Filtering Dominant Charge State

Filtering Dominant Charge State meyermr  2015-11-25
Hi Skyline Team,

I have a peptide tree that is filtered to contain only sequences and charge states that are present in an imported spectral library. If there are multiple charge states observed for a peptide, is Skyline capable of further filtering a peptide tree by dominant charge state?

Thank you,
Brendan MacLean responded:  2015-11-25
Hi Matt,
Good suggestion. It is not currently available. I have posted an issue to review several possible additions to the Edit > Refine > Advanced form, with this among them.

Thanks for your feedback.

Tobi responded:  2019-01-24
Dear Skyline Team,

is there nowadays a solution to the above mentioned issue? We work with targeted acquisitions based on an inclusion list made from a survey full scan on isotope labeled peptides. They exist in dominant charge states between 2 and 5, but only the dominant charge states for each peptide are interesting to build inclusion lists.

Would it be possible to load the survey scan with a target list of all possible charge states, quickly check for correct peak picking by RT and then remove uninteresting charge states which are e.g. <90% of the most intense charge state within each peptide? (Or another workaround which makes manual charge state deletion more feasable, in the best case peptide search independent)

Looking forward a short reply.