Issue 716: When light and heavy precursors have different sets of transitions, all quantifiable transitions should be summed when calculating Light:Heavy ratios

issues
Status:closed
Assigned To:Guest
Type:Defect
Area:Skyline
Priority:3
Milestone:21.1
Opened:2020-02-04 by Nick Shulman
Changed:2020-12-19 by Nick Shulman
Resolved:2020-10-22 by Nick Shulman
Resolution:Fixed
Closed:2020-12-19 by Nick Shulman
2020-02-04 Nick Shulman
Title»When light and heavy precursors have different sets of transitions, all quantifiable transitions should be summed when calculating Light:Heavy ratios
Assigned ToGuest»Nick Shulman
Type»Defect
Area»Skyline
Priority»3
Inspired by this support request:
https://skyline.ms/announcements/home/support/thread.view?rowId=43696

When Skyline calculates the light to heavy peak area ratio for small molecules, Skyline tries to create a correspondence between the transitions in the light precursor and the transitions in the heavy precursor.
Part of the reason that Skyline does this is to be able to calculate the "ratio dot product".
The other part of the reason is so that if a user removes a peak from a light chromatogram (because of, perhaps, interference), the corresponding peak in the heavy chromatogram does not get added to the total.

This behavior is not what users expect for small molecules. Skyline's heuristic for matching transitions between light and heavy is not robust unless the small molecule transitions have been given names.

The most likely fix that we will do is to make it so this matching of light and heavy transitions if any of the transitions do not have a Name.

2020-02-04 Nick Shulman
Milestone»20.2

2020-10-05 Brendan MacLean
Milestone20.2»21.1

2020-10-22 Nick Shulman
resolve as Fixed
Statusopen»resolved
Fixed in pull request #1264.
There is now a "Simple Ratios" checkbox on "Molecule/Peptide Settings > Quantification".

2020-12-19 Nick Shulman
close
Statusresolved»closed
Assigned ToNick Shulman»Guest