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RuSirius

Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.

IMPORTANT: THIS IS ACTIVELY DEVELOPED.

RuSirius (spelled R-U-Sirius (are you serious)) is an R package that provides an interface to the Sirius software, enabling seamless integration of xcms preprocessing results with Sirius.
It is built upon RSirius, the REST API library for the R programming language, which you can find here.

Installation Instructions

Option 1: Install Sirius and R-api via Conda

  1. You can install both the Sirius software and the R API using conda with the following command:
conda create -n sirius conda-forge::r-sirius-ms
conda activate sirius
  1. Then, in an R session, install RuSirius and it’s dependencies :
library(remotes)
install_github("RforMassSpectrometry/RuSirius")

Alternatively, you can manually install Sirius and then RuSirius:

  1. Download the Sirius software from the official releases page. RuSirius is dependent on Sirius 6.3, please ensure you have the right version downloaded.
  2. Install RuSirius and it’s dependencies (which includes the R-api) by running the following code in R:
library(remotes)
install_github("RforMassSpectrometry/RuSirius")

Usage

RuSirius comes with five vignettes to help you get started:

  1. Getting Started with RuSirius This vignette covers the basics of connecting to Sirius and managing projects.

  2. Importing Spectra into Sirius This vignette shows a basic example for importing spectra data into Sirius.

  3. Retrieving Results from Sirius This vignette explains how to retrieve and interpret different result types.

  4. Using Custom Databases This vignette demonstrates how to create and use custom databases for structure search.

  5. Importing Chromatographic Peaks from xcms This vignette demonstrates how to import chromatographic peaks from xcms and use them in Sirius.

Testers Needed

We’re looking for testers to help refine and enhance the functionality of this package, focusing on what users need most. Your feedback is crucial to ensuring the package meets user expectations and operates smoothly.

Key Areas for Testing:

  1. Ease of Installation Start by testing the installation process. Let us know if you encounter any issues, especially with package dependencies.

  2. Exploring Basic Functionalities Run the first two vignettes to familiarize yourself with connecting to Sirius and importing spectra data. This will give you a solid foundation for understanding how the package works.

  3. Adapting to Your Dataset If you’re working with custom datasets or want to import chromatographic peaks from xcms, try the third vignette. It provides the necessary code and steps for more advanced use cases.

Why Your Feedback Matters

The current implementation is in its early stages, focusing on basic functionality. Your input is essential to making the integration between xcms and Sirius seamless and user-friendly. Whether you have suggestions, encounter issues, or need additional features, don’t hesitate to reach out. Your insights will directly shape future updates.

Known Issues

This is the early stage of integrating Sirius with RforMassSpectrometry, and there’s ongoing development to enhance the implementation.

Current Issues:

  • Vignettes require Sirius login: Vignettes cannot be built automatically in CI as they require Sirius authentication. Pre-rendered vignettes are available on the pkgdown site.

  • Importing features can be time-consuming. To speed up testing, import only a few features at first and limit the process to one MS1 spectrum per feature. Further details are provided in the vignettes.

If you encounter other issues, please let us know so we can improve the package!

Docker

A pre-built Docker image is available on Docker Hub, based on the official Bioconductor docker image bioconductor/bioconductor_docker:RELEASE_3_22. It includes RuSirius, all dependencies, and Sirius 6.3.3 (downloaded directly from the official GitHub releases). The Sirius REST API starts automatically on port 9999 when the container launches.

Pulling the image 

docker pull rformassspectrometry/rusirius:latest

Running the container

Start an RStudio Server session:

docker run -e PASSWORD=yourpassword -p 8787:8787 rformassspectrometry/rusirius:latest

Then open RStudio Server at http://localhost:8787 (user: rstudio, password: as set above).

Or start an interactive R session directly:

docker run -it rformassspectrometry/rusirius:latest R

Sirius login

Sirius starts automatically inside the container on port 9999. Connect and log in from the R console:

library(RuSirius)
srs <- Sirius(projectId = "my_project",
              username = "your_email",
              password = "your_password",
              port = 9999)

Note that Sirius requires a valid account — you can register for free at https://bright-giant.com.

Building the image locally (advanced)

If you prefer to build the image from source instead of pulling from Docker Hub:

docker build -t rformassspectrometry/rusirius .

This builds the image using the Dockerfile in the repository root.

Thanks

Many many thanks to Markus Fleischauer for his work on the Sirius SDKs, many more Jonas Emmert who made the R-API usable. And Marcus Ludwig for the help and support in implementing RuSirius.