AIM:To detect the protein compositions in human lens by mass spectrography. METHODS:Prefractionation of complete lens proteins were carried out for reduction of complexity of samples. Then the proteins were separated by one-dimensional sodium dodecyl sulfate polyacrylamide gel(1D SDSPAGE), the gels were divided into slices in accordance with Coomassie brilliant blue staining,after digestion in the gel with trypsin,coupled with reversed phase high-performance liquid chromatography(RP-HPLC) separation and linear ion trap tandem mass spectrometry(LTQ) for analysis of eluted peptides.Bioinformatics tools were used for metabolic process analyses of identified proteins. RESULTS:A total of 574 lens proteins were identified.A number of unknown lens proteins and proteins isoforms were identified,including 38 proteins analogous to some proteins,56 uncertain proteins,27 uncharacterized proteins,42 proteins known molecular weight but unknown functions.Meaningful results about metabolic process analyses were obtained by bioinformatics analyses for identified proteins. CONCLUSION:This study provide abundant data analyses of many unknown proteins of human lens and their corresponding metabolic processes.