Dear Hitoshi theoretically any protecting group compatible with your reaction conditions and the other PGs along the chain can be employed.

It also depends on what you are going to do after this first reaction.

In case any acidic treatment doesn´t disturb the next step(s) or the chemical integrity of your final product, you might want to use Boc as Lys side chain PG, being after removed by acid treatment in organic solvent and appropriate scavengers.

Otherwise I would go for the Z grup, removable by cat. Hydrogenation on Pd/C, under neutral condition (provided that no double bonds or Alloc are present in the structure as they would be likely reduced).

As for the C terminal Carboxylic acid, it must be protected to avoid self coupling (still as tert butil, Fm, or Methyl ester (with the last being removed under really harsh conditions)).

If the last point is a matter of concern, you can preactivate the polisaccaride C terminal carboxylic acid, as pentafluorophenyl ester, which in presence of a organic base and cathalytic amount of HOBT selectively reacts with the free amine.

It could be interesting to use a Z group for the Lysine side-chain and a benzyl ester for the carboxylic acid. A hydrogenation step could remove both in one step :) 

Thank you Luigi and M for your thoughtful responses.  My main concerns were in trying to find a protecting agent that would preferentially react with the lysine side chains without appreciably reacting with the N-terminus, and removing the groups without hydrolyzing the polysaccharide, which is moderately acid and base sensitive.