visit this link

https://mzmine.github.io/mzmine_documentation/index.html

Actually, I followed these steps either documented in link or videos but the results don’t appear.

I tried it in MZmine2, it worked and identified the metabolites but another problem; the online database search as pubchem and KEGG identified the metabolites as synthetic metabolites but they are metabolites extracted from plants.

Yasmin Mounir Based on your description, it seems that you are experiencing an issue with the MZmine 3 software during the annotation step, specifically with the spectral identity showing up empty even after uploading or importing a MONA database from MassBank. While I can provide some insights, it's important to note that the specific cause of the issue may require further investigation.

Here are a few possible reasons why the spectral identity might be empty in MZmine 3:

1. Compatibility: Ensure that the MONA database you imported from MassBank is compatible with MZmine 3. Different versions or formats of the database might have varying compatibility, so double-check if the database format is supported by MZmine 3.

2. Database Format: Verify that the MONA database is in a format that is recognized by MZmine 3 for spectral library search. MZmine 3 typically supports formats like mzML or mzXML for spectral libraries. If the database is not in the correct format, you might need to convert it to a compatible format using appropriate tools or software.

3. Parameters Configuration: Review the parameters you have set for the spectral library search. Ensure that the search parameters, such as precursor mass tolerance, fragment mass tolerance, or scoring thresholds, are properly adjusted for your specific dataset and analysis. Adjusting these parameters might improve the identification results.

4. Database Quality: Consider the quality and completeness of the MONA database itself. If the database does not contain matching spectra or has limited coverage of your experimental data, it may result in empty spectral identities. Check the database's content and verify if it includes spectra relevant to your sample.

Regarding your question about whether the issue is related to Java or R software, MZmine 3 is primarily developed in Java and utilizes various libraries for data processing and analysis. It is less reliant on R software. However, to utilize certain advanced functionalities or data analysis methods, MZmine 3 can integrate with R scripts. In this case, the issue with empty spectral identity is unlikely to be directly related to Java or R, but rather with the specific configuration or compatibility of the software and data.

To troubleshoot further and find a solution, you can consider the following steps:

1. Consult MZmine 3 Documentation: Review the official MZmine 3 documentation, user guides, or tutorials to ensure that you are following the correct steps for annotation and spectral library search. The documentation may provide specific instructions or troubleshooting tips for the issue you are facing.

2. MZmine 3 User Community: Reach out to the MZmine 3 user community through forums, mailing lists, or online groups. Other users might have encountered similar issues and could provide insights or suggestions based on their experiences.

3. Software Updates: Ensure that you are using the latest version of MZmine 3. Check for any available software updates or bug fixes that might address the issue you are facing. Updating to the latest version could potentially resolve the problem.

4. Contact the Developers: If you have followed the above steps and are still unable to resolve the issue, consider contacting the developers or support team of MZmine 3 directly. They will have a deeper understanding of the software and may be able to provide more specific guidance or assistance.

Remember to provide detailed information about your data, the steps you have followed, and any error messages or warnings you have encountered. This will help the community or developers better understand the issue and provide relevant solutions.