Hi,

Considering the reactivity of a maleimide moiety is much lower towards amines/amides, having a cysteine thiol in your peptide will automatically make it selective for that residue.

If your pH is between 6.5 and 7.5, the reaction is so favourable to thiol than amides you typically will not see any side reactions.

I used to do tagging of proteins with chromophores via maleimide - thiol reaction. They were wonderfully efficient.