mzML quant error : Index was outside the bounds of the array. about flashlfq HOT 8 OPEN

Hi Patrick.

Based on the error log you provided, it seems that the .mzml file is the problem. Could you provide some more details about the how the mzml file was generated and/or send the file?

from flashlfq.

Thanks for the fast reply. It is a mzML that is automatically generated by MSFragger during a timsTOF .d search. I saw that there was some support for Bruker data, perhaps that could be an option?

I could share the mzML in a PM if you like.

Thanks

from flashlfq.

We're still experiencing some problems reading in .d files, so no guarantees.

If you could share the .mzml (and the .d file as well, if possible) via PM, I'll try to find and fix the issue.

from flashlfq.

You can reach me here: [email protected]

from flashlfq.

You can reach me here: [email protected]

Ok thanks! Uploading now.

from flashlfq.

Sorry to come back to this. Is there are any solution? I have also been trying to use the raw .d Bruker directories, but I get

"Error: No spectra files were found"

Although the .d files are named accordingly the File Name.

Thanks
Patrick

from flashlfq.

Thank you for your patience on this!

I took a look at the .mzML file you shared, and it appears that the file doesn't contain any MS1 scans. This would preclude analysis with FlashLFQ.

Does the .d file contain MS1 scans?

Thanks,
Alex

from flashlfq.

Thank you for the help! Sorry, I should have noticed this in the first place, I will try some other mzML conversion.

Alternatively, how can I make FlashLFQ read the .d file itself?

Thanks!

from flashlfq.