Does peeling, cooking or pureeing fruits and vegetables change the FODMAP content? Short version: this common questions does not have a good answer at this time.
Traditional nutrient database show little difference between cooked and raw fruits and vegetables. Published data from more complete FODMAP analysis has not yet explored many of these subtler variations in fruit and vegetable preparation.
It makes sense that peeling and cooking would affect certain FODMAPs in food, but there isn't enough info to be specific except in a couple of cases. We know that fructans in vegetables are water soluble and leach out into the cooking water, which is why onions and garlic in a soup or stew are potential problems even if you pick them out. We don't know specifically how many grams change, though. This effect could be useful for vegetables like broccoli and cabbage, I would think, suggesting that boiled and drained vegetables would have less fructans than raw or sauteed, but there is no data to prove it.
Peeled v. unpeeled apples and pears were analyzed in two studies by researchers at Monash University, Australia. Overall, peeled apples and pears by % weight actually had slightly more fructose than unpeeled (we might conclude fructose must be in the flesh of the fruit rather than the peel). Two varieties of apples were analyzed for polyols, peeled v. unpeeled . Peeled Granny Smith's had slightly more sorbitol than unpeeled. Peeled Pink Lady's had slightly less sorbitol than unpeeled. No generalization can be drawn, apparently. I have not seen any FODMAP data on cooked v. uncooked fruits.
It is hard to imagine any way that pureeing would change the fructose or polyol composition of fruits or vegetables. I am not aware of any specific data about whether pureeing can break down fructans in vegetables. My guess is that it can't break the molecular bonds of fructose links in fructans. Even if it could, would that be an advantage? Breaking down fructans, for example, would just mean the puree would be higher in fructose, which is also a FODMAP! (Might be helpful for someone without fructose malabsortion.)
What about food preparation methods that involve fermentation? Theoretically, the bacteria and/or yeast in fermented food could reduce the FODMAP content of the food before you eat it (instead of after you eat it, in your gut!). So far, we know that sourdough breads have less fructans than breads leavened with baker's yeast. The traditional two-day sourdough fermentation is what counts, not the word "sourdough" in the name or the flavor of the bread. These will usually be artisan breads from specialty bakeries. One clue to identifying a bread made by the sourdough process: there will be no baker's yeast in the list of ingredients.
Those are my thoughts on the subject, what about yours?
Updated 12/17/2012

Hey.
I've done a little experimentation.
I've braised 6 g shallots, in white wine vinegar, approx. 1 hour and subsequently added carrot, celery and tomatoes to make a Bolognese sauce. I had no problems.
2 days later I fried 2 g shallots to eat on the side for a steak. I became very ill.
It was the same shallots!
I think that boiling in acid solution fructans breaks down into fructose and that I can better tolerate a little fructose (<3 g) than fructan (<0.5 g)
I have read about the critical amounts in an article from Monash University. Unfortunately I cannot remember which one.
Greetings Bente
Posted by: Bente Jarmon | April 02, 2012 at 12:41 PM
Is there a registered, licensed dietician in Oakland or Berkeley (San Francisco Bay Area) who I could contact? The closest person on the list posted here is too far for me to drive (I have Multiple Sclerosis in addition to IBS). I've had success with the Basic Elimination Diet and two challenges but would like to work with a professional to go forward. Thanks for your help with this!
Posted by: Patrice Wagner | April 02, 2012 at 05:20 PM
This really is intriguing. If anyone else repeats this experiment please write in with results!
Posted by: Patsy Catsos | April 02, 2012 at 09:32 PM
I don't know of anyone personally but suggest you try the "find a dietitian" link on the earight.org web site. Filter it by selecting dietitians that do one-on-one consults, digestive health, and food sensitivities and intolerances and perhaps you will find someone with some familiarity.
Posted by: Patsy Catsos | April 02, 2012 at 09:34 PM
I have a problem with whey and all of the fodmap categories when I tested them. But I have noticed that when an onion is cooked for a very long time, it does not seem to bother me as much as if it is uncooked or cooked until it changes color. That has gotten me to wonder if cooking onions changes the fructan somehow and I read a bit about maybe it changing into fructose? But I don't know much about that. Would be curious to see if there is a set time that it takes to break down the fructans so it makes it easier for me to digest!
Posted by: Sonya | October 20, 2012 at 08:09 PM
A lot of people share your observation that cooked onions do not bother them as much as raw ones. No published data on the difference though. We do know that fructans are water soluble so we can picture how boiling and draining would reduce fructans. But the same would not apply to sauteed onions. Guess we will have to wait for answers on this.
Posted by: Patsy Catsos | October 20, 2012 at 08:21 PM
This is interesting. I've been noticing that I can tolerate steamed kale (well kale cooked in a pressure cooker with water, so I guess it's more boiling) better than I can cooked any other method. But if I drink the water too, I have more problems. I've also tried blending it, but that makes it much, much worse. I have FM and also seem to be sensitive to fructans, so I'm not sure whether its a fructose or fructan issue - but something definitely changes with both boiling and blending!
Posted by: Sarah | November 06, 2012 at 06:11 AM