For the study of the dynamics of the omics, the MS based omics strategy provides more sensitive, high throughput and accurate result in terms of better identification confidence and quantification accuracy. In our work, the MS-based omics approach was applied applied to study the dynamics of intracellular and intercellular signaling events. In our study, we have demonstrated the mass spectrometry based approaches can successfully applied to the discovery of new phosphorylation events involved in the T-cellular signaling and the quantitative phosphoproteomics approach was successfully applied to the study of important physiological function of spermatozoa. With the further combination of multiplex proteomics approach, the dynamics of the cellular signaling and the traffic of the proteome can be elucidated in more detail. The mass spectrometry is also a powerful technology for the study protein conformation, by the combination of ion mobility and the mass spectrometry, not only the protein-protein or protein-small molecular interaction but the conformation change of the structure can be determined. With the development of new MS omics platforms that integrate better mass analysis strategy, ultra high performance separation efficiency and high throughput, data processing system, a more detail information of the cellular signaling dynamics will be revealed.