Issue 403: Make it possible to choose top N transitions for quantification

issues
Status:open
Assigned To:Brendan MacLean
Type:Todo
Area:Skyline
Priority:1
Milestone:4.3
Opened:2015-03-21 by Brendan MacLean
Changed:2018-11-01 by Brendan MacLean
Resolved:
Resolution:
Closed:
2015-03-21 Brendan MacLean
Title»Make it possible to choose top N transitions for quantification
Assigned To»Nick Shulman
Notify»Birgit Schilling
Type»Todo
Area»Skyline
Priority»3
Milestone»3.2
It has been requested that we make quantification in group comparisons more flexible on the transitions that get used. Specifically, the Gibson lab has found performance of MS1 filtering is improved by using only the monoisotopic peak. One can also imagine that users might want to extract many ions for DIA and PRM but only quantify by the top 3 or even just the top 1, as in MS1.

As a general rule of thumb, including ions without interference should improve quantification, but the less selective methods (MS1 and DIA) run greater risk of including interference with each transition included, which may outweigh the benefit of adding more transitions. Also, DIA and PRM allow extraction of so many ions that it may useful to limit them.

It seems like dropdown lists like:

Quantify by:

Top MS1 ions: Top Fragment ions:
[ 1 |\/] [ All |\/]
  All
  1
  2
  3
  4
  5


2017-06-10 Brendan MacLean
Priority3»1
Milestone3.2»4.1
We really need to come up with a strategy that allows users to specify "quantitative" and "qualitative" transitions. This came up at ASMS a lot this year. Users don't always want to quantify by all transitions in the document, which is all we offer at the moment.

2018-11-01 Brendan MacLean
Assigned ToNick Shulman»Brendan MacLean
Milestone4.1»4.3