noenzyme setting

noenzyme setting egulyas  2020-04-27

Dear Brendan,

I would like to do peptidomics study. The identified peptides have no specificity on any side. How can I set it in the "digestion" ? (both side unspecific or no enzyme)


Brendan MacLean responded:  2020-04-27

You can always add any peptides you want to the Targets view as lists of peptides without protein associations by pasting a line separated list of their amino acid sequences, or using Edit > Insert > Peptides. If you have a spectral library, you can use the Add and Add All buttons in the Spectral Library Explorer (View > Spectral Libraries) to add any peptide sequence in the library regardless of cleavage.

Finally, if you really want these unspecified cleavage peptides to have a protein association in the Targets view (i.e. to be associated with a full protein sequence from a FASTA file) then you likely have to use Refine > Associate Proteins to provide the FASTA sequences after adding the peptides to the Targets list. This should make the associations through straight string matching without regard to any cleavage settings.

There is no way to tell Skyline to generate all possible peptides residue by residue without and cleavage pattern.

Thanks for posting to the Skyline support board.