Infection of human immunodeficiency virus type (HIV) 1 in an infected individual affects many physiological processes, eventually leading to the development of acquired immune deficiency syndrome (AIDS). For efficient replication, the virus utilizes its accessory proteins to modify many physiological aspects of the infected cells and the individual as a whole.1-3 Immense studies have been carried out to study HIV infection such as the role of HIV accessory proteins in the intracellular processes affected by HIV infection and mRNA changes in the infected cells.4-7 However, it is only recently that the proteome changes are being studied.8 Proteomics can be defined as “the systematic study of the many and diverse properties of proteins in a parallel manner with the aim of providing detailed description of the structure, function

and control of biological systems in health and disease”.9 The most valuable information on the system being studied is the differential expression of proteins in cells, tissues or body fluids of different states. Hence, proteomic analysis needs to be quantitative. Some of the most common approaches employed in quantitative proteomics are introduced in the following section and the principle associated with each approach is briefly discussed. Various quantitative proteomic methods have been employed in the study of HIV infection. In the rest of this chapter, examples of HIV research utilizing quantitative proteomic analysis will be provided. As the research is much diversified, the examples are grouped according to the sample type. The proteome of T cells can be monitored for changes in response to HIV infection. The cultured HIV-infected macrophages can be analyzed, or the plasma of infected individuals can be used to study whole body responses to HIV infection. Cerebrospinal fluids from infected patients can be analyzed.