Combination antiretroviral therapy (cART) has vastly improved the quality of life of those suffering from HIV. However, interruption of therapy leads to re-emergence of the virus from the latent cellular reservoirs that include macrophages, dendritic cells and particularly CD4+ T cells. J-Lat cells are a well-established CD4+ T cell line (derived from Jurkat cells) that harbour one integrated copy of the HIV provirus. These cells have been used to study both the factors that help maintain latency and to identify signals that can break latency and lead to viral reactivation. Previous studies have examined this at the transcript-level or attempted limited protein pull-down experiments. As a first step towards understanding the persistence of HIV and activation of latent provirus, analysis of the changes in host cell protein expression at the early stages of activation is crucial and may provide vital clues to develop new ways to control or eliminate viral reservoirs as well as defining the mechanisms that maintain HIV persistence. This study has provided a comprehensive quantitative protein expression map of latently infected J-Lat cells and follows changes in protein expression after viral reactivation of J-Lat clones by TNF-alpha. More than 9000 proteins and their modifications were identified and quantitated in latent and reactivated cells, making this study the largest of its kind. Unexpectedly, statistical analyses of the data revealed perturbation of several pathways in latently infected cells including proteins involved in cell signalling, energy generation and key transcription factors. This data highlights that latently infected cells are not “invisible” or indistinguishable from uninfected cells and that they have a discrete proteomic signature which has unveiled new drug targets and immunotherapeutic targets that could be used to eliminate HIV.