I am using the 'Import DDA peptide search' wizard to import results from a dataset generated by msfragger/fragpipe. The dataset contains peptides from human and a couple of viruses, with all the detected proteins included in the fasta library that I used during loading of the dataset into skyline. All viral peptides are in the generated spectral library, but none of them - and none of the proteins - made it into the target list, only the human proteins/peptides are there. I am wondering if I overlooked a setting that may have this effect. Any help would be greatly appreciated.
I am using skyline-daily v22.1.9.208.
Thank you,
Janos