Processing Bruker TIMS-ToF raw data in MS-Dial needs better description in MS-Dial tutorial

[GerdBalcke]

Dear Hiroshi and Team,
I would like to process Bruker TIMS-ToF .d project data in MS-Dial.

Currently, the MS-Dial tutorial only says:

Bruker: Go to https://www.bruker.com/service/support-upgrades/software-downloads/mass-spectrometry.html. You have to register first and obtain the installer. Finally, download and install the version compatible with your operating system environment (32-bit or 64-bit).

I did, and I assume I need to download the: CompassXtract but opening the Bruker webpage it does not appear anywhere.
I also searched for it using the "SEARCH" function ....but nothing came up.

Steffen Neumann from my institute provided a version 3.2.01, which is presumably too old.

We should have a working description in the tutorial how to download the correct version of CompassXtract.
Can I help by contacting Bruker and disucussing the issue with them?

Kindly,

Gerd

[Maringa93]

Dear Gerd, Hiroshi and Team,

I have encountered the exact same issue when trying to process data from a Bruker Impact II acquired with bbCID method. I also couldn't find the specified tool (CompassXport/CompassXtract) in the Bruker download portal, even after registering.

Additionally, I'm facing the same problem with data from a new timsMetabo (IM-TOF-MS) recently installed at my center.

Happy to help testing or contacting Bruker if needed!

Best regards,
Marc

[MarkusPiotrowski]

With MSDIAL Version 5 you don't need the CompassXtract tool.

However, I also had a hard time in importing my .d format data, because there is no .d option in the file menu.

The solution is, however, quite easy: Just drag & drop your .d folders in the file table:

[yslproteomics]

Hi, I am also facing some issues with the .d files (nanoLC-TIMS-PASEF). It seems like the alignment step cannot be performed correctly, as the alignment always gets stuck and runs forever. Does anyone know what the bottleneck is? Is MSDIAL actually compatible with TIMS-PASEF?

[GerdBalcke]

Try dragging and dropping the .d folder. That may help. Dr. rer. nat. habil. Gerd Balcke Tel: E-Mail: ORCID: +49 345 5582 1713 ***@***.*** ***@***.***> https://orcid.org/0000-0002-0475-0672 [https://mailtasticcdn.azureedge.net/img/images/siglinks/company/71639e11-6a7d-4a5d-bcf0-0b3dad2b4943/u_logo-TcV2hig3uu.png] Leibniz-Institut für Pflanzenbiochemie Weinberg 3 | 06120 Halle | Deutschland Tel. +49 345 5582 0 | www.ipb-halle.de<https://www.ipb-halle.de/> <https://app.mailtastic.de/api/linkserve/campaign/d8d4d3b2-434b-4d90-a272-57ad4c21efb7/74830> From: yslproteomics ***@***.***> Sent: Tuesday, April 14, 2026 8:26 PM To: systemsomicslab/MsdialWorkbench ***@***.***> Cc: Balcke, Gerd ***@***.***>; Author ***@***.***> Subject: Re: [systemsomicslab/MsdialWorkbench] Processing Bruker TIMS-ToF raw data in MS-Dial needs better description in MS-Dial tutorial (Issue #721) [https://avatars.githubusercontent.com/u/186743280?s=20&v=4]yslproteomics left a comment (systemsomicslab/MsdialWorkbench#721)<#721 (comment)> Hi, I am also facing some issues with the .d files (nanoLC-TIMS-PASEF). It seems like the alignment step cannot be performed correctly, as the alignment always gets stuck and runs forever. Does anyone know what the bottleneck is? Is MSDIAL actually compatible with TIMS-PASEF? - Reply to this email directly, view it on GitHub<#721 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BAR4EQM5HBVMJHO7MGC3WZD4VZ7CXAVCNFSM6AAAAACW5TVFS6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DENBWGIYDSNJVG4>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>

[yslproteomics]

Dear Gerd,

Thank you for the suggestion, but that does not help. We don't have any trouble opening the .d files and submitting the analysis. The problem is in the alignment step, in which MS-DIAL gets stuck forever.

To make myself clear, I am wondering why that is, and if anyone has tried MS-DIAL with TIMS-PASEF data (untargeted lipidomics) and made it work.

Our data can be processed in Metaboscape and Mzmine, but we are currently trying to explore different options for data analysis.

Thank you.

[mecolley]

I have been using MS-DIAL with TIMS DDA-PASEF data for years and this is my workflow:

• Convert timsTOF data with ibfconverter.exe (included in older versions of MS-DIAL e.g. 4.90)
• Use the new IBF files in MS-DIAL (4.90 works for me)

Known issues on my end:

• Unconverted Bruker .d in version 5.5 (latest release) uses too much ram and locks up my computer
• Using IBFs in version 5.5 process but the GUI locks up when trying to click around in the interface (I created an issue for this).

So far stability for tims-TOF data from me is:

• Use IBFs
• Use version 4.90