Issue 73: Add error message when incompatible isotope modifications are chosen

issues
Status:open
Assigned To:Brendan MacLean
Type:Defect
Area:Skyline
Priority:4
Milestone: 
Opened:2011-07-27 by Brendan MacLean
Changed:2014-01-08 by Brendan MacLean
Resolved:
Resolution:
Closed:
2011-07-27 Brendan MacLean
Title»Add error message when incompatible isotope modifications are chosen
Assigned To»Brendan MacLean
Notify»absterga@u.washington.edu
Type»Defect
Area»Skyline
Priority»4
Milestone»1.2
Recently someone chose the following isotope modifications together:

Label:13C(6) (K)
Label:13C(6) (C-term K)

With no peptides containing internal Lysine residues, this is really just specifying the same modification twice. Perhaps he meant to have the more common combination of:

Label:13C(6) (C-term K)
Label:13C(6) (C-term R)

But with no peptides ending in Argenine failed to notices the mistake.

Skyline does blindly convert this to K[+6] and K[+6] twice resulting in K[+12]. This is nonsensical, because the modifications replace all 12C atoms in Lysine with 13C... twice! Which doesn't really result in a +12 Da change.

Clearly it would be helpful if Skyline detected the case when chosen isotope modifications end up replacing the same atoms multiple times. This would only happen when the LabelAtoms property (i.e. atom labeling checkboxes) are used, and not when a formula is used. With a formula, the user may be replacing atoms that are not even part of the base amino acid, but part of a structural modification. This too could be worked out from the chosen modifications, but probably not worth the extra effort.

For now a simple error message can be shown when the same atoms on the same residue are specified as being replaced by 2 different modifications, which in this case would have saved the user a lot of instrument time and head-scratching.

2013-08-09 Brendan MacLean
Milestone1.2»3.1

2014-01-08 Brendan MacLean
Milestone3.1»