Flyability ratios for PSII peptide ions and their phosphorylated cognates.

The thylakoid peptide mixtures were treated with alkaline phosphatase for 0, 10, 20 and 40 min to obtain samples with varying degrees of phosphorylation. The signal intensity of each peptide ion was obtained using LC-MS and flyability ratio for each peptide/phosphopeptide pair was determined as (IB−IA)/(IpA−IpB), were IpA and IA are the ion intensities of the phosphorylated and non-phosphorylated peptides at 0 min time point, and IpB and IB are the corresponding ion intensities at the 10, 20 or 40 min time points. An average flyability ratio for each peptide/phosphopeptide pair was calculated from the data corresponding to all time points of alkaline phosphatase treatment. Ac-, N-terminal acetylation; lower case t, phosphorylated threonine residue in peptide sequence; z, the charge state of the peptide ion.