light intensity channel doubling

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light intensity channel doubling erik.soderblom  2018-01-10 06:32
 
I observed an odd issue within Skyline where if I change which peak I want to integrate, it actually changes the light channel intensity (increases it by quite a bit). I've tried to capture this on the attached slides. I was hoping it was just a visualization thing, but I exported the numerical data and confirmed the actual intensity value is changing. It doesn't appear to be happening on all peptides.
Thanks in advance for looking into this.

Skyline-Daily: 64b. 4.0.9.11707
 
 
Brendan MacLean responded:  2018-01-10 15:40
Hi Erik,
Thanks for your time today supplying files and showing me the problem over screen sharing. As we discussed on the phone, I now think that the problem is limited to the summed chromatograms that Skyline displays in Totals mode, when you have a peptide selected with multiple precursors without having Split Graph mode turned on. If you turn on Split Graph mode, you should again feel that nothing in the chromatograms changes when you change peak integration.

This is, of course, a bug, and we will fix it as soon as we can, probably before the next Skyline-daily, but not before Skyline 4.1, because we believe the same bug existed in Skyline 3.7 and you are the first person to report it.

Thanks for reporting it, though, and for working with us to understand the problem.

More once we have a fix and can say exactly what caused this display issue.

--Brendan
 
Brendan MacLean responded:  2018-01-10 15:55
Thanks to Nick, we now have a simple fix. It was possible to include a transition chromatogram twice in the loop that summed the intensities for the chromatogram totaling. With a simple check for that case, the chromatograms stay constant.

It is such a simple fix that we are going to include it in both 4.1 and the next Skyline-daily.

Thanks again for pointing it out, Erik.

--Brendan
 
erik.soderblom responded:  2018-01-11 09:38
Fantastic! Thanks for your prompt investigation and explanation.
Erik