Skyline spectral library export

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Skyline spectral library export Helian  2018-05-16 02:44
 

We often use the option in Skyline to export spectral libraries based on experimental data, but we're wondering how does it work when there are multiple raw files imported. In most cases the peptide is found only in one of the samples. When I export the spectral library does it base it on the best peak (the sample where the peptide was actually found and should be found in) or does it combine all results into one?

Thanks,
Helian

 
 
Nick Shulman responded:  2018-05-16 15:26
I believe the spectrum that ends up in your spectral library uses the peak areas that come from the first replicate in your Skyline document.

You can change the order of your replicates by going to:
Edit > Manage Results
and whichever replicate is at the top of that list is the only one that affects what the spectra look like in an exported spectral library.
 
Helian responded:  2018-05-17 00:13
Thanks for the answer! I'm not sure if it will simplify my work a lot, but it is very good to know how it works, because the spectral library export is a very useful function.