| Tool | MetaboAnalyst(R) [1], [2] | W4M [3] | xcmsrocker [4] | patRoon [5] | OUKS [6] |
|---|---|---|---|---|---|
| Language | R, Java, etc. | R | R, Py, etc. | R, C++, JS, etc. | R |
| Type | R script, Web server | Web server | R scipt | R script | R script |
| Experimental Design and Randomization | ○ | ○ | ○ | ○ | ● |
| Integration & Alignment | XCMS | XCMS | XCMS, X13CMS, apLCMS | XCMS, OpenMS, enviPick, DataAnalysis, KPIC2, SIRIUS, SAFD | XCMS |
| Optimization of Integration | MetaboAnalyst | ○ | IPO, Autotuner, xMSanalyzer, Warpgroup | ○ | IPO, Autotuner, MetaboAnalyst, Warpgroup, ncGTW, Paramounter, cpc, XCMS |
| Missing Values Imputation | 7 | ○ | 6 | ○ | 17 |
| Artifacts Removal | ○ | ○ | ○ | ○ | MetProc |
| Filtration | 8 | 1 | 5 | 10 | 11 |
| Signal Correction / Quality Metrics |
11/1 | 5/3 | 5/2 | ○ | 34/18 |
| Normalization / Quality Metrics |
7/2 | 3 | 2/2 | ○ | 6/5 |
| Transformation / Scaling | ● | ● | ● | ○ | ● |
| Adjust Variation | ○ | ○ | ○ | ○ | LM, LMM, GAM, GAMM |
| MWAS, ANCOVA | ○ | LM, LMM | ○ | ○ | LM, LMM, GAM, GAMM, DRC, GLM, GLMM, correlation |
| Annotation | CAMERA | CAMERA | CAMERA, xMSannotator, RAMClustR, nontaget, mzUnity, Rdisop, InterpretMSSpectrum | CAMERA, nontarget, RAMClustR, OpenMS, cliqueMS | CAMERA, xMSannotator, RAMClustR, mWISE, metID, MetaboAnnotation |
| Database Searching | ● | ● | ● | ● | ● |
| Identification | ○ | MetFrag, SIRIUS, CSI:FingerID | MetFrag | MetFrag, SIRIUS, CSI:FingerID, GenForm, Bruker | ○ |
| Molecular Features Clustering | ○ | ○ | pmd, classyfireR | rcdk | NoTaMe, pmd, CROP |
| Feature Selection / Filtering | 8 | 1 | 4 | ○ | 20 |
| Univariate Analysis | Parametric, Non-parametric, FC | Parametric, Non-parametric | Parametric, Non-parametric | ○ | Parametric, Non-parametric, FC, Moderated |
| Multivariate Analysis | SAM, EBAM | MANOVA | ○ | ○ | MANOVA, PERMANOVA |
| Multigroup Analysis | LM, MEBA, ASCA | LM, LMM, ASCA | ○ | ○ | LM, LMM, GAM, GAMM, DRC, ASCA, PLS, sPLS, 2D FDR, PVCA, PC-PR2 |
| Repeated Measure | ○ | LMM, sPLS-DA | ○ | ○ | LM, LMM, GAM, GAMM, DRC, sPLS-DA |
| Time Series | LM, MEBA, ASCA | LM, LMM, ASCA | ○ | ○ | LM, LMM, GAM, GAMM, DRC, PVCA, PC-PR2, MEBA, ASCA, DROmics, TOXcms, timeOmics, polyPK |
| Signal Modeling | LM | LM, LMM | ○ | ○ | LM, LMM, GAM, GAMM, DRC |
| Distance Analysis | ● | ● | ● | ○ | ● |
| Correlation Analysis | ● | ● | ● | ○ | ● |
| Outlier Detection | ○ | ○ | PCA based | ○ | PCA based |
| Sample/Effect Size and Power Calculation | ○ | ○ | ○ | ○ | ● |
| Classification Analysis | PLS, oPLS, sPLS, RF, SVM, ROC | PLS, oPLS | ROC, gWQS, caret models | ○ | PLS, oPLS, RF, SVM, PAM, ROC, GLM, gWQS, Penalized, Stepwise, caret models |
| Regression Analysis | ○ | ○ | LM, gWQS, caret models | LM | LM, GLM, Penalized, Stepwise, gWQS, caret models |
| Plot data | ● | ● | ● | ○ | ● |
| Unsupervised Data Projection | PCA, HCA, Heatmap, K-means, SOM | PCA, HCA, Heatmap | PCA, HCA, Heatmap | ○ | PCA, HCA, Heatmap, K-means, t-SNE, HCA on PCA, DBSCAN, HDBSCAN, Spectral Clustering, UMAP, MCLUST, MDS, LLE, IsoMap, Laplacian Score, Diffusion Maps, kernel PCA, sparse PCA, ICA, FA, NMF, PAM, CLARA, Fuzzy Clustering, Validation clustering |
- Pang, Z., Chong, J., Li, S., & Xia, J. (2020). MetaboAnalystR 3.0: toward an optimized workflow for global metabolomics. Metabolites, 10(5), 186.
- Pang, Z., Zhou, G., Ewald, J., Chang, L., Hacariz, O., Basu, N., & Xia, J. (2022). Using MetaboAnalyst 5.0 for LC–HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data. Nature Protocols, 17(8), 1735-1761.
- Guitton, Y., Tremblay-Franco, M., Le Corguillé, G., Martin, J. F., Pétéra, M., Roger-Mele, P., … & Thévenot, E. A. (2017). Create, run, share, publish, and reference your LC–MS, FIA–MS, GC–MS, and NMR data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy online infrastructure for metabolomics. The International Journal of Biochemistry & Cell Biology, 93, 89-101.
- Yu, M., Dolios, G., & Petrick, L. (2022). Reproducible untargeted metabolomics workflow for exhaustive MS2 data acquisition of MS1 features. Journal of Cheminformatics, 14(1), 1-10.
- Helmus, R., Ter Laak, T. L., van Wezel, A. P., de Voogt, P., & Schymanski, E. L. (2021). patRoon: open source software platform for environmental mass spectrometry based non-target screening. Journal of Cheminformatics, 13(1), 1-25.
- Plyushchenko, I. V., Fedorova, E. S., Potoldykova, N. V., Polyakovskiy, K. A., Glukhov, A. I., & Rodin, I. A. (2021). Omics untargeted key script: R-based software toolbox for untargeted metabolomics with bladder cancer biomarkers discovery case study. Journal of Proteome Research, 21(3), 833-847.