SIRIUS 4 End Of Life

After more than 4 successful years and over 300 million queries to our web services, SIRIUS 4 will reach its end of life on 31th of December 2022.

What does this mean for you? We will shut down the web services behind SIRIUS 4, so fingerprint prediction, structure database search and compound class prediction will not be possible with SIRIUS 4 anymore. Switching to SIRIUS 5 will solve the problem for you. As always, if you have a running long term project that exceeds the end of life date and cannot switch to SIRIUS 5 please contact us.  

SIRIUS email account verification failed, what now?

Dear SIRIUS users,
when creating a new SIRIUS account the link checkers of some email tools seem to execute the verification link before the user can click the link manually. In such cases the link will already be used (invalid) when the user is clicking it manually and the server returns an error message. In such cases the account has already been verified successfully, regardless of the error message. Just ignore the error and try login into SIRIUS. 

We are currently working on a solution to ensure that the verification can only be performed by the user itself.

SIRIUS 4.0.1 End Of Life

After 2 and a half successful years and over 35 million predicted fingerprints, SIRIUS 4.0.1 will reach its end of life on Friday the 30th of April 2021.
What does this mean for you? We will shut down the web service for CSI:FingerID, so no fingerprint prediction and structure database search will be possible with SIRIUS 4.0.1 anymore.

SIRIUS 4.7.0 Released

We are happy to announce that SIRIUS 4.7.0 is now available for download . This release is all about fixing bugs and performance optimization. To all who had problems with the ILP solvers, a freezing GUI, high memory consumption or long running times: This update should make your life way easier. For a full list of changes see the Changelog.

We further integrated the option to compute fragmentation trees only with our heuristic algorithm (no ILP involved) to speedup molecular formula identification for high mass compounds.
Together with applying timeouts on compound level this should make the processing of large datasets much more feasible.


SIRIUS screener
SIRIUS 4.7.0

SIRIUS online documentation now available!

We are happy to announce that the new online documentation for SIRIUS is now available at

The content is completely written in Markdown which makes contributions by the community very easy. No programming skills required!
Help us with your contributions to make this documentation more comprehensive and useful for the community. See our GitHub repository for 
detailed information on how to contribute.

SIRIUS 4.4.21 – Can now be used along with 4.0.1

Some of you may have noticed problems where SIRIUS 4.4 GUI did not start without reporting any error.
This might be due to old incompatible configs (.sirius directory) from version 4.0.1. SIRIUS 4.4.21 fixes this problem and now uses a separate config directory (.sirius-4.4). It is now possible to use version 4.0.1 and 4.4.x along on the same system without interfering each other.

SIRIUS 4.4 is coming soon!

It’s been a while since SIRIUS 4 received its last update. We are excited to announce that SIRIUS 4.4 is coming soon.
It comes with many new features, e.g.:

  • Project-Space: A standardized persistence layer shared by CLI and GUI that makes both fully compatible.
  • Redesigned Command Line Interface: SIRIUS is now a toolbox that contains different sub-tools that can be combined to “tool-chains”.
  • New (and newly integrated) tools:
    • ZODIAC: Improve Molecular Formula Identifications by re-ranking SIRIUS molecular formula annotations using Bayesian statistics. ZODIAC optimizes annotations on a whole dataset taking advantage of the fact that compounds usually co-occur in a network of derivatives.
    • PASSATUTTO: Is now part of SIRIUS and allows you to generate dataset specific decoy spectral libraries from computed fragmentation trees.
    • lcms-align: SIRIUS supports mzML/mzXML format to process whole LC-MS/MS runs. The lcms-align preprocessing tool performs feature detection and feature alignment based on the available MS/MS spectra.
    • Other handy standalone tools, e.g. compound similarity calculation.

To provide user friendly but also flexible and customizable access to the different tools we completely redesigned the command line interface (CLI).
We know that this might break your workflows and therefore we provide you an early access version of the CLI that can be used for testing and adapting your workflows:
You will also find an updated version of the manual which is still work-in-progress but contains already an updated section on the new CLI.

No worries, even when SIRIUS 4.4. will be released (as soon as the GUI is ready) version 4.0.1 will still be available for some time.

If you find bugs or have any feedback feel free to open an issue on the SIRIUS GitHub repository or contact us via .

Meet us at ISMB 2019

Meet Markus at the ISMB/ECCB 2019 in Basel.

On Tuesday, Markus will give a talk about “SIRIUS 4: turning tandem mass spectra into metabolite structure information”.
There is also a corresponding poster in Session A (J-06) which will be presented on Tuesday 6:00pm-8:00pm.

SIRIUS 4.0.1 released

A new version of SIRIUS 4 is available for download.
SIRIUS 4.0.1 brings many bugfixes, user interface polishing and improved stability of the CSI:FingerID backend.

  • SIRIUS 4.0.1 now supports JAVA 9 and higher
  • The structures used to train CSI:FingerID are now available via the web service:

See our changelog for further details .

You can download SIRIUS with CSI:FingerID here.

SIRIUS 3 is not longer supported

We found a major bug in the web service of SIRIUS 3 which can also affect the stability of the new SIRIUS 4. Therefore we decided to shut down the web service of SIRIUS 3 immediately.

Please contact us () if you need to finish work that can only be done with SIRIUS 3. We will try to find a solution then.

Sirius release 3.4 is coming soon

During the next few days we will release Sirius 3.4

This will be a major release containing several changes on the command line interface.
You may have to adjust existing scripts to get them work with the finalized command line interface.