Inquiry Regarding MS1 + DDA Spectra Processing

MetaboAnalyst
1

I have an issue using the “Spectra Processing” functionality in MetaboAnalyst 6.0 for an MS + DDA experiment.

Despite following the guidelines, I am unable to obtain any MS/MS data in the results, only putative annotations based on the scan.
Here is a summary of my workflow:

  1. I am working with test samples (n=3) acquired in DDA mode on a Thermo Q Exactive instrument.
  2. The raw files were converted using ProteoWizard’s MSConvert (MS level 1 → 2), following the provided guidelines. I also created copies renamed with the “MS2_” prefix of the same files.
  3. In the parameter settings for MS2 processing, I selected “All features” as the target option.
  4. After processing, I noticed that the results do not include any MS/MS-related data or annotations, only putative identifications based on MS1 scans.

I have reviewed the guidelines and tried troubleshooting the issue, but I have not been able to resolve it. Could someone provide guidance on what might be causing this issue?
Thank you

2

Hi GiulianDS,

Please follow the 3rd example from the data uploading page, and remember to label the MS2 group as “MS2”.
If you still have the same issue, please share your detailed steps and dataset with me.

Bests,
Zhiqiang