithms in metabolomics
  • MS2toImg - CNN approach converting MS/MS spectra to images for identification
  • Multipass CCS Refiner - Shiny app for calibrating multipass CCS measurements from cyclic ion mobility
  • NP Analyst - Open platform mapping bioassay activity to MS features for natural product discovery
  • NPFimg - Image processing and ML method identifying chemo/biomarker features in chromatography-MS
  • Pickaxe - Flexible biochemical reaction prediction tool for generating enzymatic reaction networks
  • ptairMS - Bioconductor suite for processing PTR-TOF-MS exhaled breath data in cohort studies
  • SMITER - Python tool simulating LC-MS/MS runs for any biomolecule using formula-based calculations
  • SPIFFED - Computational method for analyzing co-fractionation MS data to construct protein interaction networks
  • Umatrix - Generative algorithm using self-organizing maps to augment small biomedical sample sizes
  • VIMMS 2.0 - Framework for developing and testing MS fragmentation strategies in silico and on instruments

📕 Spectral Library

  • CIeaD - Open-access plant metabolite spectral library with complementary CID and EAD fragmentation spectra
  • DNA Adduct Portal - Curated database and portal for DNA adduct mass spectrometric detection and characterization
  • EMBL-MCF 2.0 - Updated LC-MS metabolite spectral library with authenticated reference standards
  • GNPS Drug Library - MS/MS reference library of drugs and metabolites for screening drug exposure
  • HighResNPS - HRMS spectral database for suspect screening of new psychoactive substances
  • In silico infrared spectral library of human metabolites - IR library
  • MassBank - Mass spectral database
  • metScribeR - R/Shiny package accelerating creation of in-house retention time metabolite standard libraries
  • mFAM - Approach for evaluating MS features at the metabolite family level for functional annotation
  • MIADB - Public MS/MS spectral database of monoterpene indole alkaloids on the GNPS platform
  • MS2extrcat - R package facilitating automated creation of MS/MS reference spectral libraries
  • PASL - High-resolution Orbitrap MS/MS spectral library of pyrrolizidine alkaloids
  • RMB-mix - Tool generating spectral libraries from complex mixtures to expand exposomics coverage
  • UCL-MetIsoLib - HILIC-based isomer-resolved HRMS/MS metabolite library with 334 annotated metabolites
  • WFSR Food Safety Mass Spectral Library - Food safety library

📈 Statistical

  • cluster-CV - Integrative approach combining univariate, multivariate, and pathway analysis for metabolomics
  • DisCo P-ad - Multiple testing correction method for controlling false discoveries in metabolomics
  • GetFeatistics - R package for calibration-based quantification and statistical analysis of metabolomics data
  • imputomics - R framework benchmarking and applying 52 missing value imputation algorithms for metabolomics
  • MAI - Multiple annotation imputation
  • MAMSI - Workflow integrating multi-assay untargeted LC-MS metabolomics for cross-assay biomarker discovery
  • MetaboLINK/ PCA-GLASSO - PCA combined with Graphical Lasso for dimensionality reduction of large metabolomics datasets
  • MetaHD - Multivariate meta-analysis model handling correlations and missing values in high-dimensional metabolomics
  • MeTEor - Interactive Shiny app for explorative analysis and visualization of longitudinal metabolomics data
  • MultiClassMetabo - Platform for multiclass metabolomics classification and biomarker identification
  • NOREVA - Protocol for evaluating and selecting optimal metabolomics data processing workflows
  • omicsMIC - Comprehensive tool comparing missing value imputation methods for MS-based omics data
  • PLSKO - Assumption-free knockoff generator for FDR-controlled differential expression in omics data
  • PredCMB - Tool predicting changes in individual metabolite levels from shotgun metagenome data
  • rMisbeta - R package for robust imputation of missing values in the presence of outliers
  • SMART 2.0 - Integrated tool for targeted/untargeted metabolomics with normalization, QC, and pathway analysis
  • SpectraX - MATLAB app for automated analysis of complex direct/ambient mass spectrometry spectra
  • wscaling.R - R script providing outlier-robust weighted scaling methods for metabolomics preprocessing

🎯 Targeted

  • automRm - R package for fully automatic MRM LC-MS data preprocessing using ML peak detection
  • CLAW-MRM - Automated platform for lipid annotation, statistical analysis, and MRM data parsing
  • MRMPro - Open-source tool for efficient MRM peak review and correction in large cohort studies
  • MRMQuant - Automated tool for accurate targeted metabolomic quantitation from MRM LC-MS/MS
  • Norm ISWSVR - Normalization method correcting batch effects and analytical drift in targeted metabolomics
  • RHermes - Formula-oriented, peak-detection-free method optimizing MS2 acquisition from raw LC/MS1 data
  • SCALiR - Tool for automated metabolite concentration calculation from LC-MS standard curves
  • TARDIS - Open-source R package for automated preprocessing of targeted LC-MS metabolomics/lipidomics data

📊 Visualization

  • ClusterApp - Web app for interactive clustering and dimensionality reduction of metabolomics data
  • EDaViS - Script for visualizing complex time-resolved volatile metabolomics data
  • GraphBio - Shiny web app providing 15 visualization methods for omics data without programming
  • lcmsWorld - 3D visualization tool for quality-control inspection of raw LC-MS data
  • MODE - Interactive Shiny app for detailed exploration of multidimensional omics data
  • MS-VIS - R Shiny tool for visualizing mass spectra and analyzing mass lists
  • PathwayNexus - Tool for mapping metabolomics data across multiple conditions onto metabolic pathways
  • RAIChU - Tool for predicting and visualizing NRPS and PKS biosynthetic pathway products
  • RDD metabolomics platform - Platform contextualizing unannotated MS/MS spectra by comparison to reference datasets
  • SpecXplore - Exploratory tool for manual annotation and visualization of mass spectral data

📄 License

This project is licensed under the terms in the LICENSE file.

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Trends in Computational Metabolomics (2021–2025)

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