Issue 688: Add Product Loss Formula column to Edit > Insert > Transitions for small molecules

issues
Status:open
Assigned To:Brian Pratt
Type:Todo
Area:Skyline
Priority:2
Milestone:19.2
Opened:2019-10-08 by Brendan MacLean
Changed:2019-12-20 by Brian Pratt
Resolved:
Resolution:
Closed:
2019-10-08 Brendan MacLean
Title»Add Product Loss Formula column to Edit > Insert > Transitions for small molecules
Assigned ToGuest»Brian Pratt
Notify»kikirkwo
Type»Todo
Area»Skyline
Priority»2
Milestone»19.2
It turns out that researchers working with singly charged small molecules producing singly charged fragment ions in MS/MS often think of the fragments in terms of the atoms lost during fragmentation as "neutral losses", similar to how Skyline currently handles neutral losses from peptides (e.g. Water Loss (DEST) and Amonia Loss (KQRN)). The loss formula may be relatively simple, e.g. H2O and NH3. Whereas, our current Product Formula field requires the researcher to do the math between the Precursor Formula and the loss to come up with a remainder formula.

We should give researchers both options "Product Formula" (as we have today) and add "Product Loss Formula" where we do the calculation to figure out the remainder.

2019-12-20 Brian Pratt
See PR #827 Skyline: adding a "Product Neutral Loss" column to small molecule transition list reader, which makes it convenient to describe fragments in terms of a chemical formula to be subtracted from the precursor's chemical formula."