SIRIUS is a Java-based software framework for the analysis of LC-MS/MS data of metabolites and other small molecules of biological interest. It integrates a collection of tools, including CSI:FingerID (with COSMIC), ZODIAC and CANOPUS. Both the graphical user interface and the command line version seamlessly integrate the CSI:FingerID, CANOPUS and MSNovelist web services, and the packaged Windows version includes the Java Runtime Environment.
What's new in 6.5.4
feature: Searchable projects & advanced filtering. Projects now carry a full text search index over their features, which is the basis for the new query and filter capabilities.
Smart query Bar: Located above the feature list with auto-complete suggestions for fields, operators, and known values (e.g., adduct spellings, lipid class abbreviations, compound class ontologies, and tags). Press Enter to apply. (GUI)
Unified filtering: Manual panel filters and typed search queries merge into a single filter. The standard filter dialog remains accessible via the funnel icon. (GUI)
Bulk cleanup: Delete all non-matching features from a project in a single step in the GUI or directly by query in a single API request--eliminating the need to fetch and send back IDs.
Index management: The search index builds automatically during data import and can be rebuilt anytime from Project Settings if out of sync. (GUI)
Query metadata endpoint: The searchable-fields endpoint exposes queryable fields, value types, word-search support, and sortability. (API)
Filter quantification tables directly using search queries. (API)
Legacy support: Existing CLI feature filter flags (--mzmin, --rtmax, --quality, etc.) remain unchanged and run independently of the search index. (CLI)
Projects created with older SIRIUS versions automatically migrate and index upon first open.
Single-click "Restore Defaults" button for feature filters. New single-adduct filter preset.
feature: Build custom structure databases using reaction rules. Choose from built-in reaction library or create own reactions. Support for multi-product reactions. Inclusion of intermediate products in the final database. (GUI)
feature: Inspect and browse the contents of custom-built structure databases directly within the GUI.
feature: Tag objects within a project to group data and compute fold changes. Tagging is used for blank subtraction and to mark PFAS candidates. Custom tag management is currently API-only (these endpoints are still experimental and may change)
feature: PFAS and special element detection: Integrated specialized PFAS candidate detection automatically detects strong polyfluorination signatures. Elements are now predicted for both de novo formula generation and exclusions in database/bottom-up searches. …
Yes. SIRIUS is free and open-source software released under the AGPL-3.0 license.
What is the latest version of SIRIUS?
The latest version is 6.5.4, released on Aug 25, 2026.
Is it safe to download SIRIUS?
The download button links to the official installer published on github.com, the same file Windows Package Manager installs. You can verify the downloaded file by comparing its SHA-256 checksum with 0254ad8fddc51196dd78e94c894c13158d328eb7c22c2047d14fb76209bed590.
Which Windows versions does SIRIUS support?
SIRIUS runs on Windows and is available for 64-bit (x64) systems.
How do I install SIRIUS silently?
Run the offline installer with msiexec /i "sirius-6.5.4-win-x64.msi" /quiet /norestart, or install it with Windows Package Manager: winget install --id=SiriusMS.SIRIUS -e --silent.
How do I uninstall SIRIUS?
Open Settings › Apps › Installed apps, find SIRIUS and select Uninstall. From the command line, run winget uninstall --id=SiriusMS.SIRIUS -e.
Alternatives to SIRIUS
Other Command Line Tools programs for Windows from different developers.
The Azure command-line interface (Azure CLI) is a set of commands used to create and manage Azure resources. The Azure CLI is available across Azure services and is designed to get you working quickly
