Issue 870: Implement special peak statistics for DDA MS/MS

Status:closed
Assigned To:Guest
Type:Todo
Area:Skyline
Priority:1
Milestone:22.2
Opened:2022-02-14 by Brendan MacLean
Changed:2022-07-20 by Brendan MacLean
Resolved:2022-07-20 by Brendan MacLean
Resolution:Fixed
Closed:2022-07-20 by Brendan MacLean
2022-02-14 Brendan MacLean
Title»Implement special peak statistics for DDA MS/MS
Assigned To»Nick Shulman
Type»Todo
Area»Skyline
Priority»1
Milestone»22.1
Currently for DDA acquisition type we make all MS/MS transitions non-quantitative, but use CrawPeaks to calculate bogus peak statistics for the MS/MS peaks. Specifically, there is no expectation that the following aspects of these peaks are at all relevant to anything:
- Peak Area
- Background Area
- Height (which is background subtracted)
- FWHM

So, we should change these as follows in this case:
- Peak Area = Height = Apex intensity without background subraction, i.e. the intensity of the MS/MS spectrum with the highest total intensity for all transitions monitored (or should it be simply the highest total intensity for the entire spectrum? This would be more consistent, but also more susceptible to interference. Alternatively, it could be the highest intensity of the last prior extracted MS1 signal, which might correspond well to some user expectations.
- Background Area = 0
- FWHM = #N/A
- Mass Error - Should it be relative to the peak that is responsible for the Height and Peak Area values, or stay the weighted average of all measurements between the integration boundaries?
- Full review of other values should also happen be part of this to make sure everything in sync.

2022-07-20 Brendan MacLean
resolve as Fixed
Statusopen»resolved
Assigned ToNick Shulman»Brendan MacLean
Milestone22.1»22.2
In the end, we decided to go with peak area for DDA, but without background subtraction, like SureQuant. Not quite sure how this impacts FWHM, but the important statistics are okay in this implementation.

2022-07-20 Brendan MacLean
close
Statusresolved»closed
Assigned ToBrendan MacLean»Guest