ssl search results not being imported

support
ssl search results not being imported solis  2019-08-16
 

Dear support team,

I'm trying to create a spectral library from an ssl file. Everything runs normally until the upload of the fasta file, where it says that the number of matches is 0. Can you help me figure out the issue?

So I'm doing this via: File -> Import -> Peptide Search. Please find the necessary files attached.

Thanks for your help!

 
 
Nick Shulman responded:  2019-08-16
You did not attach any files.

Files that are less than 50MB can be attached to this support request.

You can upload larger files here:
https:/skyline.ms/files.url

--Nick
 
solis responded:  2019-08-16
Thanks for the reply, Nick.

There'll be no need; I found the reason of the problem. In order to match the FASTA file with the spectral library created with the SSL file, this one should contain a column named "protein". However, that's not specified in here:

 https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BiblioSpec%20input%20and%20output%20file%20formats

It would be very kind if you do so for future users with the same problem.

Thanks!
 
Nick Shulman responded:  2019-08-16
I am not sure that I understand what you are saying.
Skyline does not normally get any information about proteins from peptide search results.
When you specify a FASTA file during "Import Peptide Search", Skyline uses your enzyme settings to digest the proteins in the FASTA file and sees whether any of those digested peptide sequences match any of the peptides sequences in your search results or SSL file.
-- Nick