Table 1 Function comparisons of IP4M and other 6 tools
From: IP4M: an integrated platform for mass spectrometry-based metabolomics data mining
Function tool | IP4M | MetaboAnalyst | W4M | Galaxy-M | XCMS online | MZmine2 | MetaBox | MS-DIAL |
|---|---|---|---|---|---|---|---|---|
Raw data preprocessing | ||||||||
LC–MS | √ | √ | √ | √ | √ | √ | – | √ |
GC–MS | √ | √ | √ | – | √ | √ | – | √ |
NMR | – | √ | √ | √ | – | – | – | – |
MS/MS | – | – | – | – | √ | √ | – | √ |
DIMS | – | – | – | √ | – | – | – | – |
Peak annotation | √ | √ | √ | √ | √ | √ | – | √ |
Peak table operations | ||||||||
Normalization | √ | √ | √ | √ | √ | √ | √ | √ |
Scaling | √ | √ | √ | √ | √ | √ | √ | √ |
Zero filling | √ | √ | √ | √ | √ | √ | √ | √ |
Transformation | √ | √ | √ | √ | – | – | √ | √ |
Ratio variable generation | √ | – | – | – | – | – | – | – |
Basic statistical summary | √ | – | √ | – | – | – | – | √ |
Retrieve rows | √ | – | – | – | – | – | – | – |
Samples and variables merging | √ | – | √ | – | – | √ | – | – |
Statistical analysis | ||||||||
Univariate analysis | √ | √ | √ | √ | √ | √ | √ | √ |
Multivariate analysis | ||||||||
PCA/(O)PLS-DA | √ | √ | √ | √ | √ | √ | √ | √ |
SVM | √ | √ | – | – | – | – | – | – |
RF | √ | √ | – | – | – | – | – | – |
Biosigner | √ | – | √ | – | – | – | – | – |
Boruta | √ | – | – | – | – | – | – | – |
Pathway and enrichment analysis | √ | √ | – | – | √ | √ | √ | |
Integrated workflows | √ | – | √ | √ | – | √ | – | – |
Other functions | ||||||||
Correlation/distance | √ | √ | √ | – | – | – | √ | √ |
Regression | √ | – | – | – | – | √ | – | – |
ROC analysis | √ | √ | – | – | – | – | – | – |
Hierarchical cluster | √ | √ | √ | – | √ | √ | – | √ |
Plotting tools | √ | √ | √ | – | √ | √ | – | – |
Power/sample size | √ | √ | √ | – | – | – | √ | – |
Network analysis | – | √ | – | – | – | – | – | – |
Omics data integration analysis | √ | √ | – | – | √ | – | √ | – |
Time series analysis | – | √ | – | – | – | – | – | – |
Developing language | R, Java, Perl | R, Java | R | R, Python, Matlab | R | Java R | R | C#, |
Local GUI/web server | Local GUI; Windows/Linux/OS | Web server; Local R package | Web server | Web server | Web server | Local GUI; Windows/Linux/OS | Local GUI; Windows/Unix/Linux | Local GUI; Windows |