There is unfortunately a bug in the "Protein Abundance Transition Summed" value.

Currently, the "Protein Abundance Transition Averaged" value has what we intended the "Protein Abundance Transition Summed" value to be-- If there is no normalization then the Protein Abundance Transition Averaged is the sum of all of the transition peak areas under that protein. The "Transition Summed" value is that sum multiplied by the total number of transitions, which is not a value that makes any sense.

We hope to fix it soon so that there is only one value in there, and it is equal to what is currently the "Transition Averaged" value.

If there is a normalization method specified on the Quantification tab at "Settings > Peptide Settings" then the protein abundance values are a little different than just the some of transition areas.
-- Nick

Thank you for your quick response. I'll wait for the bug to be fixed to obtain the normalized protein abundance.
To clarify, is this bug limited to the live report document grid or results grid, and does it not affect Live Report > Group Comparison results, such as fold change or adjusted p-value at the protein level?
Also, is there documentation available that explains the back-end calculations for fold change and adjusted p-values in group comparisons? I'd like to ensure our manual calculations match Skyline's calculations before proceeding.
Please let me know if you have any questions or need additional information.
Happy 4th of July!
Dhaval