While the official shorthand nomenclature of lipids is a first and important step towards a reporting quality tool, an additional point score reflects the quality of reported data at an even more detailed granularity. Thus, the Empirical Point Score Model for MS-based Lipidomics (EPoS-MoL) is a lipidomics scoring scheme which takes into account all the different layers of analytical information to be obtained by mass spectrometry, chromatography and ion mobility spectrometry and awards scoring points for each of them.
EPoS-MoL is an R-package and also provides a Shiny app for the calculation of the EPoS-MoL score.
Citing EPoS-MoL
Please reference the Introduction of a Lipidomics Scoring System for data quality assessment and EPoS-MoL by citing the following publication:
Hoffmann, N. et al., Introduction of a Lipidomics Scoring System for data quality assessment. Journal of Lipid Research, 100817, April 2025, doi: 10.1016/j.jlr.2025.100817
Using EPoS-MoL
A public instance of EPoS-MoL is available at https://apps.lifs-tools.org/p/app/eposmol. The app allows you to upload your lipidomics data in either long or wide format and calculate the EPoS-MoL score. It also contains a sample spreadsheet file containing two examples (long and wide format) that should cover the most common output formats of lipid identification tools, or at least a good approximation thereof. The intention is to have a format that is easy to create and process. The wide format may be easier for manual editing, while the long format may be more suitable for a compact representation and for automated creation by tools.
Installing the package
The package can be installed from GitHub using the following command:
devtools::install_github("lifs-tools/empirical-lipid-ms-score")If you want to install a particular release version, use the following command:
devtools::install_github("lifs-tools/empirical-lipid-ms-score@v1.0.0")in this case for the tag version v1.0.0
Using the package
Please see the package vignette for a detailed description of the package functionality.
vignette("eposmol", package = "eposmol")Documentation is also available at https://lifs-tools.github.io/empirical-lipid-ms-score/
Accessing the Shiny Webapp
A public version of the EpOs-MoL Shiny app can be accessed at the following URL:
Running the app from RStudio
In order to load the packages, without the need to build and install it:
devtools::load_all()You can then use the regular “Run App” button within RStudio to launch the Shiny app.
Alternatively, you can install the package, as shown above, then load it and run:
library(eposmol)
run_eposmol_app()After that, the app is accessible from your browser. Please check your R console output for the exact URL and port. The following is just an example. The port may be different on your system:
Listening on http://127.0.0.1:6097Building the Docker image
The Docker image can be built using the following command:
docker build -t eposmol .If you use buildx, you will need to instruct the image builder to load the created image into the local docker:
docker build --load -t eposmol .Alternatively, you can use the build.sh script:
bash build.shwhich will run those steps for you using the buildx builder by default. This will build and tag the eposmol image as docker.lifs-tools.org/lifs/eposmol:latest.
Running the Docker image
The Docker image can be run using the following command using the tagged image (eposmol or docker.lifs-tools.org/lifs/eposmol:latest):
docker run -p 3838:3838 eposmolThe Shiny app will then be available at http://localhost:3838/eposmol/
Alternatively, you can use the provided compose file to automatically sync local changes during development to the RShiny application. You will need to reload your browser for changes to become effective:
./run.shOr use docker compose directly:
docker compose -f docker-compose-eposmol.yml up --watchThe Shiny app will then be available at http://localhost:3838/eposmol/