The cell's proteome (protein profile) is constantly changing due to active degradation by the proteasome system, which is the main proteolytic system in the cell. Degradation by the proteasome system is a highly-regulated process implicated in numerous cellular events including transcription, differentiation, proliferation, and death. Identifying the cellular "active degradome", meaning all proteins actively being degraded by the proteasome at a given time, can therefore reflect the cellular condition, provide substantial insights into cellular programs and state, and present novel therapeutic possibilities. Current methods to detect the cell's active degradome, which mainly rely on mass spectrometry (MS) analysis, have low sensitivity and fail to detect low abundance proteins and proteins with rapid turnover (e.g. transcription factors). Therefore, there is an unmet need for a method to better detect, analyze, and profile degraded proteins inside cells.

The proteasome is isolated by immunoprecipitation under reversible cross-linking conditions that maintain the peptides that are being degraded within it. Subsequently, solid-phase extraction and MS analysis identifies these peptides (Figure 1). MAPP can be used to study patterns of protein cleavage and proteasomal regulation induced by defined stimuli or under different pathologies such as cancer and inflammation. For example, since proteasomes are known to be upregulated in cancer cells, MAPP can be used on biopsies to identify specific "fingerprints" of the transformed tumor, enabling personal tailoring of the most potentially effective treatment. Another example is the immunoproteasomes, a unique proteasome that is activated by cells under inflammatory conditions. Applying MAPP on cells following a viral or bacterial infection will identify an infection-induced 'active-degradome' signature. This can be used to identify pathogenic proteins that are targeted for either antigen presentation or other cellular functions, which holds significant therapeutic potential. Of note, proteasomes can also be isolated from biological fluids (i.e. blood, cerebrospinal fluid); therefore, proteasome profiling provides an accessible tool for analyzing different pathologies.