Rapid and effective removal of perfluorooctanoic acid from proteomics samples

Abstract

We recently demonstrated that perfluorooctanoic acid (PFOA), a volatile surfactant, is as effective as sodium dodecyl sulfate (SDS) at solubilizing membrane proteins. PFOA can be removed by repeated evaporation prior to mass spectrometry analysis. However, removal of PFOA by evaporation is a lengthy process that takes approximately 6 hrs. Toward the goal of decreasing the length of time required to remove PFOA from protein digests, we tested the efficiency of PFOA removal and subsequent peptide recovery using strong cation exchange (SCX) chromatography, hydrophilic interaction chromatography (HILIC), fluorous solid phase extraction (FSPE), and anion exchange chromatography (ANX). We found that all these chromatographic techniques except ANX chromatography remove PFOA thoroughly from protein digest. Peptide recovery rates from SCX chromatography varied widely; non-acidic peptides were recovered at rates of up to 95%, and acidic peptides were recovered at rates of less than 10%. On the other hand, acidic peptides were recovered well from HILIC, while peptides whose pIs are greater than 6 were recovered poorly. Peptide recovery using FSPE was considerably lower, less than 10% for most of the peptides. These results indicate that SCX and HILIC chromatography provide a more rapid alternative to the evaporation method for applications in which recovery of entire set of peptides is not required.