Adding peptides manually in spectral library

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Adding peptides manually in spectral library mdshadman abid  2020-11-30
 

I am using software PEAKS for the peptide search in my samples and also using these database search from peaks as the spectral library in skyline. However there are some peptides present in the sample but peaks could not detect somehow. That is why when I am generating a spectral library, I am missing those peptides. Is there any way to add/input peptide sequence manually in the spectral library?
I tried by going to Edit- Inset-peptide- then just manually typed the peptide sequence to add the peptide in the library, but I think it's not proper way of what I want to do.
In case I am unable to ask my question, I am giving an example. I know the peptide LYQNKPRRPYIL is present in my sample but PEAKS software couldn't detect it, so it is also missing in spectral library as I am generating library from PEAKS. How can I manually add this peptide in my spectral library?

 
 
Nick Shulman responded:  2020-11-30
There is nothing wrong with doing "Edit > Insert > Peptides" to get peptides into your document that were not in your spectral library.

Skyline is not going to know which charge states and precursors to choose for those peptides, so you might need to right-click on them in the Targets tree and use the menu item "Pick Children".

I am not sure why you would want to add these peptides to a spectral library. In order to add peptides to a spectral library you need to have some way of specifying what the spectra for these peptides would look like.

After you have extracted chromatograms in your Skyline document, you can use the menu item "File > Export > Spectral Library". This will create a .blib file containing all of the peptides in your document, and the "spectra" in the library use the m/z's from the transitions in your document and the "intensities" in those spectra are the integrated peak areas from the chromatogram.

If you want to merge this exported .blib file with the .blib file that you already have, you can go to:
Settings > Peptide Settings > Library > Build
and then, as input files, instead of using peptide search results, you can use the two .blib files that you already have.

If you want to create a spectral library from a list of peptides, you can use the "spectrum sequence list" format (.ssl), which is specified here:
https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BiblioSpec%20input%20and%20output%20file%20formats

However, in order to use this .ssl format, you would need to specify which spectrum from your raw files Skyline should put in the spectral library.

I am not sure that I understood your question but I hope this helps.
-- Nick