Overintegration problem

Overintegration problem luzalonsodasques  2024-05-27 07:50

Good afternoon, my name is Luz Alonso

I am writing to you because I have the following problem with Skyline (64-bit) version (e59d0dc56).

The baseline of my chromatogram, instead of being fixed at zero, starts at another point on the y-axis.

Therefore this influences my peak integration process due to it not only integrates the peak but also from the y-axis point to zero.

I attach a picture of my problem.

Looking forward to your early response



Nick Shulman responded:  2024-05-27 08:00
Skyline is probably handling this scenario correctly.

When Skyline calculates the chromatogram area, Skyline decides that the background level is the lowest of the chromatogram intensity at either the start or end of the peak. In your screenshot the dark red shaded area is the "background" and only the lighter red shaded area about that is what is reported as the "Area".

There are some diagrams showing how Skyline calculates these things here:
-- Nick
luzalonsodasques responded:  2024-05-27 08:28
First of all, thank you very much for your quick response.

I wanted to ask you again if there is any way to manually define the baseline?

Looking foward to your early response,


Mike MacCoss responded:  2024-05-27 15:21
You can adjust the boundaries to whatever points you want. The boundaries will be used to define the area and the background. You can use the mouse to click below the X-axis and drag the mouse to select the boundaries. As Nick pointed out, if you move the left boundary just a little left the background level will drop a bit, but I would imagine the effect is going to be small. It is definitely worth doing an experiment to see how adjusting the boundaries affects the area, precision, and accuracy. We recommend having replicates of a calibration curve to assess the effect quantitatively.

luzalonsodasques responded:  2024-05-29 06:00
Good afternoon again,

I just wanted to ask what means the number near the baseline.


Luz Alonso Dasques.
Mike MacCoss responded:  2024-05-29 09:50
That number and the associated red dashed lines are the number of points between the integration boundaries.