I have prepared a porphyrin-HYNIC derivative by the reaction of porphyrin alkyl amine with NHS-HYNIC-BOC. Basically it's an -NH2 and -COOH condensation reaction. I got the Mass of the purified product. However, after BOC deprotection (using TFA) I am not getting Mass of the final product.
Did you neutrallize the molecule after Boc deprotection? You're using ESI, so the peak your're getting depends on the charge of ionised particle. Porphirin should have at least 4 basic nitrogens than can react with TFA making salt, so you may be getting the salt signal, which is quite erratic.
Also, did you monitor reaction progress? We usually remove Boc in harsher conditions (pure tfa or hot methanolic HCl), so it may not have been sufficient, especially if some of it was bound to base.
Also, what solvent system are you using for mass spec? If you are using Formic acid in your solvent A or B then free amine might give you a formic acid adduct. If you see your desired weight plus a mass of 46, it might be the case.
Mikhail Nekrasov I have not tried the neutralization. I will try surely. I checked the progress of the reaction by IR. In IR I am not getting peak because of t-butyl group. so I assumed the reaction is complete. I used DCM/TFA 1:1 ratio (rt stirring for overnight) for deprotection.
Try TLC with ninhydrin stain if possible, solvent with ammonia or 1% TEA (dried before staining), probe neutrallized before the plate. This stain reveals amino groups so you should be able to see the product quite brightly, and it should be significantly lower than the source compound.
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