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. Author manuscript; available in PMC: 2016 Sep 22.

Published in final edited form as: Proteomics. 2014 Dec 17;15(2-3):419–433. doi: 10.1002/pmic.201400259

(A) Top panel; Representative MS/MS fragmentation spectrum of the singly phosphorylated (pY647) FGFR3 activation loop peptide. Bottom left panel; MS spectrum of singly phosphorylated (pY647) FGFR3 activation loop peptide isotopes. Bottom right panel; Extracted ion current of pY647 peptide from Myr (+) and Myr(−) of FGFR3^K650E cells ±PTPN1 or PTPN2 knockdown. (B) Top panel; Representative MS/MS fragmentation spectrum of the doubly phosphorylated (pY647/pY648) FGFR3 activation loop peptide. Bottom left panel; MS spectrum of pY647/pY648 peptide isotopes. Bottom right panel; Extracted ion current of pY647pY648 peptide from Myr (+) and Myr(−) of FGFR3^K650E cells ±PTPN1 or PTPN2 knockdown. (C) Quantification of integrated extracted ion current (XIC) for pY647 and pY647/pY648 in cells expressing FGFR3^K650E–Myr(−). Abscissa represents ratio of integrated XICs, Myr(−):Myr(+). (D) Quantification of integrated XIC for pY647 and pY647/pY648 in cells expressing FGFR3^K650E-Myr(+) ±PTPN1 or PTPN2 knockdown. Abscissa represents ratio of integrated XICs, shPTP:shNEG. (E) Quantification of integrated XIC for pY647 and pY647/pY648 in cells expressing FGFR3K650E-Myr(−) ±PTPN1 or PTPN2 knockdown. Abscissa represent ratio of integrated XICs, shPTP:shNEG. Error bars represent standard deviations; n ≥4. P values were generated from paired, 2-tailed Student's t-tests.

(A) Top panel; Representative MS/MS fragmentation spectrum of the singly phosphorylated (pY647) FGFR3 activation loop peptide. Bottom left panel; MS spectrum of singly phosphorylated (pY647) FGFR3 activation loop peptide isotopes. Bottom right panel; Extracted ion current of pY647 peptide from Myr (+) and Myr(−) of FGFR3^K650E cells ±PTPN1 or PTPN2 knockdown. (B) Top panel; Representative MS/MS fragmentation spectrum of the doubly phosphorylated (pY647/pY648) FGFR3 activation loop peptide. Bottom left panel; MS spectrum of pY647/pY648 peptide isotopes. Bottom right panel; Extracted ion current of pY647pY648 peptide from Myr (+) and Myr(−) of FGFR3^K650E cells ±PTPN1 or PTPN2 knockdown. (C) Quantification of integrated extracted ion current (XIC) for pY647 and pY647/pY648 in cells expressing FGFR3^K650E–Myr(−). Abscissa represents ratio of integrated XICs, Myr(−):Myr(+). (D) Quantification of integrated XIC for pY647 and pY647/pY648 in cells expressing FGFR3^K650E-Myr(+) ±PTPN1 or PTPN2 knockdown. Abscissa represents ratio of integrated XICs, shPTP:shNEG. (E) Quantification of integrated XIC for pY647 and pY647/pY648 in cells expressing FGFR3K650E-Myr(−) ±PTPN1 or PTPN2 knockdown. Abscissa represent ratio of integrated XICs, shPTP:shNEG. Error bars represent standard deviations; n ≥4. P values were generated from paired, 2-tailed Student's t-tests.