Yes you can, but take about your freeze dryer after that. However your protein will be in chloride form. To totally removed it you should exchange chloride ions into another ones. Form my experience cholride counteriones are safe for cells, enzyme ect.

Thanks a lot adam.. How can you exchange chloride ions with protons..?

No.

You will get rid of the water but not the ions. That's why people use 'volatile' buffers - such as ammonium acetate - but even to get rid of these by speed-vac takes several repetitions.

I would recommend either repeated 'concentrate dilute with water' cycles with a micro-concentrator (such as 'Centrion') OR buffer exchange by a small gel filtration column (such as a PD-10)

this is also dependent on amount of protein/peptide you have. desalting is accompanied with loss of protein/peptide, the centricon type concentrators are supposed to give a recovery of 80% but I never got those. also how much HCL is in the protein solution, will aid in better suggestions

1M HCl in a aprotein concentration of 400ug/ml...