I make my coffee every morning. I leave it to rest for 20-30 minutes, mix it with some milk, and pour it into a plastic bottle. I drink the coffee from that bottle during the day.
Am I doing it right? Does the quality or the amount of caffeine decrease, if I store it in a plastic bottle?
A short answer is "not significantly", assuming you just store your drink for the day, and there is no sharp changes in storage conditions (strong heat, freeze, etc.)---except warming up the amount you want to drink.
Coffee drinks are unstable, though, and a simple, freshly passed drip coffee tastes different (quality changes) with time. So quality will actually change over a day, although the difference is hard to notice (except people with very acute taste sense).
You are also adding milk, which softens the overall taste, so I think noticing changes in the coffee flavour is even harder.
Every vending machine around me (every 100m or so) sells coffee drinks in PET bottles. These bottles are stored for several weeks, and they sell pretty well. They taste fine for that price point and quality, and they are very stable. Of course, they do not include only coffee. They include milk, sugar, and hard-to-spell things. The last category does contain taste stabilizer, etc., so that is unfair comparison. I am just thinking it is interesting to see that coffee in plastic bottles in actually pretty common, especially for relatively short times.
I have found various health-scare articles online such as this and this about the effects of bisphenol A (BPA) on the body, a chemical which can be leached from a plastic container in to the coffee, though they're probably not reputable sources of information. As for the effect on flavour, when I was on a work experience placement I was given a plastic container for my coffee when I arrived (priorities!) and it did affect the flavour slightly in my opinion. The answer here is that it is highly subjective, as implied by Eric Platon, and if you are happy with it then that's fine. As for the effect on the quantity of caffeine, I'm pretty sure it will have no effect.
The flavor of the coffee will be affected far more by the choice of beans; the roast; the expiration date; the grind; the span of time between grinding and brewing; and last but certainly not least, the brewing method, than by the vessel into which it is put for a short period just prior to drinking it. If you are gearing up for a long car ride, the flavor will degrade somewhat faster in a plastic container, but that wouldn't affect the decision for me. If you've ever been in a Flying J, you probably know that truck drivers almost invariably fill huge plastic mugs with coffee. As far as the caffeine levels, that might be affected slightly (on microscopic levels) depending on how long you keep it in there. The slightly more porous plastic will accumulate infinitesimal quantities of coffee on the sides, which is why plastic typically stains faster than glass or metal.
P.S. I wouldn't be too worried about health effects since even super paranoid worry-worts drink from aluminum cans and plastic bottles.
