Background It is necessary to develop some innovative methods to reveal and discover the novel (SLE)-related protein molecules.In the present study,matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDITOF MS) was employed to detect the differential expression of serum polypeptides in the patients with systemic lupus erythematosus (SLE) presenting with a family history or complicating with kidney injury so as to identify the proteins associated with the genetic factors and kidney injury in SLE.Methods The subjects recruited were divided into four groups,that is,a group of SLE patients with both family history and kidney injury,a group of SLE patients with only kidney injury but no family history,a group of SLE patients with neither family history nor kidney injury,and a control group consisting of healthy volunteers.By adopting MALDI-TOF MS analysis,the serum samples obtained from the three groups of SLE patients were examined and compared with those from the control group; the categorized peptide fingerprint profile was established via the biological data collected from the samples.Results The expression of protein with a m/z of 4207 Da increased significantly in SLE patients; the protein with a m/z of 2658 Da was expressed in all SLE patients; three proteins (with m/z of 1465,5332,and 5900 Da respectively) were expressed in the SLE patients complicated with kidney injury and the protein with a m/z of 1943 Da was expressed in SLE patients with family history.Conclusion A number of differential proteins were successfully detected and identified through MALDI-TOF MS detection and these proteins may be associated with the genetic basis of SLE and the complicating kidney injury.