Issue 954: some interesting small molecule transition list weirdness

issues
Status:open
Assigned To: Brian Pratt
Type: Defect
Area: Skyline
Priority: 3
Milestone: 4.3
Opened:2023-05-10 09:07 by Brian Pratt
Changed:2024-02-20 14:36 by Brian Pratt
Resolved:
Resolution:
Closed:
2023-05-10 09:07 Brian Pratt
Title»some interesting small molecule transition list weirdness
Assigned To»Brian Pratt
Type»Defect
Area»Skyline
Priority»3
A couple of users struggling with what seem to be garbage transition lists, but which we could still handle better:
https://skyline.ms/announcements/home/support/thread.view?rowId=61026
https://skyline.ms/announcements/home/support/thread.view?rowId=60980
(files attached here)

ideas for improving there, or at least getting user to the problem sooner
1) if we see "null" as a value, treat it as an empty string
2) if adduct description contains things like water loss, and we have no chemical formula, don't do the "can't remove atoms that aren't there" check
3) read charge "positive" as +1, "negative" as -1, in the absence of any other hints
4) adopt some of these headers as knowns in the source code
 
 neum0807185.txt

2023-05-18 14:54 Brian Pratt
Also it would be good to be able to parse the "MSMS spectrum" column, which itself a list of fragment mz/intensity pairs.

2024-02-20 14:36 Brian Pratt
And even more interesting flavors in support issue https://skyline.ms/announcements/home/support/thread.view?rowId=62955