Objective To investigate the aberrant expression of phosphoproteome analysis of peripheral blood mononuclear cells( PBMCs) in patients with systemic lupus erythematosus( SLE) . Lay the foundation for further re-search of mechanism and treatment in patients with SLE. Methods Phosphopeptides were enriched using TiO2 from PBMCs of patients and healthy subjects, then analyzed by automated LC-MS/MS analysis. Phosphorylation sites were identified and quantitated by MASCOT and MaxQuant. Differential expressed proteins and peptides were screened based on the bioinformatics analysis. Results 1 035 phosphorylation sites were identified from SLE com-prared with normal subjects, 618 corresponding genes were screened out in annotation proteins. Pathway analyses showed 12 signaling pathways were identified. There were the most difference phosphorylation sites in mitogen acti-vated protein kinases( MAPK) signaling pathway. Conclusion Differently phosphorylated proteins and peptides can be detected in patients with SLE, which can be used as a mechanism of reference and supplement combined with metabolic pathway, and might be used as a potential target for treatment and research of SLE.