Markus Fleischauer

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:
  • https://www.csi-fingerid.uni-jena.de/webapi/trainingstructures.csv?predictor=pos
  • https://www.csi-fingerid.uni-jena.de/webapi/trainingstructures.csv?predictor=neg

See our changelog for further details .

You can download SIRIUS with CSI:FingerID here.

On July 8, 2018, the CSI:FingerID web service has passed five million compound queries. Awesome!

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.

Our new version, Sirius 3.5, comes with several advancements. Download and use it here.
We have a new overview tab for CSI:FingerID hits which displays results of structure search for multiple molecular formulas.
You can examine the predicted fingerprint of each compound (and molecular formula) independently of any database.
We now offer the possibility to create and search in custom structure databases.
Besides, we have a new bayesian networks scoring function for CSI:FingerID which considers dependencies between different molecular properties.
This and much more.

A new Sirius version is available. We included new features to enable a more intuitive workflow. We hope you’ll like it. Download and use it here.
We provide element prediction using isotope pattern. CSI:FingerID now predicts more molecular properties which improves structure identification.
Besides we fundamentally changed the structure of the result output generated by the command line tool to its final version. This means you might have to adjust  your workflow.

SIRIUS+CSI:FingerID is no available for Mac. You can download it here. A few highlights of the new version:

• Searching your tandem mass spectra in molecular databases using CSI:FingerId
• Restrict the SIRIUS molecular formula identification to formulas appearing in molecular databases – or search through the whole space of possible formulas. It’s up to you.
• Sort you identification results by confidence such that more reliable identifications (e.g. from high quality spectra or easy recognizable compounds) are separated from bogus identifications.
• Predict structural features and substructures from tandem mass spectra and visualize them in your candidate structure list.

Don’t hesitate to give us your feedback, report bugs or suggesting new features. Just write to