n-Dodecyl-β-D-maltopyranoside (DDM)-Assisted Resolubilization Enhances S-Palmitoylation Proteomics

This study demonstrates that adding the non-ionic surfactant n-dodecyl-β-D-maltopyranoside (DDM) during protein resolubilization improves the identification of hydrophobic peptides and proteins in bottom-up proteomics. DDM's effectiveness in overcoming the challenge of losing hydrophobic proteins after precipitation from strong detergent lysis buffers was investigated. Using immortalized mouse macrophages (IMMs), DDM (0.05% or 0.1%) to resolubilization buffers, both with and without 8M urea in 50 mM ammonium bicarbonate (ABC) were added, for global and acyl-biotin exchange (ABE) proteomics (targeting S-palmitoylation). Key findings revealed that the addition of 0.1% DDM increased the identification of total peptides, proteins, and especially membrane-associated proteins in global proteomics compared to urea alone. Gene Ontology (GO) analysis showed that proteins uniquely identified with DDM were enriched in critical cellular processes. In ABE proteomics, 0.1% DDM enhanced the identification of hydrophobic and candidate S-palmitoylated peptides. DDM also increased the number of ABE-enriched proteins, with those uniquely identified by DDM being involved in cellular transport and localization known functions of S-palmitoylated proteins. In conclusion, incorporating DDM during protein resolubilization is a simple and effective method to enhance the coverage of hydrophobic proteomes in various bottom-up proteomics applications.