Markus Fleischauer

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.  

We are happy to announce that a major version upgrade of SIRIUS is available! Scroll to the bottom to get a visual impression of the changes.

SIRIUS 5 now includes the following new features and improvements:

• Lipid class annotation with El Gordo: Lipid structures that have the same molecular formula (usually belonging to the same lipid class) can be extremely similar to each other, often only differing in the position of the double bonds. These extremely similar structures may be even not differentiable by mass spectrometry at all. SIRIUS 5 now predicts the lipid class from the spectrum; when performing CSI:FingerID database search, all structure candidates that belong to this lipid class are tagged.
• Sub-structure annotation with Epimetheus: For experimentalists, CSI:FingerID search may seem like a black box. If you want to perform manual validation of CSI:FingerID structure candidates, Epimetheus now provides a direct connection between structure candidates and your input MS/MS spectra. Sub-structures of the structure candidate of your choice are generated by a combinatorial fragmenter and assigned to peaks in the MS/MS spectrum. The new Epimetheus view allows you to directly visualize and inspect these sub-structure annotations.
• Feature-rich spectrum viewer: Improved functionality of the SIRIUS spectrum viewer, including mirror plots of measured vs predicted isotope pattern.
• New LC-MS view: A new view in SIRIUS 5 that shows the extracted-ion chromatogram of a compound, including its detected adducts and isotopes. A traffic light allows for quick spectral quality assessment.
• CANOPUS now fully supports Natural Product Classes (NPC).
• Advanced filtering options on the compound list, including the new lipid class annotations.
• Support for additional spectrum file formats (.msp, massbank, .mat)
  
  

If you were previously using SIRIUS 4, please be aware of the following breaking changes:

• User authentication: A user account and license is now needed to use the online features of SIRIUS. The license is free and automatically available for non-commercial use. If your account is not automatically verified because your non-commercial research institution is not whitelisted yet, please contact us at . 
• New project space compression: Method level directories are now compressed archives to reduce number of files and save storage.
• Changed summary writing: Summary writing has been made a separate sub-tool (write-summaries). Summary files format has slightly changed. 
• Prediction / DB search split: The fingerid/structure sub-tool has been split into a fingerprint (fingerprint prediction) and a structure (structure db search) sub-tool. This allows the user to recompute the database search without having to recompute the fingerprint and compound class predictions. It further allows to compute CANOPUS compound class prediction without having to perform structure db search.
• Updated fingerprints: Updated fingerprint vector. Fingerprint related results of SIRIUS 4 projects may have to be recomputed to perform certain analysis steps (e.g. recompute db-search). Reading the projects is still possible and formula results are not affected.
• Custom database format change: Custom database format has changed. Custom databases need to be re-imported.
• GUI column rename: Some views in the GUI have been renamed to better reflect their position and role in the workflow.

For a quick overview on these new features and changes, visit our YouTube channel. Please refer to our online documentation for a more comprehensive overview and help us squash all remaining bugs by contributing at our GitHub!

SIRIUS 4.8.0 is out and releases the COSMIC confidence score to the wild. For more details on COSMIC see here.

We are happy to announce that a new version of SIRIUS is available. With that, CANOPUS now supports negative ion mode data. Additionally, we included more structure databases CSI:FingerID can search in, such as COCONUT (Sorokina & Steinbeck, 2020) and NORMAN (Brack et al., 2012). And in case an important database is missing: With the new version, you can import custom databases using the GUI.

Even more features:

• All molecular structures have been standardized using the PubChem standardization service, to make structures more consistent. This update was already reported for version 4.4 but kept bugging us; it should now be solved for good. The standardization has a (small but measurable) positive impact on CSI:FingerID’s performance. More importantly, you will find fewer cases where CSI:FingerID is doing “something really strange”; this strange behavior was often due to un-standardized structures.
• Breaking news: We renamed a few columns in the SIRIUS project space (see Changelog), to make column names more descriptive. Sorry about that; please make sure your downstream analysis is reading in the right columns.
• CSI:FingerID now uses the molecular formula-specific Bayesian network scoring from our ISMB 2018 publication. Integrating this new score was a huge effort, but again has a positive impact on CSI:FingerID’s performance.
• To allow for a smooth transition, you can continue to use SIRIUS 4.4 and the corresponding CSI:FingerID web service until November the 30th.
• Please help us to make SIRIUS great again: Report bugs using the SIRIUS GitHub repository, or send an email to .

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 .

A preprint of our paper “ZODIAC: database-independent molecular formula annotation using Gibbs sampling reveals unknown small molecules.” is now available: https://doi.org/10.1101/842740

ZODIAC takes advantage of the fact that an organism produces related metabolites. ZODIAC builds upon SIRIUS and reranks molecular formula candidates, optimizing annotations on whole datasets. By applying ZODIAC to multiple datasets we greatly increased the number of correct annotations and identified novel molecular formulas which are not present even present in PubChem.

ZODIAC will be made available in an upcoming release of the SIRIUS software.