It has been pointed out again that our amino acid numbering is zero-based, which is not the norm in Proteomics.
The norm is 1-based, and that got pointed out first over a decade ago, but I left it zero-based so as not to create problems for anything that might have already relied on the 0-based value.
The user posting the support request above suggested we add an option to control whether or not the legacy zero-based option gets used or a more normal 1-based value.
This seems like an easy enough thing to do. We could just add it to the Peptide Settings - Digestion tab between the Enzyme and the Background Proteome. Something like:
[ ] Use zero-based amino acid positions (legacy)
New documents by default would have this unchecked, but old documents would have it checked.
And then all AA position calculations would respect this boolean.