Yes. This is possible by using the protocol search result export instead of the standard protocol export feature.
This export option is not yet supported by the API.
To export a section of protocol analyzer results, first place a timing marker pair around the region you would like to export.
Then click the gear icon next to "Decoded Protocols" on the right.
Select "search between the timing markers."
Select your timing marker pair.
Open the decoded protocols menu again.
Select "Export search results."