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

issues
Status:closed
Assigned To:Guest
Type:Todo
Area:Skyline
Priority:1
Milestone:20.2
Opened:2015-03-21 06:14 by Brendan MacLean
Changed:2022-02-14 14:16 by Brendan MacLean
Resolved:2022-02-14 14:15 by Brendan MacLean
Resolution:Fixed
Closed:2022-02-14 14:16 by Brendan MacLean
2015-03-21 06:14 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 06:24 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 14:44 Brendan MacLean
Assigned ToNick Shulman»Brendan MacLean
Milestone4.1»4.3

2022-02-14 14:15 Brendan MacLean
resolve as Fixed
Statusopen»resolved
NotifyBirgit Schilling»
Milestone4.3»20.2
We have made a lot of progress on this, such that it is now possible to describe to someone how to achieve this through the Document Grid by including the columns:

- Quantitative
- Isotope Dist Rank
- Library Rank

It is then possible to filter ions by rank and turn Quantitative off and on for all of the ions that match the filter.

2022-02-14 14:16 Brendan MacLean
close
Statusresolved»closed
Assigned ToBrendan MacLean»Guest