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Paolo Bonini²,Tobias Kind¹,Hiroshi Tsugawa³,Dinesh Barupal¹,Oliver Fiehn¹

¹FiehnLab,²NGAlab,³Riken

Published 10 May 2020 inAnalytical Chemistry

Please cite:

Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765

Retip 2.0 was updated and released in June 2024 byoloBion.

Retip is a tool for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis, available as both anR package and aPython package. Retention time calculation can be useful in identifying unknowns and removing false positive annotations. TheR package uses six different machine learning algorithms to built a stable, accurate and fast RT prediction model:

• Random Forest: a decision tree algorithms.
• BRNN: Bayesian Regularized Neural Network.
• XGBoost: an extreme Gradient Boosting for tree algorithms.
• lightGBM: a gradient boosting framework that uses tree based learning algorithms.
• Keras: a high-level neural networks API for Tensorflow.
• H2O autoML: an automatic machine learning tool.

Retip also includes useful biochemical databases like: HMDB, KNApSAcK, ChEBI, DrugBank, SMPDB, YMDB, T3DB, FooDB, NANPDB, STOFF, BMDB, LipidMAPS, Urine, Saliva, Feces, ECMDB, CSF, Serum, PubChem.1, PlantCyc, UNPD, BLEXP, NPA and COCONUT.

Retip 2.0 requires R 4.4.0 and it is recommended to use RStudio IDE to run it.

1. Download and install R from theCRAN (64 bit version recommended)
2. Download and installRStudio
3. Download and installJava JDK

Run the following command lines to install Java in Ubuntu.

sudo apt updatesudo apt install default-jresudo apt install default-jdksudo R CMD javareconf

It is also possible thatr-cran-rjava needs to be installed.

4. Download and installRtools (Windows)
5. Download and installpython3 (required to use Keras model)

Run the following command line to installpython with R.

reticulate::install_python(version = 3.10)

6. Run the following command block to install all required packages, as well as the Retip packages and Retip library.

install.packages('rJava', repos='http://cran.rstudio.com/')install.packages('devtools', version='2.4.5', repos='http://cran.rstudio.com/')install.packages('caret', version='6.0-94', repos='http://cran.rstudio.com/')install.packages('ggplot2', version='3.5.1', repos='http://cran.rstudio.com/')install.packages('rcdk', version='3.8.1', repos='http://cran.rstudio.com/')install.packages('rcdklibs', version='2.9', repos='http://cran.rstudio.com/')install.packages('doParallel', version='1.0.17', repos='http://cran.rstudio.com/')install.packages('stringi', version='1.8.4', repos='http://cran.rstudio.com/')install.packages('lattice', version='0.22-5', repos='http://cran.rstudio.com/')install.packages('randomForest', version='4.7-1.1', repos='http://cran.rstudio.com/')install.packages('xgboost', version='1.7.7.1', repos='http://cran.rstudio.com/')install.packages('brnn', version='0.9.3', repos='http://cran.rstudio.com/')install.packages('lightgbm', version='4.3.0', repos='http://cran.rstudio.com/')install.packages('h2o', version='3.44.0.3')install.packages('gtable', version='0.3.5', repos='http://cran.rstudio.com/')install.packages('grid', version='4.4.0', repos='http://cran.rstudio.com/')install.packages('gridExtra', version='2.3', repos='http://cran.rstudio.com/')install.packages('reticulate', version='1.37', repos='http://cran.rstudio.com/')devtools::install_github('olobion/Retiplib')devtools::install_github('olobion/Retip')

⚠️ It is not possible to install Retip in conda enviroment becauserJava requires NVIDIA drivers.

You will find a tutorial in theRetip app as well as in the examples folder of theGitHub repository.