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Topic: Question about Bruker QTOF raw data in MS-DIAL (Read 1769 times) previous topic - next topic

Question about Bruker QTOF raw data in MS-DIAL

Hi there,
I am using MS-DIAL to process data coming from an older qTOF compact we have in our institution. We have encountered some issues with these data when converting to mzXML/mzML using msconvert, wherein the conversion incorrectly uses the uncalibrated precursor m/z in MS2 scans, which meant a lot of MS2 spectra ended up being unconnected to corresponding MS1 peaks.

I wonder, since MS-DIAL seems to read bruker .d natively, can we assume that this issue is handled correctly when processing the datafiles (assuming they are calibrated before processing)?

Best,
Silas

Re: Question about Bruker QTOF raw data in MS-DIAL

Reply #1
In my experience, you can get around this issue in one of three ways.
1. Take the Bruker .D file and load it when creating the project just make sure to switch from ABF files to all files and find your Bruker .D files.

2. You can also use the IBF converter for your .D files, which will also keep any ion mobility data if your Bruker supports this. In my experience, this works great for lipidomics. This is included with the MS Dial Application folder.

3. MS-Dial does recommend that you use the ABF converter and convert your .D files there.

If you have any more questions, please let me know.

Re: Question about Bruker QTOF raw data in MS-DIAL

Reply #2
Hello! I have a related follow-up question and would really appreciate any guidance. I similarly have TIMS-TOF-PASEF data, with data-independent acquisition on a Bruker system.

I have tried to use the ABF converter after downloading both Compass Xtract and the TDF-SDK library from Bruker. Is there something that needs to be done to those intermediaries after they are downloaded, or does the ABF converter just 'know' to search the program files for the dll and library files they contain? Because even after those downloads, the ABF converter is still telling me that the .d files are not an accepted format.

Re: Question about Bruker QTOF raw data in MS-DIAL

Reply #3
A quick revision to my previous post - I realized my error (trying to drag and drop the .tdf file, rather than the .d folder from Bruker). But unfortunately, the ABF converter is still telling me it can't convert the .d file folders to .abf because CompassXtract isn't installed. I've installed, uninstalled, and reinstalled it multiple times now. Has anyone else had this issue?

 

Re: Question about Bruker QTOF raw data in MS-DIAL

Reply #4
I received an answer to the above question from the ABF converter developer, and am posting it in case it helps others. The converter currently can't process .tdf or .tdf_bin files because CompassXtract does not recognize them. There is a new converter in the works designed to do so, but a release date hasn't been announced. For now it seems it isn't possible to process IMS data in MS-DIAL, and files should be converted to a more general format (like mzXML) directly from Bruker software.