It sounds like Skyline is giving you one row per precursor because your report includes the "Total Area" column (or maybe "Total Area MS1") which lives on the PrecursorResult object.
You would get one row per peptide if you used the "Normalized Area" column (it's under "Quantification" which is on the "Peptide Result").
By default, the Normalized Area of a peptide is the sum of all of the areas of the Transitions under the unlabeled precursors under the peptide. The Normalized Area might be a different value if you chose a different normalization method on:
Settings > Peptide Settings > Quantification

In Skyline 4.1, we added some grouping and totaling features that would make it possible to sum the precursor areas for each peptide. Here are some PowerPoint slides showing how to use the pivot editor in Skyline:
https://skyline.ms/wiki/home/software/Skyline/download.view?entityId=79611505-d8fa-1035-b3d9-e465a39397c8&name=SkylinePivotEditor.pptx

(you might also want to look into using the Pivot Table in Microsoft Excel-- it's a really good way to roll up multiple rows of data in the way that you describe)

Hi Nick,

Thank you, the pivot table feature was exactly what we needed!

Randall