Crosstalk between PTM sites on different proteins  A. Density gradient diagram of the Log₂ ratio of proteins in WCP and the Log₂ ratio of PTM sites in different PTM proteomes of RAW264.7 cells. Orange and cyan represent 0.5 h and 2 h after LPS stimulation, respectively. Orange and cyan numbers (percentages) on the left and right represent the number and percentage of regulated proteins/PTM sites at the two time points, respectively. B. Heatmap showing the Log₂ M/L values of proteins quantified in both the WCP and all three PTM proteomes in RAW264.7 cells. Only proteins with Log₂ M/L ≥ 1 or ≤ −1 are shown, and the colors of proteins in PTM proteomes indicate the mean Log₂ M/L value of all PTM sites in the protein. C. iceLogo plots showing the difference of amino acid frequency at positions flanking the LPS-regulated PTM sites compared to unregulated PTM sites with P ≤ 0.05 in RAW264.7 cells. D. Interaction network for proteins with regulated PTM sites in RAW264.7 cells. Blue dots indicate the proteins with no interacting partner, while red dots indicate the proteins interacting with other proteins. The size of the dot indicates the number of regulated PTM sites.