That link isn't working for me - "User does not have permission to perform this operation."

Can you zip the Z:\instruments\TIM\Data\Tao\20250221-GSL-MS2\2024GLY00161-GSL-A01_GA2_1_433.d directory and upload it to http://skyline.ms/files.url ? I'm guessing the problem can also be diagnosed with msconvert, which uses the same underlying reader code.

That error message doesn't appear in our own code so it's probable that the error message is coming from the Bruker-supplied reader library, but we'll know more once we can look at the data.

Thanks for using the Skyline support board,

Brian Pratt

Agnes & Brian,

I do see that error message in some code that we have for interfacing with Bruker:
https://github.com/ProteoWizard/pwiz/blob/master/pwiz_aux/msrc/utility/vendor_api/Bruker/timsdata_cpp_pwiz.h#L214

Here's what the code looks like:

if(required_len > 16777216) // arbitrary limit for now...
    BOOST_THROW_EXCEPTION(std::runtime_error("Maximum expected frame size exceeded."));

I am not sure whether fixing this is as simple as increasing that number.

I did download the "2024GLY00161-GSL-A01_GA2_1_433.d" folder from Panorama:
https://panoramaweb.org/_webdav/Leiden University Medical Center - Tissue Glycomics/Troubleshooting/%40files/RawFiles/2024GLY00161-GSL-A01_GA2_1_433.d/
However, I am getting the error "2024GLY00161-GSL-A01_GA2_1_433.d\analysis.tsf_bin doesn't exist." so I think that folder might be missing some necessary files.

-- Nick

Dear Brian & Nick,

Thank you for looking into this.

Edited:
MSConvertGUI (Version: 3.0.25055-ff3d22ec, automated build) can convert the file; however, the resulting mzXML file still produces the "Maximum expected frame size exceeded." error. This suggests that the issue is indeed related to conversion.

My apologies—there was an issue with the initial file upload to Panorama. I have now ensured that all files are correctly uploaded to the 2024GLY00161-GSL-A01_GA2_1_433.d folder: (https://panoramaweb.org/Leiden University Medical Center - Tissue Glycomics/Troubleshooting/project-begin.view?pageId=Raw Data).

Please see the attached screenshot for reference.

At the moment, I have found a workaround: exporting mzXML files directly within DataAnalysis Version 6.1 (Build 119.2.0) allows me to open the file in Skyline without errors. However, I would appreciate any further assistance in importing the raw file into Skyline.

Please let me know if you need any additional information.

Kind regards,

Agnes

Thanks for the files.

Working with your file I see that this is a misleading message - the actual problem is that the reader DLL supplied by Bruker is complaining about a corrupt file ("bdal::io::tims::CorruptFrameDataError"). It's interesting that you were able to convert it with DataAnalysis - were there no warning messages given?

Best regards,

Brian

Dear Brian,

No error message was prompted in DA. Is this something you suggest I should take up with Bruker?

Kind regards,
Agnes

Try converting with peakpicking enabled. It shouldn't be required because it should fall back to centroided spectra if profile are unavailable, but that looks like a bug on our end.

Dear Matt,

Thank you for your help. I have tested multiple conversion settings but would prefer to import raw data directly into a Skyline template.

Bruker support (TC developers) explained that they could read the file without any problems using the TDF-SDK and recommended acquiring spectra in profile mode. The latest file (in profile mode) allows Skyline to import the file without error messages.

However, upon further inspection and considering your previous comments, I wonder if there might be an issue with the peak-picking algorithm or some sort of file reading error. In Skyline-daily (64-bit) version 24.1.1.398 I have uploaded the Skyline example file (Example_A04_Profile.sky.zip) and raw data file (2024GLY00161-GSL-A04-OLC_GA2_1_530.d) to https://panoramaweb.org/Leiden University Medical Center - Tissue Glycomics/Troubleshooting/project-begin.view.

Specifically, when selecting transition m/z 634.2200 (H2S1) and examining the chromatographic peak apex, the isotopic pattern appears distorted at Scan#3866, while Scan#3906 displays a more expected isotopic distribution. The spectra displayed in the Full Scan window are actually from MS2 scans (precursors 700.158 and 634.237). The extracted ion chromatogram (EIC) does not reflect the anomalies observed in the Full Scan peaks, yet something seems to be going wrong.

Could you please take a look and provide further guidance? I have also attached images illustrating the issue.

Kind regards,
Agnes

I am able to reproduce your issue when using your sky.zip file, but if I reimport with the current Skyline-daily the problem goes away. What version did you import with? If you use the latest Skyline-daily and reimport does that resolve the issue?

Dear Matt,

Thanks again for your help. Previously, reimporting did not resolve the issue. However, I attempted it again just now, and this time it was successful.

After changing the Transition Settings > Full Scan 'Precursor mass analyzer' from Centroided to TOF, I encountered a similar issue again. This time a mixture of MS2 and MS1 scans are depicted in the Full Scan panel. I have uploaded the file to Panorama "Example_A04_Profile_TOF_20250325.sky.zip", please see m/z 634.2200 as an example—Scans #3772-3906 are MS2 spectra, whereas Scans #3911-3984 depict MS1 spectra. This time, I reimported twice, but the issue persists.

Zip file link: https://panoramaweb.org/Leiden University Medical Center - Tissue Glycomics/Troubleshooting/project-begin.view
Skyline version: Skyline-daily (64-bit) version 24.1.1.398

Yeah I can reproduce that too with the TOF analyzer. Weird. Will look into it next week. I think you should use Centroided though because timsTOF is always acquired as centroid data.