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Why does importing skyline from mzml /4D format fail?

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Why does importing skyline from mzml /4D format fail? z15839328872  2025-07-23 23:41
 

Dear skyline team,
I used the first MS Amanda method you recommended and it still failed, and then used the second method you recommended 4D method to import still failed, and the computer kept stuck and restarted, and the data import was unsuccessful for 11 hours, and the same is true when I changed to a new computer. My data is the non-targeted identification of protein peptides done in the early stage, and the FASTA file obtained is 4D (converted into mzml format), I hope to get your reply.
Zhouyana
 
 
Nick Shulman responded:  2025-07-23 23:53
Can you send us your files?
You can upload your files here:
https://skyline.ms/files.url

It would be helpful if you could send us your .mzML file as well as the FASTA file that you are using to search.
It would also be helpful if you could send us the Bruker .d folder that the .mzML file was created from.

Most people use the .d folders directly with Skyline. It is usually not necessary to convert the .d folder to mzML to work with Skyline.

Many people have experienced errors similar to the ones that you are getting. Hopefully we will be able to figure out a solution after we see your files.
-- Nick