Changelog

SIRIUS 6

6.0.6 (2024-09-28)

fixed: When importing large mzml/mzxml runs, the feature list filter is not refreshed properly after import.
fixed: Problem when deleting feature via GUI filtering
fixed: Empty list of affected Compound and feature IDs when importing mzML/mzXML files via /import/ms-data-files API endpoint.
fixed: Error handling for fiels with empty values for given key in .mat/.msp parser
fixed: Number of explained peaks incorrect for in-source losses.
fixed: Enforced adducts ignored during formula computation
fixed: GNPS FBMN does not work with SIRIUS files (https://github.com/sirius-ms/sirius/issues/167)
fixed: Cannot enforce adducts for features detected as multimere
fixed: Missing Ids in API fragtree export (https://github.com/sirius-ms/sirius/issues/199)
fixed: ZODIAC score is missing from the formula_identifications file.
fixed: MGF parser cannot parse CHARGE=- or CHARGE=+`
fixed: Formula candidates and adducts introduced by spectral library search are not reset correctly during recompute
fixed: Adducts from LCMS preprocessing may be ignored if not part of detectable adducts.
fixed: SDF custom database import with spectra cancels the import if one compound in the file has invalid spectrum data.
improvement Show all detected adducts in the GUI
improvement Export summary in ChemVista compatible csv format.
improvement Export summary files as CSV and XLXS
improvement Scrollable Quality assessment panel
improvement Temprorary unavailable custom-dbs are no longer permanently removed from SIRIUS.
improvement Sort features by RT in summary files
improvement: data quality summary renamed to feature quality summary
improvement https://github.com/sirius-ms/sirius/issues/159
improvement Renamed SIRIUS java sdk package to sirius-sdk
Known Issues: Sometimes all jobs of a computation are finished but the Gui compute button and feature list stays in compute state. This issue has *not- yet been resolved but a workarount has been added to reset the state and make the gui controllable again when clicking Cancel all. However, after doing so SIRIUS needs to be restarted to work properly again.

6.0.5 (2024-09-02)

improvement: new export options and file formats for writing summaries in the CLI and GUI
improvement: export of data quality summaries
improvement: lcms-align is automatically executed in the CLI when importing .mzML / .mzXML files

6.0.0 (2024-06-03)

feature: de novo generation of candidate structures through MSNovelist
feature: spectral library matching
feature: expansive search allows for structure database searches in user-selected databases with a confidence score-based fallback on PubChem
feature: additional molecular formula generation strategy via bottom-up serach
feature: SIRIUS service via REST API including Python SDK
improvement: CANOPUS is automatically executed together with the fingerprint prediction
improvement: entire adduct is now used already for the first step of the annotation workflow
improvement: updated fingerprint model; now consistent between positive and negative ion mode
improvement: LCMS data preprocessing also include MS1-only features
improvement: LCMS quality tags for features
improvement: compute dialog has been streamlined to improve clarity
improvement: transition from a file-based project space to a Nitrite database

SIRIUS 5

5.8.4 (2023-11-04)

fixed problem with summary files writing of CANOPUS predictions
fixed bug where filtering of features would result in omitting features with no available confidence score
added option to ignore molecular formulas during file import in the GUI

5.8.0 (2023-07-01)

breaking: rankings and ranking cloumn names of summary files have changed
improvement: added feature id support from several input formats.
improvement: added feature id as separate fields to project wide summary files
improvement: change display name of ConfidenceScore from COSMIC to Confidence
improvement: added support for .mat PEAKID field
improvement: added support of 1-/1+ charge notation in mgf parser
fix wrong ranks in summary files
fix: missing adducts in CanopusSummaryWriter
fix: missing adducts in FormulaSummaryWriter
fix: bug with wrong NPC classes in Canopus summary files
fix: null value problem with MS-Dial msp/mat files

5.7.3 (2023-06-14)

improvement: Buffered parallelization for Fingerprinter subtool
improvement: use internal browser as fallback for User Portal if system browser not available.
- fix: fixes bug where account creation and management not possible with conda version of SIRIUS

5.7.2 (2023-05-26)

build: SIRIUS docker Image not on dockerhub
fix: Fixed maxRetentionError getting too small, introduced minError

5.7.1 (2023-05-20)

feature: Added compound quality flags to Scripting API
improvement: db import dialog, error handling and description
Fix: Fixed MS1<->MS2 switch bug

5.7.0 (2023-05-19)

//todo coming soon

5.6.3 (2023-01-12)

improvement: compounds can now be filtered by cosmic/confidence score (GUI)
improvement: added .version file to project-space that contains SIRIUS version information.
fix: unreachable availability check url for authentication server which prevented the login request message from occurring.
fix: fixed bug when selecting all database flag in cli. I behaves now like selecting all databases in the GUI.
fix: fixed some missing default values in the GUI.
fix: fixed handling of preset molecular formulas. .ms and .mgf inputs should now behave equally.
fix: fixed custom db handling in sirius/formula step. custom database can now be used as formula candidate list instead of denovo.
fix: fixed custom database import which did crash in 5.6.2
fix: fixed some typos
5.6.2 (2022-11-03)
fix: bug that prevents accepting license terms caused by mising content-length header in the request.
5.6.1 (2022-10-28)
feature: improved progress information for background computations.
feature: new scheduling of remote jobs that reduces computation time and improves local cpu utilization.
feature: A Beta version of the new SIRIUS background service is now included in the respective build (service suffix).
feature: support for MS1 only data in GUI (Isotope Pattern analysis only).
- MS1 only data from Agilent CEF format can now be imported
feature: command line autocompletion support for Linux and MacOS. See sirius --help for details.
feature: allow to write uncompressed (legacy) project-spaces via --no-compression pearameter
improvement: improvements on feature finding and feature alignment
improvement: more robust custom database importer. Support to import existing DBs into the GUI.
fix: fixed bug in feature finding that changed negative ion mode data to positive ion mode
fix: fixed inconsistent indexing of aligned and not aligned mzml/mzxml data that caused an invalid FBMN output.
- possibly breaking change: SIRIUS internal compound index does now start at 1 instead of 0
fix: several smaller fixes and improvements

5.5.2

fix: Collsion energy parsing bug
feature: Update checker

5.4.1

breaking: User Authentication. A user account and license is now needed to user the online features of SIRIUS. The license is free and automatically available for non-commercial use, details here.
breaking: New project-space compression. Method level directories are now compressed archives to reduce number of files and save storage.
breaking: Summary writing has been moved to a separate sub-tool (write-summaries). Som summary files have slightly changed. Usually just additional columns if at all.
breaking: 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.
breaking: Updated Fingerprint vector. Fingerprint related results of SIRIUS 4 projects might have to be recomputed to perform some modification (e.g. recompute db-search). Reading the projects is still possible and formula results do not affected.
breaking: Custom database format has changed. Custom databases need to be re-imported
feature: Tool - El Gordo lipid class annotation.
feature: GUI Tool - Epimetheus sub-structure annotation. Combinatorial fragmentation of CSI:FingerID candidates to assign fragment peaks to sub-structures of the candidate.
feature: GUI View - New feature rich spectrum viewer. Mirror-plot to compare Isotope pattern and Simulated isotope pattern (e.g. ).
feature: GUI View - LC-MS view to review chromatographic peak and data quality report for a given feature/compound
feature: CANOPUS now fully supports NPC classes (prediction, GUI and output)
feature: GUI advanced filtering options
feature: GUI scaling factor can be defined by the user (setting panel)
feature: Additional file formats for spectrum import supported (.msp, massbank, .mat)

SIRIUS 4

4.9.3

fix: prevent Null-pointer in CANOPUS View filter box
improvement: allow storing project-space copy as directory (not compressed)

4.9.2

fix: error when using external path for custom dbs in the CLI (#4)

4.9.1

fix: wrong log directory that might prevent SIRIUS from starting.

4.9.0

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

4.8.2

critical-fix: custom database importer wrote cache files to working directory instead to the usual casche dir

4.8.1

fix: problems with the deletion and creation of custom databases (GUI)
improvement: local database cached can be cleare from the settings panel (GUI)

4.8.0

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)

4.7.4

fix: intensity bug in FBMN export

4.7.3

fix: CONFIG already exists error during background computations (FBMN export, custom-db import)
fix: .cef file extension missing in file import dialog

4.7.2

fix: java.util.ConcurrentModificationException when computing subtool separately with the CLI

4.7.1

fix: fixed missing jar/zip provider in bundled jre -> Zipped project-spaces are now working again
fix: fixed ignored custom.config and config inheritance

4.7.0

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

4.6.1

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

4.6.0

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

4.5.3

fix: ZODIAC crash caused by empty spectra

4.5.2

fix: invalid project-space (not importable) due to empty detected adducts
fix: uncatched exception during adduct resolution (GitHub issue #9)
Merry X-Mas

4.5.1

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

4.5.0

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.

4.4.29

fix: Error when parsing FragTree json with non numeric double values
fix: layout of screener progress bar on Mac

4.4.28

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 compound.info 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

4.4.27

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

4.4.26

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

4.4.25

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

4.4.24

feature: ms2 istotope scorer now available in cli and gui

4.4.23

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

4.4.22

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

4.4.21

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

4.4.20

fix: some more fixes on MacOS GUI freezes

4.4.18

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

4.4.16

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

4.4.15

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

4.4.14

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.

4.4.(0-13)

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

4.0.1

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

4.0

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
SIRIUS 3

3.5
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

3.4

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

3.3

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

3.2

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

3.1.3

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

3.1.0

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

3.0.3

fix crash when using GLPK solver

3.0.2

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

3.0.1

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

3.0.0

release version

Changelog

SIRIUS 6

6.0.6 (2024-09-28)

6.0.5 (2024-09-02)

6.0.0 (2024-06-03)

SIRIUS 5

5.8.4 (2023-11-04)

5.8.0 (2023-07-01)

5.7.3 (2023-06-14)

5.7.2 (2023-05-26)

5.7.1 (2023-05-20)

5.7.0 (2023-05-19)

5.6.3 (2023-01-12)

5.6.2 (2022-11-03)

5.6.1 (2022-10-28)

5.5.2

5.4.1

SIRIUS 4

4.9.3

4.9.2

4.9.1

4.9.0

4.8.2

4.8.1

4.8.0

4.7.4

4.7.3

4.7.2

4.7.1

4.7.0

4.6.1

4.6.0

4.5.3

4.5.2

4.5.1

4.5.0

4.4.29

4.4.28

4.4.27

4.4.26

4.4.25

4.4.24

4.4.23

4.4.22

4.4.21

4.4.20

4.4.18

4.4.16

4.4.15

4.4.14

4.4.(0-13)

4.0.1

4.0

SIRIUS 3

3.5

3.4

3.3

3.2

3.1.3

3.1.0

3.0.3

3.0.2

3.0.1

3.0.0