The Boc group will fall off. You will have to use acetic acid or ammonium acetate (better), or some other ion pairing agent that is not so acidic. even with 0.1% TFA, when you go to concentrate the sample, the TFA will remove the Boc group. Acetic acid will have more of a background, but if you have some longer UV absorbing chromophore, then you can use 260-280 nm for detection instead of 215 or 220 nm.

Exactly - the BOC is very acid sensitive. You can use lithium trifluoroacetate if you want to be as close to TFA as possible.

I have done this with 0.1% TFA and it works fine. However, for evaporation of solvent, I would suggest immediate lyophilization of the pooled fractions, rather than rotary evaporation, since rotary evaporation will take much longer and require heat (40oC), further accelerating Boc removal. The Boc group is slowly removed under these conditions (ACN/H2O/0.1%TFA) if you allow your fractions to stand around - I recall something like 10% cleavage after 4 hours or so. Anymore TFA is going to make this deprotection even quicker, obviously.

We have used 1% TFA for cleavage of trimethoxybenzyl group in presence of Boc. It required about 30 min and immediate neutralization with TEA. About 20-40% cleavage was observed.

I agree with Steven Fletcher, we have used RP HPLC with 0.1% TFA followed by lyophilization, and it works fine. For standard purifications 0.1% is OK. You could also use formic acid, which is less acidic, but the resolution and overall performance will not be as good as with TFA (in my opinion, not worth replacing the TFA).

As an extra precaution you can freeze your collected fractions as they come out of the HPLC and keep them frozen until freeze drying.

I have used RP HPLC with 0.1 % TFA to purify BOC- protected peptides with no evidence of BOC deprotection during purification. I completely agree with Vasquez and Fletcher.

I have used previously and I found problems under rotavapor conditions when just a few ml were on the flask, so remove under liophilization and during purification don´t keep the molecules under this condition too much time and keep it at low temperature (5ºC). Trick: you can add small amounts of HPLC water-ice to the test tubes.

In summary follow the sugestions of Vazquez, Fletcher and Claudio.

I usually add some drops of TEAB (triethyl ammonium bicarbonate) right into the target fraction just to reach pH 5-6 and then evaporate it by using a rotavapor at 45-50 C. It's fast (at this temp) and safe method. I wouldn't recommend liophilization of any TFA solutions just because it cause corrosion of metal parts in my equipment.

NBoc protectiong group is stable under this HPLC analysis conditions even for the preparative one.

However be carefull with evaporation. Lyophilisation will be more appropriate to remove TFA.