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Importing MSAmanda mzid.gz file "Error getting score type for this file"

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Importing MSAmanda mzid.gz file "Error getting score type for this file" nicole pontarin  2023-07-17 18:55
 

Good morning Skyline team,

And thanks in advance for considering this support request.

I am using MS Amanda standalone version to expand my search to 5 amino acid-long peptides. I think that Skyline uses the default MS Amanda settings, searching for 6-30 aa-long peptides. I would like to receive your support on:

  • either how to modify the min and max peptide length in the Skyline "Import peptide search" from .raw data;
  • or how to resolve the "Error getting score type for this file" when I try to import files generated by MS Amanda. I tried both Skyline and Skyline daily in their up to date versions.

With thanks and regards,
Nicole
 
 
Nick Shulman responded:  2023-08-02 15:25
Sorry for the late reply.

When I step through the Skyline code, it looks like the setting that it is using for minimum and maximum peptide lengths are 0 and 60, but it is possible that the values that I am looking at are not the ones that actually get used by MSAmanda.

When Skyline runs MSAmanda, Skyline also runs Percolator in order to generate q-values. In general, you need to have q-values in order to be able to generate a spectral library from peptide search results so that BiblioSpec knows which spectra to include in the library.
I am not sure how to run Percolator on MSAmanda search results, but I might be able to ask around and find out from someone.
-- Nick
 
Juan C. Rojas E. responded:  2023-08-03 02:19
Hi Nicole,

I am sure the Skyline team can eventually find an answer to your problem.

But as a temporary workaround you could try running MSAmanda within SearchGUI+PeptideShaker (http://compomics.github.io/projects/peptide-shaker). You can export results for spectral library creation in Skyline.

Hope this helps!
Sincerely,
Juan C.
 
nicole pontarin responded:  2023-08-06 15:50
Hi Nick and Juan,

Thanks so much for your responses!

Juan, I came up with the same workflow, but did not know I could export results in Skyline! I'll write back here if I can't find the way to do this. Thanks for the suggestions!

Best wishes,
Nicole