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:
https://bio.informatik.uni-jena.de/repository/list/dist-snapshot-local/de/unijena/bioinf/ms/sirius/4.4.0-SNAPSHOT/
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 .

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.

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+CSI:FingerID for Mac OSX

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

Gastvorlesung Ivo Große

Ivo Große von der Universität Halle wird uns am 13. Januar besuchen und eine Gastvorlesung zum Thema Motif Finding und EM-Algorithmus halten – klassische Themen der Bioinformatik, die in Jena leider nicht mehr gelehrt werden.

Die Vorlesung findet am Mittwoch den 13. Januar von 9:30 bis 12:00 Uhr im Seminarraum 119, August-Bebel-Str. 4 statt.

Die Veranstaltung ist für alle Studierenden der Bioinformatik, insbesondere für alle Master-Studenten interessant. Alle Interessierten sind herzlich eingeladen.