Issue with AIF Mode in MS-DIAL for Bruker QTOF-MS Data (bbCID Mode)

[pelagialekka]

I’m currently facing an issue while processing my Bruker QTOF-MS data using MS-DIAL (5.5.250404) and would appreciate any insights or suggestions.

Instrument and Acquisition Info:

• Instrument: Bruker QTOF-MS
• Acquisition mode: bbCID
• MS1 collision energy: 4 eV
• MS/MS collision energy: 25 eV

This setup aligns with what is generally referred to as All-Ions Fragmentation (AIF).

Problem Description:
I have converted the original Bruker .d files into .mzML using ProteoWizard, since MS-DIAL does not seem to support native Bruker files. When I process the data in MS-DIAL using the AIF mode, I receive an error (attached below). Even when the process completes, no deconvoluted spectra are generated, and no reference matches are reported.

However, when I run the exact same .mzML file in SWATH mode, MS-DIAL does provide deconvoluted spectra and reference matches successfully.

My Questions:

1. Has anyone successfully used MS-DIAL with Bruker bbCID (AIF-style) data?
2. Is there something specific in the AIF settings I might be missing?
3. Should bbCID mode data actually be processed using SWATH mode in MS-DIAL, despite being all-ions-like?
4. Is there a better way to handle Bruker .d files directly or improve compatibility?

I’d be very grateful for any advice or shared experience. Let me know if you need more details about my acquisition parameters or processing workflow.

Thank you in advance!