I’m a new user of PEAKS and I have a question regarding mutation filtering. I run a search to identify mutations in a purified protein and upon analysis I see that the major filter playing a role in the identification of mutation is using either minimal intensity or minimal Ascore. Given that I would like to identify only very robustly identified mutations because I need to produce this protein, which filter would you use between these two? And eventually which threshold would you use? 20% of ion intensity!? 20 as minimal Ascore?!
Thanks a lot in advance