Peptide recovery from acid-precipitated sodium deoxycholate pellet

Sodium deoxycholate (SDC) is MS-compatible ionic detergent which is compatible with in-solution tryptic digestion. SDC is removed from tryptic digested mixtures easily by acid precipitation and it has been demonstrated its capacity to increase trypsin activity. Additionally, and on the contrary to urea, SDC does not generate carbamylation side-products. Here, we report an optimized SDC-based shotgun proteomics sample preparation methods for blood-based protein biomarker research applied to human plasma. We show that an important subset of peptides was co-precipitated with the SDC salts and was recovered by a sequencial extraction of the SDC pellet by re-solubilization and precipitation.