In section Designing a PQA monitoring method in the Chromeleon CDS software, you created the processing method that can analyze the attributes of your peptide based on data acquired with the instrument method that performs a full-MS scan followed by ddMS2 scans. Now you can adjust this method so that it is suitable for monitoring the selected peptide attributes based on data from a full-MS scan without ddMS2 scans.
IMPORTANT
The following adjustments of the processing method must be tailored for data acquired with a full-MS-only method. Whether your PQA monitoring uses a different MS instrument or the same one that you used for characterizing the PQAs, you need to have data acquired with the simpler instrument method to adjust the processing method for PQA monitoring.