Skyline Results grid - peptide results

support
Skyline Results grid - peptide results Tomas Vaisar  2018-04-10 09:44
 
Would anybody know if it is possible to get a Skyline quantification report where would be for a replicate included "calculated concentration", "ratio to standard", as well as Total fragment ion area for measured peptide and Total fragment ion area for the Standard.
In the Results grid I can get a view which gives me the former two, but does not allow to include also the actual peak area responses used in the calculation of the Ratio to standard and the Calculated Concentration.

Is there a different view?

Thanks,

Toams
 
 
Nick Shulman responded:  2018-04-10 11:37
The Results Grid shows a set of data that is filtered down to only show you results for whatever peptide/precursor/transition you have selected in the Targets tree. It is always possible to show the same data in the Document Grid as you see in the Results Grid.

In the Document Grid, you could include the "Total Area" column (it's under Proteins > Peptides > Precursors > Precursor Results > Total Area). Once you have added that column to your view, in the Customize View dialog, you can check the "Pivot Isotope Label" checkbox, so that your light and heavy total areas will appear next to each other.

I am not sure that I understood your question. It might help if you sent us your Skyline document.

In Skyline you can use the menu item:
File > Share > (complete)
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:
https://skyline.ms/files.url
 
Tomas Vaisar responded:  2018-04-10 11:51
Nick,
Might be simpler to show you what I would like to get.
I understand that Results Grid shows the data filtered down to peptide/precursor/transition. And that is what I want. But I do not see a way to show in that summary/report actual peak area (whether for peptide - total area of whatever you choose) for the measured species and for the standard that are used in the calculation of the Ratio to Heavy and of Calculated Concentration (after applying the calibration curve). I attach PPT to show that.

I know how to do this through Document Grid, but the things get pretty messy once you have lot of samples.

Tomas
 
Nick Shulman responded:  2018-04-10 12:23
It sounds like you want to see the "Total Area" column for the light and heavy precursors in the Results Grid.

There is no way to see those two columns in the Results Grid at the same time. In order to see the "Total Area" column in the Results Grid, you would need to have a precursor selected in the Targets tree, but if you had the light precursor selected, you would not be able to see the Total Area of the heavy precursor, or vice-versa.

When we first implemented the Document Grid, we thought about giving it the ability to filter itself down to whatever was selected in the Targets tree, but it never seemed like anyone needed that feature.
 
Tomas Vaisar responded:  2018-04-10 13:10
Thanks Nick, I think the easiest workaround will end up being to filter the Document view with the desired data on individual peptide.

Tomas