Identification of amino acid preferences in Adi3 phosphorylated peptides

In order to determine amino acid preference in peptides phosphorylated by Adi3, the sequences from the top 63 peptides showing the highest mean signal intensity in the first and second subarray images of the phosphorylated Ser-peptide chip were used. To analyze the amino acid composition of the top 63 peptides, the percentage of a single amino acid within the 63 peptide sequences was compared to the percentage of the respective amino acid in the whole peptide library. Additionally, to determine position-dependent amino acid preference within the top 63 peptides, the frequency of each amino acid at a given position was counted and divided by the total count of the respective amino acid. This was done for the composition of the top 63 peptides and for all peptides present in the library. Finally, the position-dependent value for all peptides was subtracted from the value for the top 63 peptides. To determine amino acid positional frequencies within the phosphorylated peptides, sequence logos of the top 10, 20, 30, 40, 50, or 63 peptides on the Ser-peptide chip and top 10 peptides on the Thr-peptide chip were generated using the WebLogo 3 server [30].