PTM proteomics had been increasingly used in studies related to inflammation and immunity, but the integrated analysis of multiple PTM was lacking. Here, we integrated WCP, acetylome, phosphoproteome and ubiquitinome datasets to identify LPS stimulation-dependent PTM events in macrophages with or without MG132. Using the SILAC quantification, we successfully identified 53,785 PTM sites and 19,726 proteins at all times in LPS-stimulated macrophages. Integration of these datasets provided a possibility to have a more comprehensive understanding of the inflammatory response.