Low pH capillary electrophoresis application to improve capillary electrophoresis-systematic evolution of ligands by exponential enrichment.

•A novel low pH CE-SELEX is proposed for interaction validation of proteins and ssDNA library.•Reverse migration of complex and unbound ssDNA makes complete protein–ssDNA complex collection without ssDNA interference.•Direct complex collection at cathode is convenient no need to exactly control collection time.•Larger amount protein–ssDNA complex collection than common CE-SELEX.