Average Mass Error PPM

Average Mass Error PPM sarah.lennon  2013-11-27
Hi Brendan,

I'm currently using skyline Daily vr. to do MS1 quantification using Maxis Impact Bruker datas. In order to apply a second filter, I wanted to export the average mass error ppm. Here, it appears, that the number reporter in the .csv file is not exactly the same than the one on the top the peak indicated in the skyline file.
Do you have an explanation? Maybe I'm not exporting what I'm thinking.

Enclosed, you will find the skyline file as well as the .csv file.

Thanks for your help,


Brendan MacLean responded:  2013-11-27
Hi Sarah,
You are right, the AverageMassErrorPPM value is a weighted average of all of the chromatogram peaks for a single precursor. Whereas, the value shown on the chromatogram graphs is the mass error of the single most intense chromatogram peak, just as the retention time value shown with it is the apex time of the most intense peak.

Maybe Skyline should offer both values in the reports. In this implementation, however, I decided to have only the average, and since the mass error for the most intense peak is much easier to derive yourself.

I will consider offering both. Thanks for your feedback.

ryan morrison responded:  2022-05-16
I ran into this same problem recently and was happy to find a previous question and good explanation.
A couple of follow up questions:
Would it be possible to display the Average PPM on the top of the peak in the chromatogram view?
Is the Average PPM from only the selected transitions and not all available? For instance, if I import data for 5 y-ions and then only display / select 3, would the Average PPM be from the 5 imported or the 3 selected?
Nick Shulman responded:  2022-05-16
I am not sure that I understand your questions.
The Average Mass Error PPM value that you can see in the Document Grid or in the Results Grid is calculating by taking the weighted averages of the mass errors of the transitions under that precursor. The mass errors are weighted by the transition peak area. If a transition has been marked as "non-quantitative" (you can right-click on a transition in the Targets tree to mark it as non-quantitative) then the transition will be excluded from the precursor's Average Mass Error PPM calculation.
I am not sure exactly what you mean about displaying or selecting only 3 of the 5 ions that you imported. When Skyline calculates the average mass error PPM for a particular precursor, that calculation is not going to be affected by what is selected in the Targets tree.
If you would like to learn more about the Document Grid and the Results Grid, you should take a look at the Custom Reports tutorial:

In the years since this question was first posted, we have added several new mass-error-related graphs to Skyline. You can see these graphs by using the menu items located at:
View > Mass Errors
I am not very familiar with exactly what you can see in those graphs, but one of them might have the information that you are looking for.
-- Nick
ryan morrison responded:  2022-05-16
Thanks for the quick response and answers, very helpful. I now understand better the Average PPM calc and how to make a transition non-quantitative as needed.
For the question about what is displayed in the chromatogram view, what I currently see is the ppm of the highest intensity transition listed just below the retention time. This is selected to be displayed by right-clicking on the chromatogram and selecting "mass error". Is there a way to change what it shows from the ppm of the highest intensity transition to the average ppm of the quantitative transitions as selected in Targets tree?