Gianluca Sigismondo

Dear all,

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

  • Edit
    Bioinformatics Solutions Inc.

    Hi Gianluca,

    Thank you for your question. AScore is a score originally created for PTMs. Technically it is not designed for mutations. AScore can be used, but I recommend using ion intensity to determine the localization of a mutation. Generally speaking, a minimum ion intensity of 5% or greater is a good cutoff. This means one major fragment ion must be found with at least 5% relative intensity before the mutation site and one must be found after. If not, it is still likely that a mutation is found within the peptide. However, the location of the mutation is questionable. If you have any more questions I'll be happy to help you.

    Kind regards,
    Dan Maloney
    Application Scientist
    519-885-8288 ex 1014