Multi-in-One: Multiple-Proteases, One-Hour-Shot Strategy for Fast and High-Coverage Phosphoproteomic Investigation

Although a multiple-protease based shotgun proteomics method was shown to improve coverage for phosphosite identification, this traditional pipeline is time-consuming and can be of low reproducibility. Here, we demonstrated a multi-in-one strategy to saturate the phosphosite coverage by combining the multiple-proteases based digestion, one-step enrichment, and one-shot data-independent acquisition (DIA) as short as 1 h. In the “three-in-one” workflow, more than 19,700 and 13,500 phosphosites could be identified in the trypsin-like and nontrypsin-like mixture, respectively. By combining and applying our “three-in-one” strategy, nearly 30,000 phosphosites could be successfully quantified with high reproducibility across samples. Meanwhile, we developed a faster and more robust method, in which over a single 66 min chromatographic method by “six-in-one” strategy, 19,445 phosphosites could be successfully localized, drastically reducing the database search time required in the traditional method. Inspiringly, this strategy further enabled us to discover 2,675 phosphorylation events on the low abundant transcription factors (TFs) in living cells with high coverage. More broadly, the multi-in-one strategy makes the multiple-protease digestion in large-scale analysis applicable, with low time-consuming, high sensitivity, improved coverage, and high reproducibility.