AbstractThe electrophoretic migration behavior of three closely related hydrophobic intrinsic membrane proteins of the photosystem II light‐harvesting complex (LHC II) was investigated in free solution capillary electrophoresis at pH 8.0–10 with running electrolyte solutions containing either anionic, zwitterionic or nonionic detergents. The complete and repeatable separation of these proteins was accomplished with a running electrolyte solution of 25 mM Tris/192 mM glycine, pH 8.8, containing either sodium dodecyl sulfate or n‐octyl β‐D‐glucopyranoside at concentration up to 5.0 and 7.0 mM, respectively. Migration times and resoltuion of the individual LHC II intrinsic membrane proteins were sensitive to the type of detergent. The effect of detergent concentration on the electrophoretic behavior of the LHC II proteins was also investigated. Electroelution of the LHC II components separated by sodium dodecyl sulfate‐polyacrylamide gel electrophoresis was used to isolate these intrinsic membrane proteins, which were then injected onto the capillary electrophoresis system for peak identification.