Complex can be separated using low pH buffer and then concentrate and purify the eluted protein using TCA or other method. To identify the binding partner better to resolve eluted protein in 2D gel or using LC MS and do the MALDI analysis, or you can also try to directly digest those whole complex (Ab-Ag), without separating, for MALDI analysis because peptides for Ag can be easily identified over Ab (this will be good for monoclonal Ab or Ab specific to single Ag). For elution optimization try this protocol http://www.gelifesciences.com/gehcls_images/GELS/Related%20Content/Files/1334615650802/litdoc18102229AE_20121107154820.pdf

Thanks a lot for your attention and help.

Sincerely,

Juliana