Similarly to how you defined better integration windows by setting one XIC as a reference for others, the same steps can help you deal with peaks that are so closely related that the detection swaps their identification in some XICs. For example, this can be the case of isoforms from peptide oxidation. This can be often resolved by selecting the XIC that contains the correct assignment as the detection reference for all the other XICs.

IMPORTANT

Changing of the detection reference XIC for a component becomes a part of the processing method. Therefore, it can affect all injections that use this processing method.

By default, component matches are assigned to the greatest peak in the RT window. In the case of closely related peaks with different proportions in different XICs, you can resolve identification issues by assigning the same RT window while specifying which component is always the first and which is always the second.