I'm managing HPLC assay analysis of a peptide drug and I've always worked with assay specifications such as 97.0% - 103.0% or 98.0% - 102.0% w/w. To my understanding, these limits are solely based on method uncertainty (+/- 3 sigma), which I have always accepted. However, our peptide has some degradation which theoretically will result in a lower assay value than e.g. 97.0%.

How is degradation considered when limits like 97.0% - 103.0% w/w are set in guidelines etc.? How can we incorporate both the method uncertainty and the degradation in our assay limit?