Online Removal of Sodium Dodecyl Sulfate via Weak Cation Exchange in Liquid Chromatography–Mass Spectrometry Based Proteomics

Biological research often requires
the use of sodium dodecyl sulfate
(SDS) to solubilize protein samples; however, this detergent is not
compatible with direct mass spectrometry (MS) analysis. Here, we report
an online high-throughput proteomics method that permits standard
in-solution digestion of SDS-containing samples followed by direct
liquid chromatography coupled to tandem mass spectrometry (LC–MS/MS)
analysis using weak cation-exchange chromatography (WCX). This approach,
called the online removal of sodium dodecyl sulfate (Online reSDS),
exploits the properties of WCX in a highly organic and mildly acidic
medium to retain positively charged peptides by both hydrophilic interaction
and electrostatic attraction while simultaneously repelling negative
SDS molecules. This method was optimized to successfully analyze complex
samples that contain up to 1% of SDS. Furthermore, online reSDS improves
the identification of peptides with post-translational modifications
(PTMs), such as deamidation and phosphorylation, without preliminary
enrichment. In conclusion, we show that reSDS can facilitate research
in proteomics by allowing the use of SDS in a wide range of LC–MS/MS
applications with simplified sample-processing procedures.