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

¹FiehnLab, ²NGAlab, ³Riken

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

Retiplib 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.

Retip library is an R library that includes a large dataset of molecules from from various databases, with calculated chemical descriptors using CDK (Chemistry Development Kit).

The databases included are: 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.

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

1. Download and install R from the CRAN (64 bit version recommended)
2. Download and install RStudio
3. Run the following command line to install Retiplib.

devtools::install_github('olobion/Retiplib')

To install the Retip package, follow these installation instructions.

The library is included in the Retip package. You only need to install Retiplib and follow the tutorial to run Retip, available in the Retip app or in the examples folder of the GitHub repository.

Alternatively, if you want to use the library by your own way, run the following command line to get the library.

Retiplib::get.retiplib()

You can also retrieve the metadata, databases, or descriptors of the library by executing the following functions.

Retiplib::get.libmetadata()
Retiplib::get.libdatabases(include_metadata=FALSE)
Retiplib::get.libdescriptors(include_metadata=FALSE)