I would like to predict the peptides of SD rat plasma after trypsin digestion. Can Skyline help? If yes, may I know how to do it? If not what do you recommend? Thanks!
Nick Shulman responded:
Do you have a FASTA file which contains the protein sequences that you would expect to find in rat plasma?
After you have such a FASTA file, then, in Skyline, you would go to:
Settings > Peptide Settings
and on the "Digestion" and "Filter" tabs make sure that those settings are appropriate for the peptides you want to see.
Then use the menu item:
File > Import > FASTA...
Skyline will read through the FASTA file and digest the proteins according to your settings, and the Targets tree in Skyline will become populated with the peptides that pass your filter criteria.
Hope this helps,
Richard Lam responded:
Any idea on where I can find the FASTA file for rat plasma? Thanks!
Otherwise, my understanding is that nearly all rat proteins can be detected in plasma if your assay is sensitive enough, so it might work if you used the complete rat proteome fasta.
You can download the complete rat FASTA here: https://www.uniprot.org/proteomes/UP000002494
Note that Skyline is not the right tool for figuring out which proteins are detectable in your sample. Skyline is very good at quantifying things that you have reason to believe are detectable in your sample.