• Sign In
  1. Requests

Bruker diaPASEF .d import failure: Failed importing results file [...]'16495.d'. error reading spectrum merged=15875 frame=5716 scanStart=1 scanEnd=702

support

View Request

view list print
Bruker diaPASEF .d import failure: Failed importing results file [...]'16495.d'. error reading spectrum merged=15875 frame=5716 scanStart=1 scanEnd=702 Lindsay Pino  2025-04-16 10:01
 

Hi team!

I've been building Skyline v 24.1 docs from DIA-NN 1.8.1 results using the “Import DIA Peptide Search” walk-through. The good news is that 4 out of my 6 files look great! The sad news is that 2 of the 6 files throw these errors. I'm not sure what could be different about these two files compared to the four that successfully imported. I'm not sure where to troubleshoot! The Skyline file is kinda big but I can get that shared if useful?

More random details if helpful:

  • Isolation scheme: Results only
  • Same error when I use Skyline-daily

Thanks!
Lindsay
 
 
Nick Shulman responded:  2025-04-16 14:21
Someone else had a similar CorruptDataFrameError a few weeks ago:
https://skyline.ms/announcements/home/support/thread.view?rowId=68400

I am not sure I follow everything that was discussed in that support request.

It looks like you might be able to work around this error by changing the Mass Analyzer settings at "Settings > Transition Settings > Full Scan" to "Centroided". Also, the behavior might be better in Skyline-daily than in Skyline 24.1.

I think we are going to look into what is causing this error.
I assume that these files can be opened just fine in Bruker Compass DataAnalysis?
It would probably be helpful if you could send us your .d folders. You can package everything up in a .zip file and upload it here:
https://skyline.ms/files.url
-- Nick
 
Lindsay Pino responded:  2025-04-16 15:17

Uploading now! Sharing the Skyline doc with the successfully imported files, and one of the failed files. They're probably gonna need some time to upload, but they're chugging along.

  • 240808_Sarthy_jr.sky.zip
  • 240805_Sarthy_DMSO_chrom_01_S2-A3_1_16495.d

It looks like you might be able to work around this error by changing the Mass Analyzer settings at "Settings > Transition Settings > Full Scan" to "Centroided". Also, the behavior might be better in Skyline-daily than in Skyline 24.1.

I already had Centroided selected, so that's unfortunately not it. Hm. I was unable to import the same two files in both Skyline 24.1 and in Skyline-daily, so at least it's reproducible?

I assume that these files can be opened just fine in Bruker Compass DataAnalysis?

I'll double check this tomorrow. These files don't live on the instrument computer anymore, so I'll have to get them onto an external drive and pop them onto an instrument computer in the morning!

Thanks again,
Lindsay
 
Lindsay Pino responded:  2025-04-21 14:11

I'm back! Confirmed that the files can be opened in Bruker Compass DataAnalysis!