Trends in Computational Metabolomics (2021–2025)

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

Collaborating

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📚 Table of Contents

• 🏷️ Annotation
• 🧪 Benchmark/Dataset
• 🧬 Biosynthetic Gene Clusters
• 💧 CE-MS
• ⚡ DIMS
• 🗃️ Database
• 💊 Drug Discovery
• 🌱 Exposomics
• 🌀 FT-ICR MS
• 🗂️ Formats
• 🔥 GC-MS
• 🔋 Holistic/Standalone Tools
• 🌈 IR
• 🖼️ Imaging MS
• 🌬️ Ion Mobility MS
• 🧮 Isotopic
• 🔭 Large Scale
• 🧬 Lipidomics
• 🕸️ Metabolic Networks
• 🗃️ Metadata
• 🔀 Multifunctional
• 🔗 Multiomics
• 🔬 NMR
• 🌱 Organism Specific
• 🛤️ Pathway, Enrichment and Ontology Tools
• 🔎 Patterns
• ⚙️ Pre-processing
• ✅ Quality Control
• ⏱️ RT (Retention Time)
• 🦠 Single Cell Metabolomics
• 🗺️ Spatial Metabolomics
• 🧩 Specialized
• 📕 Spectral Library
• 📈 Statistical
• 🎯 Targeted
• 📊 Visualization

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🏷️ Annotation

🧪 Class | Property Prediction

• CANOPUS - Class annotation tool
• Mass Spectrum Transformer - Transformer-based mass spectrum analysis
• MWFormer - Molecular weight prediction
• Spec2Class - Spectrum to class prediction

🔍 De Novo Generation

• DiffMS - Diffusion model for MS
• MASSISTANT - Mass spectrometry assistant
• MS-BART - BART model for mass spectrometry
• MS2Mol - MS/MS to molecule prediction
• MSGo - Mass spectrometry structure generation
• MSNovelist - De novo structure elucidation
• Mass2SMILES - Mass to SMILES conversion
• MassGenie - Fragment generation
• OMG - Optimal molecule generation
• SEISMiQ - Structure elucidation
• Spec2Mol - Spectrum to molecule
• TeFT - Transformer for fragmentation

🧠 Learned Spectrum Representations

• ChemEmbed - Chemical embeddings
• CLERMS - Contrastive learning for MS
• DeepMASS - Deep learning for mass spectrometry
• DreaMS - Deep learning representations
• LSM1-MS2 - Language-spectrum model
• MS2DeepScore - Deep learning similarity scoring
• MS2DeepScore 2.0 - Updated deep learning similarity
• MSBERT - BERT for mass spectrometry
• NaFM - Neural attention foundation model
• 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 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 - 3D molecular property embedding
• BAM - Biotransformation-based annotation method
• ChemWalker - Annotation propagation via random walks
• ConCISE - Consensus classifications
• E-SGMN - Enhanced structure-guided molecular networking
• IIMN - Ion identity molecular networking
• IMN4NPD - Integrated molecular networking for natural products
• MCN - Molecular community networking
• MMSA - Multiple mass spectral alignment
• ModiFinder - Modification site localization
• MolNotator - Mass spectral feature to molecule workflow
• MS-Net - MS networking
• 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 - Metabolite annotation
• MCheM - Multiplexed chemical metabolomics
• MetaboAnnotatoR - All-ion fragmentation annotation
• MMST - Multimodal spectral transformer
• MS2DECIDE - Decision theory for annotation
• mWISE - Metabolite identification
• NetID - Network-based identification
• OrbiFragsNets - Orbitrap fragmentation networks

🔍 Spectral Similarity Retrieval

• BLINK - Fast spectral similarity
• compareMS2 2.0 - MS/MS comparison
• falcon - Fast spectral clustering
• FastEI - Fast EI spectral matching
• Flash entropy search - Entropy-based search
• MASST+ - Enhanced mass spectrum search
• metID - Metabolite identification
• mineMS2 - MS/MS mining
• MolDiscovery - Molecule discovery
• MS/MS spectral entropy similarity - Entropy-based similarity
• Reverse Spectral Search - Reverse search algorithm
• SimMS - Similarity for mass spectra
• TransExION - Transformer for ion extraction
• Weighted spectral similarity for library search - Weighted similarity

⚗️ Spectrum Prediction

• 3DMolMS - 3D molecular MS prediction
• CFM-ID 4.0 - Competitive fragmentation modeling
• CIDMD - Collision-induced dissociation via molecular dynamics
• DeepCDM - Deep collision dissociation model
• ESP - Enumerated substructure prediction
• FIORA - Fragmentation prediction
• fragnnet - Fragmentation neural network
• GrAFF-MS - Graph attention for fragmentation
• HDSE-MS - High-dimensional spectral encoding
• ICEBERG - In silico chemical biology
• MARASON - Mass spectrum prediction
• MassFormer - Transformer for mass spectra
• MassKG - Mass spectrometry knowledge graph
• MS2Compound - Compound identification
• ms-pred - Mass spectrum prediction
• NPS-MS - Novel psychoactive substances MS
• PPGB-MS2 - Pathway-guided prediction
• QC-GN2oMS2 - Quantum chemistry MS prediction
• SingleFrag - Single fragmentation prediction

🧰 Workflow Tools

• ENTAiLS Toolkit - Annotation toolkit
• MetaboCoreUtils, MetaboAnnotation and CompoundDb - R packages for annotation
• MetaFetcheR - Metabolite fetching
• MS2Query - Query-based annotation
• mscompiler - MS compiler
• mspepsearchr - Peptide search
• PS2MS - Protein to MS
• RapidMass - Rapid mass analysis
• Scannotation - Scan annotation
• ShinyMetID - Shiny app for metabolite ID
• SiMD - Similarity-based metabolite discovery

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🧪 Benchmark/Dataset

• MassSpecGym - Mass spectrometry benchmark
• MetaBench - Metabolomics benchmarking

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🧬 Biosynthetic Gene Clusters

• antiSMASH 8.0 - Biosynthetic gene cluster detection
• iPRESTO - Prediction of secondary metabolites
• MariClus - Marine cluster analysis
• MIBiG 3.0 - Minimum information about BGCs
• NPClassScore - Natural product classification scoring
• NPLinker - Natural products linking
• NPOmix - Natural products omics

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💧 CE-MS

• MobilityTransformR - Mobility transformation
• PeakMeister - Peak detection for CE-MS

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⚡ DIMS

• EASY-FIA - Flow injection analysis
• rIDIMS - R package for DIMS
• Tidy-Direct-to-MS - Tidy workflow for direct MS

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🗃️ Database

• AMDB - Antimicrobial metabolite database
• BinDiscover database - Binary discovery database
• CCDB - Compound class database
• COCONUT - Natural products database
• DNA adduct database - DNA adducts
• EnzyMine - Enzyme mining
• foodMASST - Food mass spectrometry
• FragHub - Fragment database hub
• 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 - Leaf metabolomics
• MarkerDB 2.0 - Biomarker database
• MassBase - Mass spectrometry database
• MassSpecBlocks - Building blocks for MS
• MCID database - Compound identification
• MedMeta - Medical metabolomics
• MetaboLights - Metabolomics data repository
• Metabolome atlas of the aging mouse brain - Mouse brain metabolome
• MetalinksDB - Metabolite links database
• MetaNetX 2025 update - Metabolic network database
• MetHoS - Metabolomics hosting
• METLIN-CCS - METLIN with CCS values
• microbeMASST - Microbial mass spectrometry
• MiMeDB - Microbiome metabolome database
• MiMeDB 2.0 - Updated microbiome metabolome database
• MSCAT - MS catalog
• MSnLib - MSn library
• Natural Products Atlas 2.0 - Natural products database
• NGlycDB - N-glycan database
• NIST23 - NIST mass spectral library
• NMRlipids Databank - NMR lipids database
• NPMine - Natural products mining
• PharmMet DB - Pharmacometabolomics
• plantMASST - Plant mass spectrometry
• Pyrfume - Olfactory metabolomics
• RepoRT - Retention time repository
• Spectraverse - Spectral universe
• TOMATOMET - Tomato metabolome

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💊 Drug Discovery

• BitBIRCH-Lean - Chemical space exploration
• ChromaQuant - Chromatographic quantification
• DMetFinder - Drug metabolite finder
• Limelight - MS data sharing
• SynFrag - Synthetic fragment analysis

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🌱 Exposomics

• CMDN - Chemical mixture detection network
• EISA-EXPOSOME - Exposome analysis
• ExposomeX - Exposomics platform
• FeatureHunter - Feature detection
• FluoroMatch IM - Fluorinated compound matching
• HalogenFinder - Halogenated compound detection
• HExpMetDB - Human exposome database
• MDRB - Metabolite-disease relationship
• MetabFlow - Metabolomics workflow
• MSThunder - MS data processing

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🌀 FT-ICR MS

• MetaboDirect - Direct analysis
• MoleTrans - Molecular transformation

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🗂️ Formats

• Aird - Aird format tools
• AlphaTims - TIMS data handling
• CloMet - Cloud metabolomics
• Dear-OMG - OMG format tools
• mspack - MS data packing
• mwtab Python Library for RESTful Access - mwTab access
• MZA - MZ archive format
• mzapy - Python mza tools
• mzPeak - Peak handling
• pyOpenMS-viz - OpenMS visualization
• rawrr R - Raw file reading in R
• SpectriPy - Spectral data in Python
• TIMSCONVERT - TIMS conversion

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🔥 GC-MS

• ADAP-KDB - ADAP knowledge database
• CRISP - GCxGC data processing
• eROI - Enhanced ROI detection
• gc-ims-tools - GC-IMS tools
• GcDUO - GC dual detection
• GCMS-ID - GC-MS identification
• isoSCAN - Isotope scanning
• MACE - Mass spectral analysis
• MetaboPAC - Metabolome pathway analysis
• mzrtsim - Simulation tools
• RIpred - Retention index prediction
• SERDA - Spectral entropy analysis
• SpecTUS - Spectral tools
• uafR - UAF R package
• UniqPy - Unique peak detection

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🔋 Holistic/Standalone Tools

• FluoroMatch 2.0 - PFAS workflow
• GNPS2 - Global natural products social networking
• MAVEN2 - Metabolomics analysis
• MAW - Metabolomics analysis workflow
• MassCube - Mass spectrometry cube
• MeRgeION - Ion merging
• MetaboReport - Metabolomics reporting
• MetaboScape 2025 - Bruker metabolomics
• Metabox 2.0 - Metabolomics toolbox
• MetEx - Metabolite extraction
• PlantMetSuite - Plant metabolomics suite
• Workflow4Metabolomics - Galaxy workflows

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🌈 IR

• Chemprop-IR - IR property prediction
• Graphormer-IR - IR prediction with Graphormer
• Spectro - IR/NMR annotation

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🖼️ Imaging MS

• 13C-SpaceM - 13C spatial metabolomics
• Aird-MSI - Aird for MSI
• Cardinal v3 - MSI analysis in R
• DeepION - Deep learning for ion images
• deepPseudoMSI - Deep learning pseudo MSI
• DIMPLE - DIMPLE imaging
• HT SpaceM - High-throughput SpaceM
• i2i - Image to image
• imzML Writer - imzML writing
• LipidQMap - Lipid quantitative mapping
• M2aia - MSI analysis platform
• macroMS - Macro mass spectrometry
• mass2adduct - Adduct detection
• massNet - Mass networking for MSI
• MassVision - 3D MSI visualization
• Met-ID - Metabolite identification for MSI
• METASPACE-ML - METASPACE machine learning
• MetaVision3D - 3D metabolomics vision
• MSI-Explorer - MSI exploration
• MSIannotator - MSI annotation
• MSIGen - MSI data generation
• MSight - MSI insight
• MSIpixel - Pixel-level MSI
• msiFlow - MSI workflow
• MSroi - MSI ROI analysis
• Multi‑MSI Processor - Multi-MSI processing
• Pew2 - MSI visualization
• rMSIannotation - R MSI annotation
• S2IsoMEr - Isotope analysis for MSI
• SagMSI - Sagittal MSI
• SmartGate - Smart gating for MSI
• SONAR-MSI - SONAR for MSI
• SpaceM - Spatial metabolomics
• SpatialMETA - Spatial meta-analysis
• SSN - Spectral similarity network
• subMALDI - Sub-MALDI analysis

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🌬️ Ion Mobility MS

• AllCCS2 - CCS prediction database
• AutoCCS - Automated CCS calculation
• AutonoMS - Autonomous MS
• CCS Predictor 2.0 - CCS prediction
• CCSfind - CCS finding
• GCIMS - GC-IMS tools
• HyperCCS - Hyperparameter CCS
• Met4DX - 4D metabolomics
• MobiLipid - Lipid mobility
• MOCCal - Mobility calibration
• Mol2CCS - Molecule to CCS
• OpenTIMS, TimsPy, and TimsR - TIMS data tools
• PACCS - CCS prediction
• PNNL PreProcessor - PNNL preprocessing
• POMICS - Proteomics and metabolomics
• PubChemLite plus CCS - PubChemLite with CCS
• SigmaCCS - Sigma CCS
• Snakemake CCS - Snakemake for CCS
• SSN-CCSPIF - Trendline-based filtering

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🧮 Isotopic

• Aerith - Isotope analysis
• CIL-ExPMRM - Chemical isotope labeling
• FAMetA - Fatty acid metabolomics
• IsoPairFinder - Isotope pair finding
• isopair - Isotope pairing
• Isoreader - Isotope ratio reading
• IsoSolve - Isotope solving
• khipu - Isotope pattern analysis
• Khipu-web - Web-based khipu
• SIMPEL - Stable isotope metabolomics

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🔭 Large Scale

• LargeMetabo - Large-scale metabolomics
• peakPantheR - Peak integration at scale

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🧬 Lipidomics

• ADViSELipidomics - Advanced lipidomics
• BATL - Batch tools for lipidomics
• DBLiPro - Lipid database profiler
• DIATAGe - DIA tagging
• Doxlipid - Oxidized lipids library
• LINEX2 - Lipid network explorer
• LipiDetective - Lipid detection
• LipiDex 2 - Lipid identification
• LipiDisease - Lipid-disease associations
• Lipid Spectrum Generator - Lipid spectrum generation
• Lipid Wizard - Lipid analysis wizard
• Lipid4Danalyzer - 4D lipid analysis
• LipidA-IDER - Lipid A identification
• LipidCruncher - Lipid data crunching
• Lipidepifind - Lipid epitope finder
• LipidFinder 2.0 - Lipid finding
• LipidIN - Lipid identification network
• LipidOne 2.0 - Lipid analysis platform
• LipidOracle - Lipid prediction
• LipidOz - Ozone-induced lipid analysis
• LipidQuant 1.0 - Lipid quantification
• LipidQuant 2.1 - Updated lipid quantification
• LipidSig - Lipid signatures
• LipidSig 2.0 - Updated lipid signatures
• LipidSigR - R package for LipidSig
• LipidSpace - Lipid space visualization
• LipidSuite - Lipid analysis suite
• LIPID MAPS - Lipid maps database
• LipoCLEAN - Lipidomics cleaning
• LORA - Lipid ontology reasoning
• LPPtiger2 - Lipid pattern prediction
• MS2Lipid - MS/MS lipid identification
• MS-RIDD - Lipid double bond analysis
• Neurolipid Atlas - Neural lipid atlas
• RefLAS - Reference lipid analysis
• RPLC-IMS-CID-MS Lipid Database - Lipid database
• RTStaR - RT standardization
• SimLipid - Lipid simulation

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🕸️ Metabolic Networks

• DNEA - Differential network enrichment
• FNICM - Flux network integration
• KGMN - Knowledge graph metabolic network
• Kiphynet - Kinetic-phylogenetic network
• M2R - Metabolite to reaction
• MetaboliticsDB - Metabolite database
• MetNet - Metabolic network
• MicroMap - Microbiome mapping
• MInfer - Metabolite inference
• MINNO - Minimal network notation
• NetAurHPD - Network auralization
• Recon8D - Reconstruction 8D
• Thermo-Flux - Thermodynamic flux

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🗃️ Metadata

• MatrixLM - Matrix linear models
• MetaXtract - Metadata extraction
• PeakForest - Peak forest database
• SMetaS - Metadata standardization

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🔀 Multifunctional

• BUDDY - Bottom-up deconvolution
• DEIMoS - Data extraction for ion mobility
• eMZed 3 - Interactive analysis
• FERMO - Feature-based molecular networking
• iMAP - Integrated metabolomics analysis
• maplet - Metabolomics analysis
• Mass-Suite - Mass spectrometry suite
• matchms - MS matching
• MargheRita - R metabolomics
• MetaboAnalyst 5.0 - Metabolomics analysis
• MetaboAnalyst 6.0 - Updated MetaboAnalyst
• MetaboAnalystR 4.0 - R package for MetaboAnalyst
• MetaboLink - Metabolomics linking
• MetDNA3 - Metabolite annotation
• MetMiner, MDAtoolkits - Metabolite mining
• MetaProViz - Metabolomics visualization
• mpactR - Metabolomics impact
• MS-DIAL 5 - MS data analysis
• MSOne - MS1-based analysis
• MZmine 3 - Mass spectrometry analysis
• NP3 MS Workflow - Natural products workflow
• OpenMS 3 - Open-source MS analysis
• OpenMS WebApps - Web applications
• patRoon 2 - Pattern recognition
• PMart - Proteomics/metabolomics
• POMAShiny - POMA Shiny app
• Punc'data - Punctured data analysis
• Rodin - Metabolomics platform
• SLAW - Sample-level analysis
• TidyMass - Tidy mass spectrometry
• TidyMass2 - Updated TidyMass
• TraceMetrix - Trace analysis
• UmetaFlow - Untargeted metabolomics
• XCMS-METLIN - XCMS online

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🔗 Multiomics

• AgeAnnoMO - Age annotation multiomics
• BATMAN‑TCM 2.0 - TCM database
• BnIR - Brassica napus integration
• haCCA - Hierarchical CCA
• HoloFoodR - Hologenome food
• INTEGRATE - Multiomics integration
• iSODA - Integrated systems omics
• iTraNet - Integrative network
• jMorp - Japanese multiomics
• MetaNet - Meta network analysis
• MiMeNet - Microbiome-metabolome network
• MODMS - Multiomics data management
• MPOD - Multiomics platform
• MultiOmicsIntegrator - Omics integration
• OmicsAnalyst - Omics analysis
• Omics Dashboard - Omics visualization
• OmicsNet 2.0 - Omics networking
• Paired Omics - Paired omics data
• SOmicsFusion - Omics fusion
• SVAtlas - Structural variant atlas
• TurbOmics - Turbocharged omics
• TurboPutative - Turbo putative annotation

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🔬 NMR

• A-SIMA/A-MAP - NMR analysis
• AQuA - Automated quantification
• ASICS - Automatic spectrum identification
• Bucket Fuser - Bucket fusion
• CASMDB - CAS metabolomics database
• COLMAR1d - 1D COLMAR
• COLMARppm - COLMAR ppm
• COLMARvista - COLMAR visualization
• CReSS - Cross-referenced spectroscopy
• DeepSAT - Deep learning for SAT
• FlavorFormer - Flavor analysis
• InRA - Integrated NMR analysis
• LAMAIS - Language model for MS
• MADByTE - Bioactivity typing
• Magnetstein - NMR processing
• MagMet - Magnetic metabolomics
• MagMet-F - MagMet fluorescence
• mcfNMR - MCF NMR
• MetaboLabPy - Python metabolomics
• MetAssimulo 2.0 - Metabolite simulation
• MixONat - Mixture analysis
• MultiNMRFit - Multi-NMR fitting
• NAPROC-13 - Natural products 13C
• NMR2Struct - NMR to structure
• NMRformer - Transformer for NMR
• NMRFx - NMR processing
• NMRhub - NMR hub
• NMRInversions.jl - NMR inversions in Julia
• NMRium - NMR in browser
• NMR molecular networking - NMR networking
• NMRphasing - NMR phasing
• NMRQNet - NMR quantification network
• nmRanalysis - R NMR analysis
• NP-MRD - Natural products MRD
• PRIMA-Panel - PRIMA panel
• PROSPRE - Prospective NMR
• Protomix - Protomix analysis
• pSCNN - Parallel spectral CNN
• PyINETA - Python INETA
• ROIAL-NMR - ROIAL for NMR
• SAND - Spectral analysis
• SMolESY - Small molecule ESY
• ukbnmr - UK Biobank NMR

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🌱 Organism Specific

• Aspergillus Metabolome Database - Aspergillus metabolome
• FoodAtlas - Food metabolomics
• GMDP Database - Gut microbiome database
• gutMGene v2.0 - Gut microbiome genes
• gutSMASH - Gut secondary metabolites
• GutUDB - Gut database
• HORDB - Herbal odor database
• IDBac - Bacterial identification
• LiqBioer - Liquid biopsy
• MDSi - Maize database
• MetaDb - Medicinal metabolome database
• MetaboSeek - Metabolomics seeking
• MiMIR - Microbiome integration
• mVOC 4.0 - Microbial VOCs
• MyxoDB - Myxobacteria database
• Omics Untargeted Key Script - OUKS
• OrchidMD - Orchid metabolomics
• PaIRKAT - Pathway integration
• PeanutOmics - Peanut omics
• PSC-db - Plant secondary compounds
• SalivaDB - Saliva database
• SmilODB - Smile odor database
• StreptomeDB 4.0 - Streptomyces database
• The Molecular Human - Human molecular network

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🛤️ Pathway, Enrichment and Ontology Tools

• ChemFOnt - Chemical ontology
• EnrichMET - Enrichment for metabolomics
• GINv2.0 - Gene interaction network
• IDSL.GOA - Gene ontology annotation
• iMSEA - Integrative MSEA
• Lilikoi V2.0 - Pathway analysis
• massDatabase - Mass database
• MBROLE3 - Metabolite biological role
• metGWAS 1.0 - Metabolite GWAS
• metLinkR - Metabolite linking
• MetChem - Metabolite chemistry
• MIMOSA2 - Microbiome metabolome
• MiNEApy - Minimal network enrichment
• MS2MP - MS to metabolic pathway
• ORA - Over-representation analysis
• PALS - Pathway activity levels
• PaintOmics 4 - Pathway visualization
• PathBank 2.0 - Pathway database
• SBGNview - SBGN visualization
• secCellFie - Cell-type metabolic functions
• Viime-Path - Pathway analysis
• WebGestalt - Web-based enrichment
• Xconnector - Cross-omics connector

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🔎 Patterns

• MCnebula - Multiple classes nebula
• Metabokiller - Pattern killing
• MS2LDA 2.0 - LDA for MS/MS
• mzBucket - m/z bucketing

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⚙️ Pre-processing

• 3D-MSNet - 3D MS network
• AriumMS - Arium MS processing
• asari - Feature extraction
• AVIR - Adduct and in-source verification
• CorrDIA - Correlation-based DIA
• CycloBranch - Cyclopeptide analysis
• DaDIA - Data-dependent acquisition
• DBDIpy - DBDI processing
• DecoID - Deconvolution ID
• DeepMSProfiler - Deep learning profiler
• DIAMetAlyzer - DIA analysis
• DNMS2Purifier - MS/MS purification
• DuReS - Duplicate removal
• Eclipse - Eclipse processing
• EVA - Enhanced visualization
• Finnee 2024 - Finnee update
• G-Aligner - Global alignment
• GCMSFormer - Transformer for GC-MS
• HeuSMA - Heuristic spectral matching
• IDSL.IPA - Isotope pattern analysis
• ImpLiMet - Imputation for lipidomics
• ISFrag - In-source fragmentation
• IsoFusion - Isotope fusion
• JPA - Joint peak alignment
• LAGF - Lag filtering
• LongitudinalProf-MSMS-Method - Longitudinal profiling
• maplet - Metabolomics mapping
• MassDash - Mass dashboard
• MassLite - Lightweight MS
• MESSES - Metadata extraction
• metabCombiner - Dataset combining
• metabCombiner 2.0 - Updated combiner
• Metabonaut - Metabolomics explorer
• Metaboprep - Metabolomics preparation
• metaboprep v2 - Updated preparation
• Metanorm - Normalization
• MOCCA - Multivariate curve resolution
• MPACT - Metabolomics processing
• MS1FA - MS1 feature analysis
• MS2Planner - MS/MS planning
• MSMCE - MS molecular connectivity
• MS-TDF Software - TIMS data filter
• msFeaST - MS feature selection
• MultiABLER - Multi-batch learning
• mzLearn - m/z learning
• mzRAPP - Rapid processing
• NeatMS - Neural network for MS
• Nextflow4MS-DIAL - Nextflow for MS-DIAL
• NP-PRESS - Natural products processing
• OpenNAU - Open NAU
• PCPFM - Python pipeline
• Peak Pair Pruner - Peak pair analysis
• PeakBot - Peak detection bot
• PeakDecoder - Peak decoding
• PeakDetective - Peak investigation
• PeakPerformance - Peak performance
• PFΔScreen - PFAS screening
• QuanFormer - Quantification transformer
• RegFilter - Regression filtering
• rtmsEcho - RT-MS echo
• Spectral Denoising - Denoising
• TopNEXt - Top-N optimization
• xcms - Peak detection and alignment

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✅ Quality Control

• ALISTER - Quality assessment
• CordBat - Batch correction
• Dbnorm - Database normalization
• hRUV - Hierarchical RUV
• iDIA-QC - DIA quality control
• InjectionDesign - Injection optimization
• MAFFIN - Mass feature filtering
• marr - Maximum rank reproducibility
• MassQLab - Mass quality lab
• MatrixQCvis - Matrix QC visualization
• MetaMOPE - Metabolomics MOPE
• MetaPro - Meta processing
• MSNORM - MS normalization
• Msquality - MS quality metrics
• MultiBaC - Multiple batch correction
• mzQuality - m/z quality
• OSCA Finder - Outlier finding
• Paramounter - Parameter optimization
• PeakQC - Peak quality control
• QC4Metabolomics - QC for metabolomics
• QComics - QC for omics
• QuantyFey - Quantification quality
• RALPS - Regularized adversarial learning
• Rapid QC-MS - Rapid quality control
• RawBeans - Raw data QC
• RawHummus - Raw data visualization
• Shinyscreen - Shiny screening
• WaveICA 2.0 - Wavelet ICA

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⏱️ RT (Retention Time)

• ABCoRT - Antibody RT prediction
• AsRTNet - Attention-based RT
• CMM-RT - CMM for RT
• DeepGCN-RT - Deep GCN for RT
• DeepRTAlign - Deep RT alignment
• GNN-RT - GNN for RT prediction
• Graphormer-RT - Graphormer for RT
• QGeoGNN - Geometric GNN for RT
• ReTimeML - RT machine learning
• retention_time_gnn - RT GNN
• RI-based-CPSC - RI-based compound prediction
• ROASMI - RT optimization
• RT-Ensemble Pred - Ensemble RT prediction
• RT-Pred - RT prediction
• RT-Transformer - Transformer for RT

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🦠 Single Cell Metabolomics

• MetaPhenotype - Metabolic phenotyping
• MMEASE - Single cell metabolomics
• scFUMES - Single cell functional metabolomics
• SCMeTA - Single cell meta-analysis

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🗺️ Spatial Metabolomics

• scSpaMet - Spatial metabolomics
• SMART - Spatial metabolomics analysis
• SMAnalyst - Spatial metabolomics analyst
• SMQVP - Spatial quality visualization
• SpaMTP - Spatial metabolomics platform

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🧩 Specialized

• Amanida - Amanita metabolomics
• arcMS - Archaea MS
• ATLASx - Comprehensive atlas
• BAGO - Bioactivity-guided optimization
• BioPKS Pipeline, RetroTide - Polyketide analysis
• BioTransformer 3.0 - Biotransformation prediction
• BitterMasS - Bitter compound prediction
• BreathXplorer - Breath analysis
• CCWeights - CCS weighting
• ChemEcho - Chemical echo
• ChemSpectra - Chemical spectra app
• COMMIT - Community integration
• COVRECON - COVID reconstruction
• DarkNPS - Dark chemical space
• DeepMet - Deep learning metabolomics
• Easy-Amanida - Easy Amanida
• ECDFormer - ECD transformer
• FORUM - Disease-chemical forum
• GlyKAn AZ - Glycan analysis
• homologueDiscoverer - Homologue discovery
• IonFlow - Ion flow analysis
• M2S - Metabolite to structure
• Maldi Transformer - MALDI analysis
• MassQL - Mass query language
• MEISTER - Metabolite identification
• MetaboliteChat - LLM for metabolites
• MetaboLM - Language model for metabolomics
• Metaboverse - Metabolic visualization
• MetCohort - Cohort metabolomics
• MetDIT - Metabolite data integration
• mGWAS-Explorer 2.0 - Metabolite GWAS explorer
• MINE 2.0 - Metabolomics MINE
• MODAPro - MODA processing
• MolSpectLLM - LLM for spectroscopy
• MSConnect - MS connectivity
• MSident - MS identification
• MS-RT - MS-RT clustering
• MS2toImg - MS/MS to image
• Multipass CCS Refiner - CCS refinement
• NP Analyst - Natural products analysis
• NPFimg - Natural products fingerprint
• Pickaxe - Reaction rule mining
• ptairMS - PTR-MS analysis
• SMITER - Structure elucidation
• SPIFFED - Spectral processing
• Umatrix - Unified matrix
• VIMMS 2.0 - Virtual metabolomics MS

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📕 Spectral Library

• CIeaD - Chemical investigation
• DNA Adduct Portal - DNA adducts
• EMBL-MCF 2.0 - EMBL library
• GNPS Drug Library - Drug spectra
• HighResNPS - High-resolution NPS
• In silico infrared spectral library of human metabolites - IR library
• MassBank - Mass spectral database
• metScribeR - Metabolite scribing
• mFAM - Mass family
• MIADB - MIADB database
• MS2extrcat - MS/MS extraction
• PASL - Pyrrolizidine alkaloids
• RMB-mix - RMassBank mixing
• UCL-MetIsoLib - UCL isotope library
• WFSR Food Safety Mass Spectral Library - Food safety library

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📈 Statistical

• cluster-CV - Cluster cross-validation
• DisCo P-ad - Discovery co-analysis
• GetFeatistics - Feature statistics
• imputomics - Imputation methods
• MAI - Multiple annotation imputation
• MAMSI - Multi-method analysis
• MetaboLINK/ PCA-GLASSO - PCA GLASSO
• MetaHD - High-dimensional metabolomics
• MeTEor - Metabolite testing
• MultiClassMetabo - Multi-class classification
• NOREVA - Normalization evaluation
• omicsMIC - Omics integration
• PLSKO - PLS knockoff
• PredCMB - Prediction for CMB
• rMisbeta - R Misbeta
• SMART 2.0 - Statistical metabolomics
• SpectraX - Spectral analysis
• wscaling.R - Weighted scaling

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🎯 Targeted

• automRm - Automated MRM
• CLAW-MRM - CLAW for MRM
• MRMPro - MRM processing
• MRMQuant - MRM quantification
• Norm ISWSVR - IS normalization
• RHermes - Targeted screening
• SCALiR - Scaling in R
• TARDIS - Targeted analysis

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📊 Visualization

• ClusterApp - Clustering application
• EDaViS - Enhanced data visualization
• GraphBio - Graph visualization
• lcmsWorld - LC-MS world
• MODE - Metabolomics data explorer
• MS-VIS - MS visualization
• PathwayNexus - Pathway visualization
• RAIChU - Chemical visualization
• RDD metabolomics platform - RDD visualization
• SpecXplore - Spectral exploration

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📄 License

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