Allow Custom Report to Export Chromatogram Time in Units of Indexed Migration Time

Allow Custom Report to Export Chromatogram Time in Units of Indexed Migration Time sstewart  2023-07-21 10:09

Right now, when building a custom report, I can only select 'Raw Time' under Chromotagrams. Instead, I'd like the option to select 'Indexed Migration Time'.

Brian Pratt responded:  2023-07-21 10:58

Just to be clear, this would be where the values are output scaled such that the first point has value 0.0 and the last has value 1.0?

Brendan MacLean responded:  2023-07-21 11:35

That is not my understanding. This is where the x-scale is what we use when the user right-clicks in the chromatogram graph and clicks "Show <iRT Calculator> Score" where <iRT Calculator> is the name of the iRT calculator currently set in the document.

Nick Shulman responded:  2023-07-22 09:45
It might be that what we should do instead is add a couple of new columns so that you would have enough information to do the conversion yourself.
That is, when you have an iRT calculator, Skyline calculates the slope and intercept for each result file that converts between iRT score and retention time for that file.
I am not sure exactly what we should call these new columns but we could certainly get something like that implemented in the next version of Skyline.
-- Nick
sstewart responded:  2023-07-24 07:34
I was imagining something like Brendan's proposal. But to be honest, all that matters is that the units (scaled or not) are consistent between export / import (my other request). I'd like to avoid redoing the calculation myself, not because of difficulty of course, but because we would then need to keep our code "in sync" with Skyline should you guys ever change the iRT calculation (even if it's unlikely that you do). I want my code to be as ignorant as possible of everything except peak integration/assignment.

tldr; All that matters to my code is that the peaks are nicely aligned across replicates. The exact units of indexed migration time don't really matter.
sstewart responded:  2023-08-03 01:11
thoughts on this? if slope/intercept fastest way to get this into next release, that's fine.
Will Thompson responded:  2023-08-04 10:21
Hey team, catching up on this thread. What happens when the user right-clicks and shows the indexed time in the graphs? Is that not a value that can be exposed in a report? I've attached an example document in case we need a test case to make this less abstract. We want to be able to export a chromatograms report and a beak boundaries report with the x-axis in the iRT-scaled time, for each run, then import a peak boundaries file which has the corrected integration times expressed still as iRT-scaled time.