|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.