FastRet

FastRet is an R package for predicting retention times in liquid chromatography. It can be used through the R console or through a graphical user interface (GUI). The package is described in Fadil et al. (2026). The package’s key features include the ability to

1. Train new predictive models specific for your own chromatography column
2. Use pre-trained models to predict retention times of molecules
3. Adjust pre-trained models to accommodate modifications in chromatography columns
4. Select a small, representative subset of molecules to re-measure on a modified column (Selective Measuring), so that an adjustment model can be trained cheaply

Installation

FastRet requires a Java SDK (for the chemical-descriptor package rcdk). Once Java is available, you can install the released version of FastRet from CRAN by entering the following commands in an R session:

if (Sys.which("java")[1] == "") stop("Please install a Java SDK first.")
install.packages("FastRet")

To install the development version from GitHub instead, use:

install.packages("pak")
pak::pkg_install("spang-lab/FastRet")

For further details see Installation.

Usage

The easiest way to use FastRet is through its GUI. A hosted version of the GUI is available at https://fastret.spang-lab.de, so you can try FastRet without installing anything. To start the GUI locally, install the package and then run the following command in an interactive R terminal:

FastRet::start_gui()

After running the above code, you should see an output like

Listening on http://localhost:8080

in your R console. This means that the GUI is now running and you can access it via the URL http://localhost:8080 in your browser. If your terminal supports it, you can also just click on the displayed link.

The GUI is organized into four modes, available as tabs in the navigation bar: Train, Select, Adjust and Predict (the tabs use short labels; hovering shows the full names Train new Model, Selective Measuring, Adjust existing Model and Predict Retention Times). By default, the GUI opens on the Train tab. For more information about the individual modes and the various input fields, click on the little question mark symbols next to the different input fields or have a look at the documentation page for GUI Usage.

Documentation

FastRet’s documentation is available at spang-lab.github.io/FastRet. It includes pages about

• GUI Usage
• CLI Usage
• Package Internals
• Contribution Guidelines
• Function Reference

Citation

To cite FastRet in publications, please use:

Fadil F, Schmidt T, Amesoeder C, Heckscher S, Schoen M, Gronwald W, Oefner PJ, Spang R, Dettmer K (2026). FastRet: Fast and Simple Retention Time Prediction in Liquid Chromatography. Journal of Chemical Information and Modeling, 66(16), 10412-10425. doi:10.1021/acs.jcim.6c01344

A BibTeX entry is available via citation("FastRet") in R.

Reproducing the paper

The code and cached results needed to reproduce all figures, tables and numbers of the paper are attached to the v1.5.2 release as freda.zip; the README inside explains how to run it.