Supplementary Figure 3: Quantification of Lck phosphorylation on both regulatory tyrosines.
From: In vitro membrane reconstitution of the T-cell receptor proximal signaling network
(a-d) Representative fragment ion spectra for peptides containing phosphorylated Y394, unphosphorylated Y394, phosphorylated Y505, and unphosphorylated Y505. LC-MS was carried out as described in Online Methods. (e) Table summarizing relevant mass spectrometry parameters, which was obtained by using a 3 ppm peptide threshold and >2 Sequest Xcorr score. % occupancy was calculated by dividing the total ion current (TIC) for the phosphorylated peptide by the sum of TIC for both the phosphorylated and unphosphorylated cognate peptide. This TIC based quantification method has been shown to have greater dynamic range than both spectral counting and isotope labeling methods2,3.
