Coming soon…
  • GUI: Better progress information for running jobs
  • more bugfixes ;-)
  • fix: prevent Nullpointer in CANOPUS View filter box
  • improvement: allow to store projectspace copy as directory (not compressed)
  • fix: error when using external path for custom dbs in the CLI (#4)
  • fix: wrong log directory that might prevent SIRIUS from starting.
  • feature: improved filtering options for the compound list in the GUI
  • feature: MS1 only data can now be imported using the CLI (--allow-ms1-only) to perform isotope pattern based molecular formula identification #28.
  • change: changed tanimoto algorithm form probabilistic to rounded to dramatically reduce running time for large structure candidate lists, see #43
  • change: --db=BIO is now the default in the CLI, see #43
  • fix: wrong adduct for adduct switch annotated spectra in project-space output.

  • dev feature: hidden parameter to skip project validation for testing purposes see, #42

  • minor bug fixes and improvementss
  • critical-fix: custom database importer wrote cache files to working directory instead to the usual casche dir
  • fix: problems with the deletion and creation of custom databases (GUI)
  • improvement: local database cached can be cleare from the settings panel (GUI)
  • feature: COSMIC - confidence score
  • improvement: new Object storage baackend
  • improvement: resizeable compound list (GUI)
  • improvement: CSI:FingerID and SIRIUS/ZODIAC scores in formula selector (GUI)
  • fix: new CLP dll should improve compatibility on windows (NO Solver found problem)
  • fix: intensity bug in FBMN export
  • fix: CONFIG already exists error during background computations (FBMN export, custom-db import)
  • fix: .cef file extension missing in file import dialog
  • fix: java.util.ConcurrentModificationException when computing subtool separately with the CLI
  • fix: fixed missing jar/zip provider in bundled jre -> Zipped project-spaces are now working again
  • fix: fixed ignored custom.config and config inheritance
  • feature: Heuristic computation for fragmentation trees to improve running times for high mass compounds (no ILP has to be computed)
  • feature/improvement: Summaries
    • new formula_identifications_adducts.tsv summary file
    • new canopus_summary_adducts.tsv summary file
    • added fromulaRank to compound_identifications.tsv and compound_identifications_adducts.tsv
    • fix: inconsistent ranking in compound_identifications.tsv and compound_identifications_adducts.tsv
  • improvement: more information about running jobs (compound information), improved log panel
  • improvement: All SIRIUS distros ship with start scripts that should handle env variables properly
  • improvement: rounded values for similarity matrix output
  • improvement: better progress information during import
  • improvement: CSI:FingerID adn CANOPUS summaries with multiple adducts (like the formula summary)
  • improvement/fix: Multithreading and performance issues of integrated CLP ILP solver
  • improvement/fix: GUI Job cancelling now works properly, even under high load
  • improvement/fix: improved caching and update mechanisms prevents GUI freezes and reduces GUI memory consumption when computing large data sets
  • improvement/fix: much lower memory consumption when writing summaries

  • fix: memory leak in jjob job manager lib - dramatically improves performance on large datasets.
  • fix: correct handling of CHARGE=-0 in mgf
  • fix: corrupted project-space caused by empty adduct detection results after mgf import
  • fix: empty project dir after wrong command
  • fix: wrong compound name in compound edit panel
  • fix: invalid valence filter error when computing positive and negative ion mode together fix: compound timeout not working reliable
  • fix: Commercial ILP solver not detected correctly even if the correct env variable was set
  • fix: CEF format import - “No proper interval given” error
  • fix: multiOS build architecture now OpenMS compatible
  • several minor bug fixes

  • upgrade: SIRIUS ships now with JRE-15 which should fix jvm crashes during heavy multi threading on linux
  • fix: CSI:FingerID results were not refreshed correctly after recomputing with different parameters in the GUI
  • fix: Parameters were not always handled correctly when recomputing with the GUI
  • fix: Index bug in fragmentation tree scoring
  • feature: standalone subtool (ftree-export) to export fragmentation trees from CLI
  • feature: --noCite command to disable bibliography print in CLI
  • improvement: bibliography is not printed when showing help message or command parsing error
  • fix: another problem with un-importable projects due to detected adducts
  • fix: ZODIAC crash caused by empty spectra
  • fix: invalid project-space (not importable) due to empty detected adducts
  • fix: uncatched exception during adduct resolution (GitHub issue #9)
  • Merry X-Mas
  • improvement: CLP native libs are now compatible with glibc 2.12+ (instead of 2.18+)
  • fix: project-space with outdated fingeprint versions (e.g. from SIRIUS 4.4) are now handled correctly and can be converted.
  • fix: database formulas could be used if candidates even if they were incompatible with the adduct
  • fix: mzml/mzxml files are now shown in input file selector
  • feature: CANOPUS: for negative ion mode data
  • feature: Bayesian (individual tree) scoring is now the default for ranking structure candidates
  • update: Structure DB update due to major changes in PubChem standardization since the last one.
    • feature: COCONUT, NORMAN and Super Natural are now officially supported
  • feature: Custom-DB importer View (GUI)

  • feature: mgf export for Feature Based Molecular Networking is now available in the GUI

  • breaking: additional columns (ionMass, retentionTimeInSeconds) have been added to project wide summary files such as formula_identifications.tsv, compound_identifications.tsv and compound_identifications_adducts.tsv
  • breaking: column names in formula_candidates.tsv have changed: massError(ppm) to massErrorPrecursor(ppm), explainedPeaks to numExplainedPeaks, medianAbsoluteMassError(ppm) to medianAbsoluteMassErrorFragmentPeaks(ppm)
  • breaking: column names describing scores now use camel case instead of underscores: ConfidenceScore, SiriusScore, ZodiacScore,TreeScore,IsotopeScore, CSI:FingerIDScore

  • fix: incompatibility with recent MaOSX version caused by gatekeeper. We now provide an installable packages.
  • fix: missing SCANS annotation in mgf-export subtool - creates now a valid input for FBMN
  • fix: un-parsed retention times in CEF format.
  • fix: Structure DB linking (wrong ids, missing link flags, duplicate entries, etc.)
  • fix: reduced memory consumption of CLI and GUI

  • JRE is now included in all version of SIRIUS
  • Many more bug fixes and performance improvements

NOTE: SIRIUS versions will now follow semantic versioning (all upcoming releases) regarding the command line interface and project-space output.

  • fix: Error when parsing FragTree json with non numeric double values
  • fix: layout of screener progress bar on Mac
  • feature: Retention time will now be imported by SIRIUS
    • RT is shown in the Compound list in the SIRUS GUI and the list can be sorted by RT
    • RT is part of the file in the project-space
  • feature: Loglevel can now be changed from CLI
  • feature: Summaries can not be written without closing SIRIUS GUI
    • Improvement: Better progress reporting when Summary writing summaries (GUI)
  • fix: Agilent CEF files without CE can now be imported
  • feature: coin-or ilp solver (CLP) is now included. This allows parallel computation of FragTrees without the need for a commercial solver.
  • improvement: Compounds without given charge are can now be imported. SIRIUS tries to guess the charge from the name (keyword: pos/neg) or falls back to positive.
  • improvement: additional parameters in compute dialog
  • improvement: commands of the ‘show command’ dialog can now be copied
  • fix: error when writing/reading fragmentation trees with new Jackson parser
  • fix: mgf exporter (CLI) now outputs feature name properly
  • fix: deadlock during connection check without internet connection
  • fix: tree rendering bug on non linux systems
  • fix: crash when aborting recompute dialog
  • upgrade (GUI): included JRE to zulu11.41.23-ca-fx-jre11.0.8
  • fix: deadlock and waiting time due to webservice connections
  • fix/improvement: Adduct Settings and Adduct detection
  • fix: memory leak in third party json lib -> Zodiac memory consumption has been reduced dramatically
  • fix: several minor bug fixes in the sirius libs
  • fix: removed spring boot packaging to
    • solve several class not found issues,
    • solve github issue #7
    • errors when importing and aligning mzml files.
    • improve startup time
  • fix: cosine similarity tool ignores instances without spectra (failed before)
  • fix: mgf-export tool skips invalid instances if possible (failed before)
  • instance validation after lcms-align tool
  • feature: ms2 istotope scorer now available in cli and gui
  • fix: wrong missing value handling in xlogp filter (some candidates were invisible)
  • improvement: less cores for computations if gui is running to have mor cpu time for GUI tasks
  • improvement: show deviation to target ion in FragTree root if precursor is missing in MS/MS
  • fix: Classloader exceptions when using CLI from the GUI version
  • fix: Wrong mass deviation for trees with adducts
  • fix: misplaced labels when exporting svg/pdf fragtrees
  • fix: some minor GUI bugs
  • fix: incompatibilities with existing configs from previous versions (.sirius)
  • fix: CANOPUS detail view has size zero
  • fix: failing CSI:FingerID computation with Zodiac re-ranking and existing Adducts
  • improvement: errors that occur before GUI is started are now reported
  • improvement: minor GUI improvements
  • fix: some more fixes on MacOS GUI freezes
  • fix: GUI Deadlock on MacOS X fixed. Mac version is now available.
  • improvement: Character separated files in project-space have now .tsv extension for better excel compatibility.
  • feature: Windows headless executable respects %JAVA_HOME% as JRE location.
  • improvement: Improved packaging and startup of the GUI version
  • fixes GitHub issues: 4 and 6
  • feature: CSI:FingerID for negative ion mode is available
    • NOTE: CANOPUS for negative mode data is not ready yet and will still take some time.
  • fix: Too small Heapsize on Windows
  • improvement: better GUI performance
  • feature: CLI Sub-Tool to export projects to mgf.
  • feature: multiple candidate number for Zodiac.
  • fix: zodiac score rendering.
  • fix: deadlock project-space import
  • fixes: tree rendering
  • improvement: import and deletion performance
  • improvement: import progress now shown
  • fix: MacOS included JRE not found.
  • fix: ignored parameters.
  • fix: recompute does not correctly invalidate and delete previous results.
  • fix: UI now correctly update when data will by deleted by the computations.


  • New (and newly integrated) tools:
    • CANOPUS:: A tool for the comprehensive annotation of compound classes from MS/MS data.
    • ZODIAC: Builds upon the SIRIUS molecular formula identifications and uses, say, its top 50 molecular formula annotations as candidates for one compound. It then re-ranks molecular formula candidates using Bayesian statistics.
    • PASSATUTTO: Is now part of SIRIUS and allows you to generate dataset specific decoy databases from computed fragmentation trees.
    • Other handy standalone tools e.g. compound similarity calculation, mass decomposition, custom-db creation and project-space manipulation.
  • Project-Space: A standardized persistence layer shared by CLI and GUI that makes both fully compatible.
    • Save and reimport your projects with all previously calculated results.
    • Review your results computed with the CLI in the GUI.
    • Handy project-space summary CSV and mzTab-M files for downstream analysis.
    • Preojects can be stored and modified as directory structure or as compressed archive.
  • LCMS-Runs: SIRIUS can now handle full LCMS-Runs given in mzML/mzXML format and performs automatic feature detection.
    • The lcms-align preprocessing tool performs feature detection and feature alignment for multiple LCMS-Runs based on the available the MS/MS spectra.
  • Redesigned Command line interface: SIRIUS is now a toolbox containing many subtools that may be combined to ToolChains based on the project-space.

  • CSI:FingerID had some massive updates, including more and larger molecular properties.
    • Structure DBs New version of the CSI:FingerID PubChem copy that now uses PubChem standardized structures.
    • NORMAN is now available as search DB
    • All available database filters can now be combined to arbitrary subsets for searching (even with custom databases).
  • Interactive fragmentation tree viewer with vector graphics export in the GUI.
  • New REST service with openAPI specification and Swagger-UI.
  • Java 11 or higher is now mandatory
    • GUI version ships with an integrated JRE
  • Many minor improvements and Bugfixes


  • Java 9 and higher are now supported
  • CSI:FingerID trainings structures available
    • Trainings structures available via WebAPI.
    • Trainings structures are flagged in CSI:FingerID candidate list.
  • SMARTS filter for candidate list (GUI)
  • Molecular Property filter for candidate list (GUI)
  • Available prediction workers of the CSI:FingerID webservice can be listed from SIRIUS
  • Improved connection handling and auto reconnect to Webservice
  • Improved error messaged
  • Improved stability and load balancing of the CSI:FingerID webservice
  • Several bug fixes


  • Fragmentation tree heuristics
  • Negative ion mode data is now supported
  • Polished and more informative GUI
    • Sirius Overview: Explained intensity, number of explained peaks, median mass deviation
    • Fragmentation trees: Color coding of nodes by intensity/mass deviation, more informative Fragmentation tree nodes
    • CSI:FingerID Overview: Number of Pubmed publication with pubmed linking for each Candidate, Visualization of CSI:FingerID score.
    • Predicted Fingerprints: Visualisation of prediction (posterior probability), predictor quality (F1) and number of training examples.
    • Several small improvements
  • CPLEX ILP solver support
  • Consider a specific list of ionizations for Sirius
  • Consider a specific list of adducts for CSI:FingerID
  • Custom ionizations/adducts can be specified (CLI and GUI)
  • Full-featured standalone command line version (headless version)
  • Improved parallelization and task management
  • Improved stability of the CSI:FingerID webservice
  • Time limit for fragmentation tree computations
  • Specify fields to import name and ID from .sdf into a custom database (GUI).
  • CSI:FingerID results can be filtered by Custom databases (GUI).
  • Better filtering performance (GUI)
  • Bug fix in Database filtering view (GUI)
  • Error Reporter bug fixed (GUI)
  • Logging bugs fixed
  • Many minor bug fixes


  • Custom databases can be imported by hand or via csv file. You can manage multiple databases within Sirius.
  • New Bayesian Network scoring for CSI:FingerID which takes dependencies between molecular properties into account.
  • CSI:FingerID Overview which lists results for all molecular formulas.
  • Visualization of the predicted fingerprints.
  • ECFP fingerprints are now also in the CSI:FingerID database and do no longer have to be computed on the users side.
  • Connection error detection and refresh feature. No restart required to apply Sirius internal proxy settings anymore.
  • System wide proxy settings are now supported.
  • Many minor bug fixes and small improvements of the GUI


  • element prediction using isotope pattern
  • CSI:FingerID now predicts more molecular properties which improves structure identification
  • improved structure of the result output generated by the command line tool to its final version


  • fix missing MS2 data error
  • MacOSX compatible start script
  • add proxy settings, bug reporter, feature request
  • new GUI look


  • integration of CSI:FingerID and structure identification into SIRIUS
  • it is now possible to search formulas or structures in molecular databases
  • isotope pattern analysis is now rewritten and hopefully more stable than before


  • fix bug with penalizing molecular formulas on intrinsically charged mode
  • fix critical bug in CSV reader


  • Sirius User Interface
  • new output type -O sirius. The .sirius format can be imported into the User Interface.
  • Experimental support for in-source fragmentations and adducts


  • fix crash when using GLPK solver


  • fix bug: SIRIUS uses the old scoring system by default when -p parameter is not given
  • fix some minor bugs


  • if MS1 data is available, SIRIUS will now always use the parent peak from MS1 to decompose the parent ion, instead of using the peak from an MS/MS spectrum
  • fix bugs in isotope pattern selection
  • SIRIUS ships now with the correct version of the GLPK binary


  • release version