Traditionally, CE with SDS (CE-SDS) places many restrictions on sample composition. Requirements include low salt content, known initial sample concentration, and a narrow window of final sample concentration. As these restrictions require buffer exchange for many sample types, sample preparation is often tedious and yields poor sample recoveries. To improve capacity and streamline sample preparation, an automated robotic platform was developed using the PhyNexus Micro-Extractor Automated Instrument (MEA) for both the reduced and nonreduced CE-SDS assays. This automated sample preparation normalizes sample concentration, removes salts and other contaminants, and adds the required CE-SDS reagents, essentially eliminating manual steps during sample preparation. Fc-fusion proteins and monoclonal antibodies were used in this work to demonstrate benefits of this approach when compared to the manual method. With optimized conditions, this application has demonstrated decreased analyst hands on time and reduced total assay time. Sample recovery greater than 90% can be achieved, regardless of initial composition and concentration of analyte.