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Can I compare documents but only looking for differences in specific fields?

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Yes.

Compare the data based on a common view as normal, double click on a document to see the document level differences, expand the Document category to expose the fields.

For each field you wish to ignore, right click on it and choose Add to Smart Filter.  

Once you've done this for all fields except the ones where you are looking for differences, enabling/disabling the Smart Filter will now include the fields you added.

For hiding different sets of fields for different situations, see Can I have more than 1 Smart Filter?

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