Selective extraction of peptides in acidic human plasma by porous silica nanoparticles for peptidome analysis with 2-D LC-MS/MS

In this study, an improved method for human plasma peptidome analysis including selective porous silica nanoparticles (MCM-41) extraction and subsequent online 2-D nano-LC-MS/MS analysis was established. Enhanced enrichment efficiency for the MCM-41 extraction was obtained by adjusting the pH of the plasma sample to 2.5. A total of 1680 unique peptides were identified in the plasma sample obtained from one healthy donor, which is nearly twice the amount identified from the native state of the plasma sample. The hydrophobic property, molecular weight (MW), and pl distribution of the identified peptides at pH 2.5 and native state of the plasma sample were systematically investigated and compared. Furthermore, many unusual cleaved peptides from plasma proteins (e.g., HSA) were observed at pH 2.5, which clearly show a ladder pattern. The cleavage patterns for all of the identified peptides at pH 2.5 were summarized, and chymosin and cathepsin D were confirmed as the possible peptidases responsible for the change of cleavage pattern in peptide profiling.