Methods to Isolate Proteins from Detergent-containing Solutions for Proteome Analysis

Abstract

The use of the detergent sodium dodecyl sulfate (SDS) to assist in the solubilization of protein samples can be highly beneficial in the proteomics workflow. However, SDS is incompatible with LC-MS. Acetone precipitation is an effective means of depleting SDS from protein samples. However, inconsistent and variable yields have limited the use of this technique as a front-end purification strategy ahead of MS. This thesis provides an in-depth characterization of protein recovery through acetone precipitation. An improved protocol is proposed, using an increased amount of ionic buffer to ensure proper protein precipitation efficiency. The use of a filter cartridge to separate the organic solvent from the protein pellet is examined. High SDS removal (99.75%) efficiency and high protein recovery (>80%) were found to be possible with this device. Overall, this work provides evidence that acetone precipitation is an effective method to deplete SDS ahead of MS analysis.