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But how do you know whether it is hidden fat or protein?

Oy, there is NO really good short answer to that one... I will say that FDA and USDA, regulations and nutrition database respectively, always calculate carbs "by difference". If it's not fat and not protein (two numbers they really want to know about) then it must be carbs. That usually works, too, because they're fussy about the cals, the proteins and especially the fats!

Sadly, we lowcarbers want to know precisely on the carbs, so we have to do this effective carb calculation we've been talking about.

If you want to know more about the whole nutrition facts label thing, go here:
ExpertFoods Inc., Super Duper Label FAQ
to get probably the best label FAQ, the basics to start with, you will find anywhere on the web (and written by a longtime lowcarber, too).

Hope this helps!