Intensity in Skyline is much higher than Xcalibur bin fang  2019-07-23
 

For the same peak, the intensity value in Skyline is much higher than the intensity shown in Xcalibur. However, if I click on the individual data points in Skyline, the spectrum will show the correct intensity.

 
 
Brendan MacLean responded:  2019-07-23

Try zooming in on the spectrum graph you have in the PowerPoint slide. I expect you will find that it is a profile spectrum. Skyline sums the signal found within your extraction range with profile data, you should find that if you are zoomed in enough to see the multiple peaks in the spectrum that if you add up the ones highlighted by the colored band, that they add up to the point shown in the chromatogram.

We actually have made no effort to make Skyline produce numbers on the same scale as Xcalibur. However, you should find that if you do a linear regression between their numbers and ours that they correspond very closely. Our numbers have been used a great deal and vetted in many papers. We are confident they produce valid quantitative results comparable to instrument vendor software, as claimed in this paper from the Hoofnagle lab:

https://www.ncbi.nlm.nih.gov/pubmed/29203474

But, our peak area numbers do not necessarily match vendor peak area numbers. Though, they should be quantitatively consistent.

Thanks for posting to the Skyline support board with screenshots of what you are seeing.

--Brendan

 
bin fang responded:  2019-07-23

Thank you Brendan for the quick reply and explanation. We've been using and publishing result from Skyline. Just didn't notice this until now.