Objective To find specific biomarkers related to HAART treatment in plasma samples of AIDS patients for clinical therapeautic efficacy evaluation and guidance for the prognosis of HIV treatment.Method Plasma samples of AIDS patients were collected from Infectious Disease Department 1 of Shanghai Public Health Clinical Center in June of 2008 to February of 2009,including 11 successfully HAART treated cases (HIV load ＞ 50 copies/ml) and 11 unsuccessfully HAART treated cases (HIV load ＜50 copies/ml).Patients' age ranged from 22 to 63.Plasma samples were treated by Bio-rad AurumTM Serum Protein Mini Kit to remove high abundant proteins:albumin and immunoglobulin were removed.The treated plasma proteins were separated by two-dimensional electrophoresis and analyzed by electrophoretogram using Imagemaster software to find differentially-expressed proteins related to therapeutic efficacy.After digestion by trypsin,the differentially-expressed proteins were identified by online reversed-phase nano-flow liquid chromatography coupled with electrospray ionization ion trap mass spectrometry.Results Low abundant proteins were efficiently enriched after the AurumTM Serum Protein Mini Kit treatment.Six differentially-expressed proteins were detected while comparing successfully and unsuccessfully HAART treated group.These proteins were accurately identified by tandem Mass spectrometry (MS), including serum transferrin, serum β-fibrinogen, etc.Conclusions Our proteomic research revealed that the differentially-expressed proteins such as transferrin,which is related to plasma virus loading in AIDS patients in the process of treatment,might be potential biomarkers evaluating HAART therapeutic efficacy.