For robust PQA quantitation, you must define a set of criteria that incorporates all possible scenarios for a particular PQA. Keep in mind that any given PQA might also involve the following related components:
- Modified peptides
- Adducts
- Glycans
- Missed cleavages
Additionally, when selecting a PQA to monitor, consider the mass tolerance and MS signal intensity threshold parameters for the experiment. If a particular component does not meet the specified mass tolerance or MS signal intensity parameters set for the experiment, it does not appear in the Results table.