Development of Techniques for Removal of Sodium Dodecyl Sulfate for Enhanced Protein Identification and Characterization

Abstract

Mass spectrometry is a powerful tool employed in proteomics; however, sodium dodecyl sulfate (SDS), a surfactant used for protein solubilization, is known to cause severe interference at concentrations greater than 0.01%. Thus, methods for SDS removal are paramount. This thesis presents the development of techniques for efficient SDS removal while maintaining high protein recoveries. Due to the lack of sensitivity and selectivity demonstrated by current high-throughput SDS quantitation methods, a negative-mode LC-ESI-MS technique was optimized (LOQ 0.5 ng, LOD 0.15 ng SDS). The Pierce Detergent Spin Removal Columns are a commercial product which efficiently removes SDS, but offers poor protein recovery. An alternate protocol is developed which maintains effective SDS removal while providing protein yields of >65%. Proteomic experiments often involve numerous samples, thus necessitating high-throughput methods for SDS removal. A fully automated strong cation exchange-reversed phase technique was therefore developed, which efficiently removes SDS while providing >75% protein recovery.