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Why does importing skyline from mzml format fail? How to solve it

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Why does importing skyline from mzml format fail? How to solve it z15839328872  2025-07-22 19:54
 

Hello,dear Skyline team
Since I targeted to do 4D before, so the generation of offline data is mzml, many attempts have failed, the attachment is my screenshot and data, I hope to solve this problem, thank you very much。
Zhou Yanan
 
 
Nick Shulman responded:  2025-07-22 22:23
The menu item that you tried to use is only for importing peptide search results into Skyline. You cannot use that menu item with .mzML files.

Skyline does have a peptide search engine called "MS Amanda". Here is the tutorial for that:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_dda_search_zh

Here is the tutorial for ion mobility (i.e. 4D):
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_ims

Can you give us more information about what sort of data you have? Is it peptides or small molecules?
-- Nick
 
z15839328872 responded:  2025-07-23 01:04
Hello, my data is peptides, and I did non-targeting in the early stage, and I got the FASTA information table about proteins and peptides and the down-to-machine data of mzml
Zhouyanan
 
z15839328872 responded:  2025-07-23 01:46

Hello, I tried the first MS Amanda method you recommended and it still failed
 
Matt Chambers responded:  2025-09-30 07:31

Hi Yanan,

Sorry for the delay. Could you share one of the mzML filse you're trying to search, and what species it is (or also share the FASTA if it's something unusual)?