Ionization suppression effect of phosphopeptides in nano-electrospray ionization quadrupole time-of-flight mass spectrometry

Protein phosphorylation is an important post-translational modification (PTM), and involves in many cell activities and disease processes. Nowadays, mass spectrometry (MS) is a powerful tool in peptide-based proteomics. But phosphopeptides, especially multiply phosphorylated peptides, are difficult to be detected by MS. One opinion is that the presence of unphosphorylated peptides lead to the ionization suppression of phosphopeptides. But contrary opinion exists. Moreover, the suppression effect caused by different types of phosphopeptides hasn't been studied yet. In this study, a set of synthetic standard phosphopeptides (singly, doubly and triply phosphorylated peptides) with the same amino acid sequence, and the unphosphorylated peptides were injected into mass spectrometer with or without mixing. Through the ratios of signal intensities of the phosphopeptides before and after mixing, we confirmed that the signals of phosphopeptides were suppressed by those of the unphosphorylated peptides. In addition, the signals of the doubly phosphorylated peptides were slightly suppressed by those of the singly phosphorylated peptides with the same amino acid sequence. The signals of the triply phosphorylated peptides were notably suppressed by the singly and doubly phosphorylated peptides with the same amino acid sequence. Therefore, the singly and multiply phosphorylated peptides should be fractionated and enriched before mass spectrometry analysis.