Issue with Metabolomics-SNETS-V2: Empty job and no networks

[Pauline Lindholm]

Hi Everyone,

I have completed my Metabolomics-SNETS-V2 job without any reported errors. However, upon downloading the associated Cytoscape file, I noticed that it is empty, with no networks present. Additionally, the job file size is reported as 0 mb. I have verified that my .mzXML files contain data, so I am uncertain about the cause of the issue. 

Has anyone else encountered a similar issue, or does anyone have insights into what might be causing this?

One potential factor could be the process used to generate the .mzXML files.

Here is the workflow I followed:

• Data was acquired on a Waters instrument.

• The data was processed using Waters' UNIFI software and exported as a .mgf file.

• The .mgf file was then converted to .mzXML using MSConvert.

• The .mzXML files were uploaded to GNPS and then used to create a new job using the Metabolomics-SNETS-V2.

Thank you for your time and assistance.

Best regards,

Pauline

[Mingxun Wang]

Likely the issue is your doing feature finding in Unifi and then clustering in classical networking. Turn off clustering in networking. 

Ming

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[TonioG]

Hi Pauline,

We have two Waters instruments, one with MassLynx and one with UNIFI. This last one can generate mzML file directly, without using MSConvert, which might be dangerous using with Waters data.

Just make sure that you use the last version of UNIFI (the unbugged one), since the previous one did not generate mzML which were usable. 

Antonio