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The function of a protein is functional through multiple protein interactions, so creating an interaction network between proteins can help us understand the composition of a protein complex or the up-and-downstream relationship between different proteins. The most common methods to identify protein interaction is yeast two-hybrid (Y2H) and Affinity-purification mass spectrometry (AP/MS). Y2H uses two proteins to see if they can interact and induce the yeast to express its reporter gene to identify. AP/MS, on the other hand, identifies the composition of the protein complex. AP/MS analysis the whole interactome and can investigate the relationship between proteins, not just to understand if two proteins can interact.

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