Issue 752: Add option to use 1-based amino acid position numbering

issues
Status:open
Assigned To:Kaipo
Type:Todo
Area:Skyline
Priority:3
Milestone:21.1
Opened:2020-09-02 by Brendan MacLean
Changed:2020-09-02 by Brendan MacLean
Resolved:
Resolution:
Closed:
2020-09-02 Brendan MacLean
Title»Add option to use 1-based amino acid position numbering
Assigned To»Kaipo
Type»Todo
Area»Skyline
Priority»3
Milestone»21.1
It has been pointed out again that our amino acid numbering is zero-based, which is not the norm in Proteomics.

https://skyline.ms/announcements/home/support/thread.view?rowId=43680

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.