Robert,

In the Document Grid, the "rdotp" value is in a column called "DotProductLightToHeavy" (on the Peptide Result) or "Ratio Dot Product" (on the Precursor Result).

If you want to delete peptides that have low dot product scores, you can use the Pivot Editor in the Document Grid to find the peptides with low rdotp's across all of the replicates, and then you can use the Actions dropdown on the Document Grid to delete those peptides.

Here's a PowerPoint showing how to do that.

There is more information about the Pivot Editor here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=PivotEditor

-- Nick