MSDIAL.v5.5.260323 failed to deconvolve timsMetabo dia-PASEF data

[ptpb781209069]

Dear MS-DIAL team,

I encountered an issue when processing timsMetabo dia-PASEF data using MSDIAL.v5.5.260323.
After downloading and extracting MS-DIAL, I had to manually update timsdata.dll in .\lib\Bruker with the latest version downloaded from Raw Data Access & API before the software could read and process the timsMetabo dia-PASEF data correctly.
Currently, MS-DIAL can successfully generate the MS1 peak table, but no MS/MS spectra are produced after deconvolution/export.
I would appreciate any explanation or suggestions from the MS-DIAL team regarding this issue.

The raw data and processing-related files are available here:
Google Drive
parameters.txt

Thank you very much for your help.

[Maringa93]

Hi @ptpb781209069,

Thanks for sharing this — I’m also working with timsMetabo data (both DDA-PASEF and DIA-PASEF) and would like to reproduce the issue on my side. Could you clarify two things?

Which raw format did you use in MS-DIAL: the original Bruker .d folders or IBF files converted with IbfConverter?

In MS-DIAL, which option did you select under "Data type selected": SWATH, AIF, or DDA?

Those two details change how MS‑DIAL performs deconvolution and MS/MS pairing for PASEF/DIA-style data, so they’re important for reproducing the behaviour you describe.

Thanks,
Marc

[ptpb781209069]

Hi Marc,

Thank you for your reply.

I used the original Bruker .d folders directly in MS-DIAL and did not convert the data to IBF format.

For "Data type selected", I chose SWATH.

With these settings, MS-DIAL successfully generated the MS1 peak table, but no deconvoluted MS/MS spectra were produced in the output.

Please let me know if any additional information or files would be helpful for reproducing the issue.

Best regards