Import transition list with modifications that have not been pre-specified

support
Import transition list with modifications that have not been pre-specified joshuasmith  2019-08-28
 

Hi, I am doing DIA to discover novel adducts on a specific residue of a certain peptide. We have previously done PRM experiments to search for pre-specified adducts to that residue (e.g., Cys adducts, or oxidation, or various electrophilic adducts), where I would manually enter each pre-specified adduct into the "structural modifications" list on the Modification tab in the Peptide Settings menu. However, now that we are doing discovery experiments, I have a lot of potentially novel adducts that i have not already entered into the structural modifications list a priori. When I try to import a (properly formatted, attached) transition list with novel adducts, I get an error message for each adduct that Skyline cannot automatically reassign to a current "structural modification" entry:

"Precursor m/z 903.4449 does not match the closest possible value 895.0976 (delta = 8.3473), peptide ALVLIAFAQYLQQCPFEDHVK. Check the Modification tab in the Peptide Settings, the m/z types on the Prediction tab, or the m/z match tolerance on the Instrument tab of the Transition Settings."

Is there a way to have Skyline automatically create new structural modification entries for novel adducts in an imported transition list?

Let me know if this isn't clear, or you need more info.

Thanks!
Josh