Phosphorylation (O-linked and N-linked) plays an important role in biological functions and cell signaling. Here, we employed a one-dimensional online alkaline-pH reversed-phase nanoelectrospray-tandem mass spectrometry (alkaline-pH-MS/MS) for the investigation of global phosphorylation. In this method, phosphopeptides were separated on a nanoflow C18 column with an alkaline-pH gradient and directly introduced to the mass spectrometer through nanoelectrospray ionization. Although the phosphosites and phosphopeptides identified by alkaline-pH-MS/MS were slightly lower than those of traditional online low-pH reversed-phase tandem MS (low-pH-MS/MS), these two methods were highly complementary to each other. This alkaline-pH-MS/MS may affect the actual polarity and CSD of phosphopeptides, consequently improving the identification of multiply phosphorylated peptides. Moreover, alkaline-pH-MS/MS was compatible with other peptide fractionation and phosphopeptide enrichment techniques, such as offline high-pH or low-pH reversed-phase liquid chromatography fractionation. The complementarity of alkaline-pH-MS/MS and low-pH-MS/MS was further demonstrated by the tandem mass tag (TMT)-based quantitative phosphoproteomic analysis of five pairs of hepatocellular carcinoma (HCC) tumors and normal adjacent tissues (NATs). Furthermore, unique information on significantly changed phosphosites was observed by alkaline-pH-MS/MS. This study provided an alternative and complementary tool for global analysis of both O- and N-phosphoproteome, which may be beneficial for the discovery of phosphoproteins with significant biological functions.
Keywords: alkaline-pH-MS/MS; charge state; fractionation; mass spectrometry; phosphoproteomics.