Issue 831: Change or add an option for MS/MS spectrum graph dotp value in mirror plot with Prosit

issues
Status:open
Assigned To:ritach
Type:Defect
Area:Skyline
Priority:2
Milestone:22.1
Opened:2021-07-29 by Brendan MacLean
Changed:2022-04-27 by ritach
Resolved:
Resolution:
Closed:
2021-07-29 Brendan MacLean
Title»Change or add an option for MS/MS spectrum graph dotp value in mirror plot with Prosit
Assigned To»ritach
Type»Defect
Area»Skyline
Priority»3
Milestone»21.2
From a user and instructor of Skyline:

"When you correlate two spectrums with the mirror option in Skyline a dotp is calculated, does it take into account the unfragmented precursor peak? I ask this question because I have noticed that PROSIT and other prediction tools (like pdeep3) do not include the unfragmented precursor intensity in the prediction and I guess this affects negatively in the dotp value. Am I right? I attach you some examples in a word document."

She also referenced this paper as a useful source:
https://pubmed.ncbi.nlm.nih.gov/33970638/

Whe should either fix what we do for dotp in this case, or add an option, if we feel what we are currently doing has some utility.
 
 correlated-spectrum.docx

2021-11-29 ritach
Milestone21.2»22.1

2022-03-31 Brendan MacLean
Priority3»2
Raising the priority, since it got mentioned again on the support board.

https://skyline.ms/announcements/home/support/thread.view?rowId=55124

2022-04-27 ritach
Notify»Brendan MacLean;Nick Shulman
It seems to me that the dotp in the Prosit mirror mode is calculated using currently annotated peaks only, so effectively user can select the ion types to be used, including the precursor. Should we decouple the two and provide a separate selection option for dotp only? Seems a bit excessive to me.
Otherwise, the only new thing to implement here is the ability to hide/show the dotp (and maybe other title elements)