There is no way to do this in Skyline right now, but I am supposed to implement this feature soon.
Specifically, the feature that I am supposed to implement is "Protein-level calibration curves" where Skyline calculates the calibration curve for a group of peptides.
In the Document Grid, there is a column that you can add to your report called "Protein Abundance". That column combines the information for all of the peptides into a single value. That is the value that we are planning on having Skyline use in the future Protein-level calibration curve feature, but for now, you would have to do that manually.
-- Nick

Nick,
Thank you for your response.
I tried to add "Protein Abundance" to my report. This gave me very strange results.
For my absolute quantification I have followed the absolute quantification tutorial. I have a standard curve of light (set as "standard" in the replicate document grid). Then I have an unknown replicate. In peptide settings I set Normalization as ratio to heavy and regression fit as "quadratic".
In the peptide ratio result of the document grid I have a value for my unknown replicate. When I add Protein abundance I have another result I am not confident in.
I attached the skyline file. Do you have any idea why ?
Thank you,
Clémence

I am not sure I understand what you think is going wrong.
Can you post a screenshot of what you are seeing?
-- Nick

Hi Nick,
Please find attached a ppt with screenshots.

Thank you,
Clémence

the ppt !

Thank you for sending the PowerPoint file.

The "Quantification" column in the Document Grid only gives you information about a single peptide. The Protein Abundance column gives you a number for a single protein. You would not expect to see the same values in those two columns.
-- Nick