When you have acquired data for your sample using the instrument method without ddMS2 scans, you need to scrutinize the results and adjust the processing method. You might need to revise the settings described in Designing a PQA monitoring method in the Chromeleon CDS software and select different parameters, thresholds, and so on.
For example, a frequent issue that causes component identification to fail are slight shifts in retention times. In this case, you can consider defining wider RT windows or, in the case of peptide modifications, you can define their retention times relatively to the native peptide.
NOTE
When you fix identification for one XIC of a component, do not forget to transfer the same settings to the other XICs by setting the fixed XIC as reference.