|How to import amino acid substitutions from ProteinPilot 5.0 search results||christof.lenz||2020-06-16|
I am looking for a systematic way to import peptide search results from SCIEX ProteinPilot 5.0 including amino acid substitutions. In 'thorough' mode, ProteinPilot allows to search peptide sequences including all amino acid substitutions. Scoring is then adjusted using an underlying BLOSUM substitution matrix and goes into scoring, so we could use a peptide score cutoff here.
I am stumped, however, on how to import the search results including the 180 or so possible AA substitutions into Skyline to look for these peptides e.g. in HR-MS1 or DIA data. Is there any good way to do this, except 'declaring' each potential substitution as a variable PTM?
Any hints or experiences much appreciated!!