Library generation using data from PeptideAtlas

[andrewlai]

Hi Vadim,

First of all, I’d like to thank you for making this great software available to everyone!

I have a question about potentially using PeptideAtlas data for library generation versus the entire human FASTA.

For example, if I am working with extracellular vesicles from human plasma, is there any advantage to using their plasma_EV build (https://peptideatlas.org/builds/human/plasma_ev/)? If so, would I simply download the peptide sequences in FASTA format, generate the library, and then reannotate the predicted library using the UniProt human FASTA file?