Functional elimination should work via inhibitory antibodies (e.g. see Unruh et al., Oncotarget, 2016 May 3;7(18):25264-75. doi: 10.18632/oncotarget.7955). Selection/isolation from a solution could be done via Immunoprecipitation (e.g. see Yamauchi et al., J Occup Health. 2015;57(2):161-8. doi: 10.1539/joh.14-0148-OA. Epub 2015 Jan 20).
You could prepare a column with the matrix conjugated to antibodies against the specific protein. Then allow the cell sup. for binding with the conjugated matrix. Them load onto column and flow through should be devoid of the protein.