University of Birmingham FAIMS and phosphoproteomics of fibroblast growth factor signalling: Enhanced identification of multiply-phosphorylated peptides

: We have applied liquid chromatography high- fi eld asymmetric waveform ion mobility spectrometry tandem mass spectrometry (LC − FAIMS − MS/MS) and liquid chromatography tandem mass spectrometry (LC − MS/MS) to the investigation of site-speci fi c phosphorylation in fi broblast growth factor (FGF) signaling. We have combined a SILAC approach with chemical inhibition by SU5402 (an FGF receptor tyrosine kinase inhibitor) and dasatinib (a Src family kinase inhibitor). The results show that incorporation of FAIMS within the work fl ow results in (a) an increase in the relative proportion of phosphothreonine and phosphotyrosine sites identi fi ed, (b) an increase in phosphopeptide identi- fi cations from precursors with charge states ≥ +3 (with an associated increase in peptide length), and (c) an increase in the identi fi cation of multiply phosphorylated peptides. Approximately 20% of the phosphorylation sites identi fi ed via the FAIMS work fl ow had not been reported previously, and over 80% of those were from multiply phosphorylated peptides. Moreover, FAIMS provided access to a distinct set of phosphorylation sites regulated in response to SU5402 and dasatinib. The enhanced identi fi cation of multiply phosphorylated peptides was particularly striking in the case of sites regulated by SU5402. In addition to providing a compelling example of the complementarity of FAIMS in phosphoproteomics, the results provide a valuable resource of phosphorylation sites for further investigation of FGF signaling and tra