Table 1.
The entire list of reviewed tools is organized by important analytical steps in metabolomics data analysis and includes details regarding their platform dependency, and implementation, e.g., programming language (R, Python, Java, C/C ++, etc.) or web browser based and their availability
| Name of the Software Tool | Category | Platform dependency | Implementation/ use dependency | Software availability | References |
|---|---|---|---|---|---|
| AlpsNMR | Platform | NMR | R | https://github.com/sipss/AlpsNMR | (Madrid-Gambin et al. 2020) |
| SigMa | Platform | NMR | MATLAB, Standalone | https://github.com/BEKZODKHAKIMOV/SigMa_Ver1 | (Khakimov et al. 2020) |
| NMRfilter | Platform | NMR | NA | https://github.com/stefhk3/nmrfilterprojects | (Kuhn et al. 2020) |
| MSHub + EI-GNPS | Platform | GC–MS | GNPS, Web | https://bitbucket.org/iAnalytica/mshub_process/src/master/; https://github.com/CCMS-UCSD/GNPS_Workflows/tree/master/mshub-gc/tools/mshub-gc/proc | (Aksenov et al. 2020) |
| RGCxGC toolbox | Platform | GCXGC-MS | R, TeX | https://github.com/DanielQuiroz97/RGCxGC | (Quiroz-Moreno et al. 2020) |
| CROP | Preprocessing | LC–MS/MS | R | https://github.com/rendju/CROP | (Kouřil et al. 2020) |
| ncGTW | Preprocessing | LC–MS/MS | R, C ++ | https://github.com/ChiungTingWu/ncGTW | (Wu et al. 2020) |
| TidyMS | Preprocessing | LC–MS/MS | Python | https://github.com/griquelme/tidyms | (Riquelme et al. 2020) |
| AutoTuner | Preprocessing | LC–MS/MS | R | https://github.com/crmclean/Autotuner | (McLean & Kujawinski, 2020) |
| hRUV | Preprocessing | LC–MS/MS | R | https://shiny.maths.usyd.edu.au/hRUV/ | (Kim et al. 2020) |
| MetumpX | Preprocessing | Any | R | https://github.com/hasaniqbal777/MetumpX-bin | (Wajid et al. 2020) |
| MetaQuac | QC | Targeted LC–MS | R | https://github.com/bihealth/metaquac | (Kuhring et al. 2020) |
| dbnorm | QC | Any | R | https://github.com/NBDZ/dbnorm | (Bararpour et al. 2020) |
| MetaClean | QC | LC–MS/MS | R | https://cran.r-project.org/web/packages/MetaClean/index.html | (Chetnik et al. 2020) |
| NeatMS | QC | LC–MS/MS | Python | https://github.com/bihealth/NeatMS | (Gloaguen et al. 2020) |
| MESSAR | Annotation | LC–MS/MS | Web | https://messar.biodatamining.be/ | (Liu, Mrzic, et al., 2020; Liu, Nellis, et al., 2020) |
| SMART 2.0 | Annotation | 2D NMR | Web | https://smart.ucsd.edu/classic | (Reher et al. 2020) |
| MetFID | Annotation | MS/MS data | NA | NA | (Fan et al. 2020) |
| CPVA | Annotation | Any | Web | https://github.com/13479776/cpvamscpva.med.sustech.edu.cn | (Luan et al. 2020) |
| NRPro | Annotation | LC–MS/MS | Java, Web | https://bioinfo.cristal.univ-lille.fr/nrpro/ | (Ricart et al. 2020) |
| MetENP/MetENPWeb | Annotation | LC–MS/MS | R, Web | https://www.metabolomicsworkbench.org/data/analyze.php | (Choudhary et al. 2020) |
| CANOPUS | Annotation | LC–MS/MS | Standalone | https://bio.informatik.uni-jena.de/software/canopus/ | (Dührkop et al. 2020) |
| MolDiscovery | Annotation | LC–MS/MS | Python | https://github.com/mohimanilab/molDiscovery | (Cao et al. n.d.) |
| MetIDfyR | Annotation | LC–MS/MS | R | https://github.com/agnesblch/MetIDfyR | (Delcourt et al. 2020) |
| Qemistree | Annotation | LC–MS/MS | Python | https://github.com/biocore/q2-qemistree | (Tripathi et al. 2020) |
| IIMN | Annotation | LC–MS/MS | GNPS, Web | https://ccms-ucsd.github.io/GNPSDocumentation/fbmn-iin/ | (Robin Schmid, Daniel Petras, Louis-Félix Nothias, Mingxun Wang, Allegra T. Aron, Annika Jagels, Hiroshi Tsugawa, Johannes Rainer, Mar Garcia-Aloy, Kai Dührkop, Ansgar Korf, Tomáš Pluskal, Zdeněk Kameník, Alan K. Jarmusch, Andrés Mauricio Caraballo-Rodrígu 2020) |
| FOBI | Annotation | Any | R, Web | https://github.com/pcastellanoescuder/FOBI_Visualization_Tool | (Castellano-Escuder et al. 2020) |
| Biodendro | Annotation | LC–MS/MS | Python | https://github.com/ccdmb/BioDendro | (Rawlinson et al. 2020) |
| AllCCS atlas | Annotation | IM-MS | Web | https://github.com/ZhuMetLab/AllCCS; http://allccs.zhulab.cn/ | (Zhou et al. 2020) |
| Binner | Annotation | LC–MS/MS | Java | https://binner.med.umich.edu/ | (Kachman et al. 2019) |
| MS-CleanR | Annotation | LC–MS/MS | R | https://github.com/eMetaboHUB/MS-CleanR | (Fraisier-Vannier et al. 2020) |
| Retip | Annotation | LC–MS/MS | R | https://www.retip.app/ | (Bonini et al. 2020) |
| QSRR Automator | Annotation | LC–MS/MS | Python | https://github.com/UofUMetabolomicsCore/QSRR_Automator/releases/tag/v1_exe | (Naylor et al. 2020) |
| MFAssignR | Annotation | LC–MS/MS | R, HTML | https://github.com/skschum/MFAssignR | (Schum et al. 2020) |
| McSearch | Annotation | LC–MS/MS | R | https://github.com/HuanLab/McSearch; http://cloudmetabolomics.ca/mcsearch | (Xing et al. 2020) |
| REDU | Annotation | LC–MS/MS | GNPS, Web | https://redu.ucsd.edu/ | (Jarmusch et al. 2020) |
| MASST | Annotation | LC–MS/MS | GNPS, Web | https://masst.ucsd.edu/ | (Wang, Jarmusch, et al., 2020; Wang, Leber, et al., 2020) |
| NPClassifier | Annotation | Any | Web | https://npclassifier.ucsd.edu/ | (kim et al. 2020) |
| patRoon | Annotation | HR MS/MS | R | https://github.com/rickhelmus/patRoon | (Helmus et al. 2021) |
| LipidLynxX | Annotation | LC–MS/MS | Python, Standalone | http://lipidmaps.org/lipidlynxx/ | (Ni & Fedorova, 2020) |
| Skyline | Multifunctional | Any | Standalone | https://skyline.ms/project/home/software/Skyline/begin.view | (Adams et al. 2020) |
| NoTaMe | Multifunctional | LC–MS/MS | R, Web | https://github.com/antonvsdata/notame | (Klåvus et al. 2020) |
| BALSAM | Multifunctional | IMS, GC–MS, LC–MS | Web, Python, HTML, Java | https://exbio.wzw.tum.de/balsam/, https://github.com/philmaweb/balsam_django | (Weber et al. 2020) |
| MRMkit | Multifunctional | Targeted LC–MS | Python, R | https://github.com/cssblab/MRMkit | (Teo et al. 2020) |
| MetaboShiny | Multifunctional | Any | R | https://github.com/joannawolthuis/MetaboShiny | (Wolthuis et al. 2020) |
| SmartPeak | Multifunctional | Many | C#, Python | https://github.com/AutoFlowResearch/SmartPeak | (Kutuzova et al. 2020) |
| MS-DIAL 4.0 | Multifunctional | LC–MS/MS, GC–MS, IMS | Standalone | http://prime.psc.riken.jp/compms/msdial/main.html | (Tsugawa et al. 2020) |
| IP4M | Multifunctional | LC–MS/MS | Java, Perl, R, Standalone | https://IP4M.cn | (Liang et al. 2020) |
| DropMS | Multifunctional | HR MS | Web | http://www.dropms.online/ | (Rosa et al. 2020) |
| Epimetal | Statistics, visualization | Any | JavaScript, Web | https://github.com/amergin/epimetal; http://epimetal.computationalmedicine.fi/ | (Ekholm et al. 2020) |
| Metabolite AutoPlotter | Statistics, visualization | Quantitative metabolomics data, any | R, Web | https://mpietzke.shinyapps.io/AutoPlotter/ | (Pietzke & Vazquez, 2020) |
| Metabolite-Investigator | Statistics, visualization | LC–MS | R, Web | https://github.com/cfbeuchel/Metabolite-Investigator; https://apps.health-atlas.de/metabolite-investigator/ | (Beuchel et al. 2020) |
| VIIME | Statistics, visualization | Any | Web | https://viime.org/#/ | (Choudhury et al. 2020) |
| struct | Statistics, visualization | Any | R | http://bioconductor.org/packages/struct | (Lloyd et al. 2020) |
| lipidr | Statistics, visualization | LC–MS/MS | R | https://www.lipidr.org/ | (Mohamed et al. 2020) |
| NOREVA | Statistics | Any | Web, R, Standalone | http://idrblab.cn/noreva/ | (Yang et al. 2020) |
| %polynova_2way | Statistics | Processed data | SAS | https://doi.org/10.1371/journal.pone.0244013.s002 | (Manjarin et al. 2020) |
| rawR | Visualization | LC–MS | R, C ++ | https://github.com/fgcz/rawR | (Kockmann & Panse, 2020)R |
| Metaboverse | Visualization | Any | Java, HTML, Standalone | https://github.com/Metaboverse | (Jordan A. Berg, Youjia Zhou, T. Cameron Waller, Yeyun Ouyang, Sara M. Nowinski, Tyler Van Ry, Ian George, James E. Cox, Bei Wang 2020) |
| JS-MS 2.0 | Visualization | LC–MS/MS | Java, JavaScript, HTML | https://github.com/optimusmoose/jsms | (Henning & Smith, 2020) |
| COCONUT | Database | Any | Web | https://coconut.naturalproducts.net/ | (Sorokina et al. n.d.) |
| METLIN MS2 molecular standards database | Database | LC–MS/MS | Web | http://metlin.scripps.edu/ | (Xue et al. 2020) |
| CSMDB | Database | NMR | MATLAB | https://github.com/cibionnmrlab/CSMDB-with-ConQuer-ABC | (Charris-Molina et al. 2020) |
| EMBL-MCF | Database | LC–MS | NA | https://curatr.mcf.embl.de/ | |
| MIAMI | Isotopic | GC–MS | C ++ | http://miami.tu-bs.de/ | (Dudek et al. 2020) |
| isoSCAN | Isotopic | GC–MS | R | https://github.com/jcapelladesto/isoSCAN | (Capellades et al. 2020) |
| LiPydomics | Lipidomics | Ion Mobility, Lipidomics | Python, HTML | https://github.com/dylanhross/lipydomics | (Ross et al. 2020) |
| LipidCreator | Lipidomics | LC–MS | C#, HTML, Skyline plugin | https://github.com/lifs-tools/lipidcreator | (Peng et al. 2020) |
| Lipid Annotator | Lipidomics | LC–MS/MS | NA | NA | (Koelmel et al. 2020) |
| Raman2imzML | MSI | Raman | C ++, R | https://github.com/LlucSF/Raman2imzML | (Iakab et al. 2020) |
| SUMMER | Multiomics | Any | R, Web | http://igc1.salk.edu:3838/summer/ and https://bitbucket.org/salkigc/summer/src/master/ | Huang et al. (2020) |
| metpropagate | Analysis, visualization | Untargeted LC–MS/MS | R, Python | https://github.com/emmagraham/metPropagate | Graham Linck et al. (2020) |
The tools generally follow their order of appearance in the manuscript text