Novel tools are necessary to explore proteins related to human immunodeficiency virus (HIV) infection. In this work, proteomic and glycoproteomic technology were employed to examine plasma samples from HIV-positive patients. Through comparative proteome analysis of normal and HIV-positive plasma samples, 19 differentially expressed protein spots related to 12 non-redundant proteins were identified by ESI-ion trap MS. Among these, the 130-kDa isoform of alpha-1-antitrypsin was found to be decreased in HIV-positive patients while another variant with a molecular weight of 40 kDa was increased. SWISS-2-D-PAGE reference gel and protein sequence comparisons of the 40-kDa protein showed homology with alpha-1-antitrypsin minus the N-terminus, and its identity was further confirmed by 1-D Western blotting and glycoproteomic analysis. In all, our results showed that proteomics and glycoproteomics are powerful tools for discovering proteins related to HIV infection. Furthermore, this 40-kDa variant of alpha-1-antitrypsin found in the plasma of HIV-positive individuals may prove to be a potentially useful biomarker for anti-HIV research according to bioinformatics analysis.