ZODIAC performs de novo molecular formula annotation on complete biological datasets (high-resolution, high mass accuracy LC-MS/MS runs). In order to use ZODIAC, please download SIRIUS 4.4; ZODIAC is integrated.  SIRIUS ranks molecular formulas for each compound individually using fragmentation trees and isotope pattern analysis. ZODIAC takes the fragmentation trees as input and reranks the molecular formula candidates by taking similarities of compounds in the dataset into account.

Please, download the appropriate SIRIUS version for your operating system, here. You need version 4.4 or higher.
The GUI version (which also includes the full command line version) requires no external JRE. Everything ist included. Download, extract, execute.
Systems should have a least 8GB of RAM (more RAM required for large datasets)


SIRIUS documentation

Demo data

Download the demo data here and extract it. Follow the step-by-step guide below to run ZODIAC (or see the README.txt for command line parameters).

Drag and drop the directory including the 2 mzML files (“mzML_dir”) into SIRIUS. Select to align both files:

Now select “compute all”

Select SIRIUS and ZODIAC. Increase the number of reported candidates for SIRIUS, to increase the chance that the correct molecular formula candidate is contained in the result list. Click “compute”.

After computations are finished, molecular formulas are ranked based on the ZODIAC score.

Some notes on your data

ZODIAC assumes that compounds co-occur in a network of derivatives. Similarities are judged based on fragments. Data quality has a direct influence on performance. MS/MS spectra should have enough fragments. Preceding blank subtraction is advised. ZODIAC is not suited for data with many chimeric compounds (MS/MS spectra of multiple compounds). Use a sufficiently small isolation window when measuring the data. Your data should contain some hundred compounds to see a reasonable effect of the ZODIAC reranking.


ZODIAC has been evaluated and considerably improves correct annotations. The evaluation data and a virtual machine for reproduction purposes is available in our data section. We used this modified OpenMS version. This is the source code of the SIRIUS CLI and the SIRIUS/ZODIAC libraries.