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MS data not supported 196310  2026-01-12 16:51
 

Dear SkyLine Team,
I am trying to upload my Thermo data (From an exploris 480) as .RAW on skyline for peptide search (DDA), but they cannot load (it says it's not a valid imput file). I have also tried to convert them into a mgf and mzML but it gives me the same error. I can open those files on FreeStyle and Proteome Disc, so I do not think they are corrupted or invalid.

How can i proceed now?

Thank you for your help,

Lorenzo Tagliazucchi from University of Parma, Italy
 
 
Nick Shulman responded:  2026-01-12 17:07
If you want to search for peptides in a .raw file, you should use the menu item:
File > Search > Run Peptide Search

It looks like you were instead trying to use the "File > Import > Peptide Search" menu item. That's the menu item that you would use if you already had peptide search results. It also used to be the menu item to run a new peptide search, but we moved that functionality to "File > Search".

When you do File > Search > Run Peptide Search, Skyline will ask you to provide your .raw files as well as a FASTA file.

You can learn about running peptide searches in Skyline here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_dda_search

-- Nick