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Import DIA Peptide Search results from Spectronaut

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Import DIA Peptide Search results from Spectronaut n prust  2023-03-29 06:12
 

Hi,

I followed the Webinar yesterday about how to use DIA results/libraries for SRM method setup/optimization.
I was now trying to do it myself using a Spectronaut output instead of EncyclopeDIA. I already asked yesterday during the webinar if this is possible and the link you provided says that I can use a csv SN output file. However I tried both building a library using the SN report file in .tsv format and using an existing library created with SN.
When trying to build the library I get the Error: Error getting score type for this file. The csv format as stated on the website https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibBuild is not even supported, so I cannot use that one.
When trying to use an existing library I am having the issue that the library format (.kit) from SN is not supported.
I feel like I am missing something here.

Do you have any information how I can Import DIA peptide search results from SN?

Cheers,
Nadine
 
 
Nick Shulman responded:  2023-03-29 07:17
Oops! The information I gave you yesterday was incorrect.
The way to get the spectronaut .csv file into Skyline is with the menu item:
File > Import > Assay Library

(Yesterday I said to use "File > Import > Peptide Search", but as far as I can tell there is no way to use a Spectronaut csv file with that).

If you are still having trouble getting this to work with the "File > Import > Assay Library" menu item you can send us that .csv file and we can figure out how to make it work. If that .csv file is less than 50MB you can attach it to this support request. You can upload larger files here:
https://skyline.ms/files.url
-- Nick
 
n prust responded:  2023-03-29 07:39
Hi Nick,

thanks for the swift reply.

Loading it via "File > Import > Assay Library" seems to work. :-)

Thanks again!

Cheers,
Nadine