Chlamydomonas CDKL5 phosphorylation in lf5 CDKL5-GFP-TG (control), lf2 CDKL5-GFP, and lf5 CDKL5K33R-GFP cells.

S4 Data shows the datasets for MS experiments 3, 4, 6, and 7. All CDKL5 peptide isoforms: a lists all the peptide isoforms (both phosphorylated and nonphosphorylated) identified in two sets of biological samples (MS experiments 3 and 4) consisting of purified CrCDKL5 from strains lf5 CDKL5-GFP-TG, lf2 CDKL5-GFP, and lf5 CDKL5K33R-GFP-TG. Column “Start position” lists the first amino acid of each peptide isoform. Column “Stop position” lists the last amino acid of each peptide isoform. Column “Phosphoisoform” shows the phosphorylated residues of each phosphopeptide; “Non” indicates peptide was not phosphorylated. Columns D–I show precursor intensities of each peptide isoform in each sample; numbers were normalized based on total peptide intensities from CDKL5. “NA” indicates that the peptide isoform was not detected. Value of 0 (“0.00E + 00”) indicates that the peptide isoform was identified but no quantitative data acquired due to low-abundance. Isoforms from the activation loop peptide (aa 155–170) are highlighted in yellow; the nonphosphorylated isoform of this peptide was consistently detected at much higher abundance in samples from the lf2 CDKL5-GFP strain than from the other two strains. Highlighted in green are phosphorylated sites detected only in samples from the lf5 CDKL5-GFP-TG strain, suggesting that these sites are auto-phosphorylated. Of these, residues surrounding only S584 match the CDKL5 phosphorylation-consensus sequence (see Fig 11). Peptides beyond amino acid 622 are from GFP. All CDKL5 peptides: a list of the sum of all the isoforms (both phosphorylated and nonphosphorylated) for the same peptide from MS Experiment 3 and 4. Value of 0 (“0.00E + 00”) indicates that the peptide was either not identified or no quantitative data acquired due to low-abundance. An empty indicates that the value for the denominator to calculate the ratio is zero. Peptide 155–170 is highlighted in yellow. CDKL5 (WT and K33R) CIP peptides: a list of the sum of all the isoforms (both phosphorylated and nonphosphorylated) for the same peptide from MS Experiment 6 and 7. Value of 0 (“0.00E + 00”) indicates that the peptide was either not identified or no quantitative data acquired due to low-abundance. An empty indicates that the value for the denominator to calculate the ratio is zero. Peptide 155–170 is highlighted in yellow. (XLSX)