I proceed to a separation of proteins n'y FPLC after which I have to do a sequencing but I can only get very little quantity. So what is the minimum protein amount to perform sequencing ?
In the low pmol (with luck high amol) range. Rule of thumb: If you do electrophoresis on a minigel with two wells (a narrow for standard and a wide for sample), blott and see a good band with Ponceau, then cutting out this band will give you enough protein for repeated, automated gas-phase sequencing by Edman's method. If you do it by hand, you need more protein.
Remember though that you need an unblocked N-terminus, in many proteins it is either naturally modified or it can be modified during isolation.