i'd posit that how you're using them makes a difference. when i'm using canned tomatoes i'm usually cooking them long enough that the stems and cores break down. but if you're using them for a quicker cook, it might be worth taking the time to remove them since the texture can be pretty unpleasant.
The best kitchen advice I can give is to always use your common sense and follow your gut. Many times while squishing whole tomatoes by hand, ill feel a particularly tough end-and I discard them.
I used to, but then figured out that they cook up well and you don't notice them in the finished dish. Not sure how I realized that--probably I didn't cut the stem out one time and discovered it didn't make a difference.
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