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

Hongyan Zhao, Debbie Cunningham, Andrew Creese, John Heath, Helen Cooper

Research output: Contribution to journalArticlepeer-review

11 Citations (Scopus)
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Abstract

We have applied liquid chromatography high-field 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-specific phosphorylation in fibroblast 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 workflow results in (a) an increase in the relative proportion of phosphothreonine and phosphotyrosine sites identified, (b) an increase in phosphopeptide identifications from precursors with charge states ≥ +3 (with an associated increase in peptide length), and (c) an increase in the identification of multiply phosphorylated peptides. Approximately 20% of the phosphorylation sites identified via the FAIMS workflow 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 identification 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 trafficking.
Original languageEnglish
Pages (from-to)5077–5087
Number of pages10
JournalJournal of Proteome Research
Volume14
Issue number12
Early online date27 Oct 2015
DOIs
Publication statusPublished - 4 Dec 2015

Keywords

  • FAIMS
  • differential ion mobility
  • FGF signaling
  • phosphoenrichment
  • phosphopeptides
  • phosphoproteomics

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