Issue 135: Implement "decrease in old protein" method of calculating half-life

issues
Status:closed
Assigned To:Guest
Type:Todo
Area:Topograph
Priority:2
Milestone:1.2
Opened:2011-12-30 by Evvie Vincow
Changed:2017-10-18 by Brendan MacLean
Resolved:2012-06-26 by Nick Shulman
Resolution:Fixed
Closed:2017-10-18 by Brendan MacLean
2011-12-30 Evvie Vincow
Title»Implement "decrease in old protein" method of calculating half-life
Assigned To»nicksh@u.washington.edu
Type»Todo
Area»Topograph
Priority»2
Milestone»1.2
As we discussed, I'd like to test whether Topograph can measure protein degradation more directly. The method would be something like this:

Calculate % new as usual.
Compare % new to raw % D3.
Assuming that the difference between those two numbers reflects protein that is new but unlabeled, calculate the percentage of the unlabeled protein that is actually new, and subtract it from total unlabeled protein.
Use the resulting figure, "% old," instead of % new, in the log plots to calculate half-life.
Create an option for this method in the drop-down on the HalfLivesForm.

2012-06-26 Nick Shulman
resolve as Fixed
Statusopen»resolved
Assigned Tonicksh@u.washington.edu»Evvie Vincow
In the latest versions of Topograph (since about March), there have been several new options for how to calculate half life.

In the "Half Life Calculation Settings", where it says "Which quantity should Topograph use to calculate the fraction of the peptide that is newly synthesized", you want to choose "The fraction of unlabeled peptide".

Then, then (small) amount that needs to be subtracted from the unlabeled peptide to account for the fact that some newly synthesized protein happens to be unlabeled is controlled by the next option:
"How should Topograph determine the precursor pool at later time points".

2017-10-18 Brendan MacLean
close
Statusresolved»closed
Assigned ToEvvie Vincow»Guest