SD Rat Plasma

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SD Rat Plasma Richard Lam  2019-04-23
 

Hello,

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!

Regards,

Richard

 
 
Nick Shulman responded:  2019-04-24
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,
-- Nick
 
Richard Lam responded:  2019-04-24
Any idea on where I can find the FASTA file for rat plasma? Thanks!

Best regards,
 
Nick Shulman responded:  2019-04-24
If you want a list of peptides that are particularly easy to detect in rat plasma, you should take a look at the Grouped Studies tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_grouped

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.

But, if you are trying to discover what might be in your sample, then you should use a peptide search engine. There is no particular search engine that we recommend, but here is the list of search result formats that Skyline understands:
https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibBuild

Once you have some peptide search results, you might find the MS1 full scan filtering tutorial useful:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_ms1_filtering
Good luck!
-- Nick