Paolo Bonini2, Tobias Kind1, Hiroshi Tsugawa3, Dinesh Barupal1, Oliver Fiehn1
Published 10 May 2020 in Analytical 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 by oloBion.
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 an R package and a Python package. Retention time calculation can be useful in identifying unknowns and removing false positive annotations. The R 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.
- Download and install R from the CRAN (64 bit version recommended)
- Download and install RStudio
- Download and install Java JDK
Run the following command lines to install Java in Ubuntu.
sudo apt update
sudo apt install default-jre
sudo apt install default-jdk
sudo R CMD javareconf
It is also possible that r-cran-rjava needs to be installed.
Run the following command line to install python with R.
reticulate::install_python(version = 3.10)
- 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')
rJava requires NVIDIA drivers.
You will find a tutorial in the Retip app as well as in the examples folder of the GitHub repository.