Different ratio-to-standard result on different computers

Different ratio-to-standard result on different computers Joerg  2021-10-14

we have encountered a very strange thing in our quantifications of metabolites. In these cases we used stabile isotope-labelled internal standards for each analyte and exported the "ratio-to-standard". We have opened the same file on two different computers and exported the "ratio to standard" both with the setting "SUM" and "MAX". On one computer the exported values are identical (and plausible looking at the peaks), but on the other computer the "SUM" setting leads to exactly 2-fold increased ratios while the "SUM" setting yields the same results as the other computer.
As the ratio-to-standard is only a single value, I expected identical values for both settings (as they are on my computer), but the other computer consistently yields two-fold higher ratios, also for other analyses files, if we use the "SUM" setting.
I hope that we are just missing something, some setting we may have altered, but two different results depending on the computer from which you export from the same file would be next to the "Xerox bug" for me...

Nick Shulman responded:  2021-10-14

I am not sure I understand what you did. Are you talking about exporting a custom report from Skyline, and was that report created using the Pivot Editor which is what the "SUM" and "MAX" are referring to?

One reason that the results would be different would be that the report definition that you are using is different on the two computers. Report definitions are usually stored along with many other Skyline settings in a "user.config" file deep under the "Users/<username>/AppData/Local/..." folder. You can also tell Skyline to include the report definition in the Skyline document by going to "Settings > Document Settings > Reports" and checking the checkbox next to the report names that you want to be included in your .sky file.

You can export report definitions to a ".skyr" file by going to:
File > Export > Report > Edit List
and then select the report whose definition you want to export and push the "Share" button.

A .skyr file is a small text file which contains a list of the columns that are in the report, as well as the operations that might have been applied using the Pivot Editor.

In Skyline, the number of rows in the report that you end up with depends a lot on which columns are included in the report. If one version of a report has twice as many rows as a different version, it often is because one version of the report definition includes columns from the Transition or Precursor level, whereas the other report only has columns from the Molecule level.

When you use the pivot editor in Skyline, the number of rows in the resulting report are reduced. If one of the value columns is using the "Sum" aggregation function, that would be affected by the number of rows that were in the report before the pivoting was applied.

If I understand your question right, it sounds like the report definitions on your two computers are different. If you export ".skyr" files on both of the computers and compare those text files you will probably be able to see the difference.

It's possible that I have misunderstood your question and your question has nothing to do with reports in Skyline and/or the pivot editor.

If that's the case, you should send us your Skyline document.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

If that .zip file is less than 50MB you can attach it to this support request. Otherwise, you can upload it here:

If this question has something to do with Reports in Skyline, you should also send us the report definition.
On way to do this is to go to "Settings > Document Settings > Reports" and check the checkbox next to the report that you are interested in. (You should this before you do "File > Share" so that the report definition gets included in the .zip file that you create).
A different way to export the report definition would be to go to:
File > Export > Report > Edit List > Share
and then you can send us the .skyr file that you create.

-- Nick

Joerg responded:  2021-10-14

Hi Nick,
many thanks for the quick reply! Yes, I was referring to a report from the Pivot Editor. I hoped that such report settings were somewhere I wasn´t aware of! Glad, this is the case. We will most likely store the report definitions with the respective Skyline file from now on!
Thanks a lot!