Issue 868: Consider generating a dictionary of less common isotopes instead of hardcoding them piecemeal in response to user requests

Status:open
Assigned To:Brian Pratt
Type:Todo
Area:Skyline
Priority:3
Milestone:4.3
Opened:2022-01-28 12:27 by Brian Pratt
Changed:2022-02-03 13:25 by Brian Pratt
Resolved:
Resolution:
Closed:
2022-01-28 12:27 Brian Pratt
Title»Consider generating a dictionary of less common isotopes instead of hardcoding them piecemeal in response to user requests
Assigned To»Brian Pratt
Type»Todo
Area»Skyline
Priority»3
We recently added support for heavy copper (C' in Skyline-speak, C65 in adduct-speak) because it appears as an adduct in a list of common mass spec contaminants.

It occurs to me that this could have been handled automatically if we used the information we already have in pwiz.Common.Chemistry,IsotopeAbundances.

For any given element X that we don't already have hard-coded, it's just a matter of identifying the most common stable isotopes and noting them as X', Xmm, X", and Xnn respectively, where mm and nn are the isotope masses rounded to the nearest integer.

2022-01-28 12:43 Brian Pratt
Of course I meant "(Cu' in Skyline-speak, Cu65 in adduct-speak)" in my initial description, oops....

2022-02-02 11:38 Brian Pratt
Note that we'll want to update the Skyline xsd so that <xs:simpleType name="heavy_isotope_symbol_type"> is a more comprehensive regex.

2022-02-03 13:25 Brian Pratt
Notify»Nick Shulman
Also this might be the time to take up Nick's idea of extending our formula notation to handle the form 13C instead of C' in formulas. This would require allowing spaces in formulas - as Nick says:
"If we allowed spaces in the chemical formula, then you could write (for very heavy glucose):
C6 2H12 18O6
but, without spaces there's no way to tell that there are not 62 carbons."

Possibly we'd want to anticipate other separators, like "_" or "+". There's not even a de facto standard for this that I've found, I can imagine a lot of variations to be handled.