FAIMS and Phosphoproteomics of Fibroblast Growth Factor Signaling: Enhanced Identification of Multiply Phosphorylated Peptides.
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.
School of Biosciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, United Kingdom.
Hongyan
H
Zhao
School of Biosciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, United Kingdom.
Debbie L
DL
Cunningham
School of Biosciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, United Kingdom.
Andrew J
AJ
Creese
School of Biosciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, United Kingdom.
John K
JK
Heath
School of Biosciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, United Kingdom.
Helen J
HJ
Cooper
D000595:Amino Acid Sequence; D002853:Chromatography, Liquid / Q000379:methods*; D000069439:Dasatinib / Q000494:pharmacology; D005346:Fibroblast Growth Factors / Q000378:metabolism*; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D008969:Molecular Sequence Data; D010748:Phosphopeptides / Q000032:analysis* / Q000378:metabolism*; D010766:Phosphorylation; D019000:Phosphotyrosine / Q000032:analysis / Q000378:metabolism; D047428:Protein Kinase Inhibitors / Q000494:pharmacology; D040901:Proteomics / Q000379:methods; D011758:Pyrroles / Q000494:pharmacology; D017468:Receptors, Fibroblast Growth Factor / Q000037:antagonists & inhibitors / Q000378:metabolism; D015398:Signal Transduction; D053719:Tandem Mass Spectrometry / Q000379:methods; D019061:src-Family Kinases / Q000037:antagonists & inhibitors / Q000378:metabolism
D010748:Phosphopeptides; D047428:Protein Kinase Inhibitors; D011758:Pyrroles; D017468:Receptors, Fibroblast Growth Factor; C105686:SU 5402; D019000:Phosphotyrosine; D005346:Fibroblast Growth Factors; D019061:src-Family Kinases; D000069439:Dasatinib
FAIMS; FGF signaling; differential ion mobility; phosphoenrichment; phosphopeptides; phosphoproteomics