Fig. 1. Strategies for studying interactomes with mass spectrometry (MS). (a) Affinity purification using antibody, epitope tags, Strep-tag, or tandem affinity purification (TAP) tags; (b) Proximity labeling process with BioID (biotin identification) or APEX (an engineered peroxidase developed from ascorbate peroxidase); (c) Global interactome analysis using co-fractionation or thermal proximity coaggregation. After enrichment or various processes, the output protein samples are analyzed by MS, bioinformatics tools are used to select for high-confident interacting proteins (HCIPs), and then the protein‒protein interaction network or interactome is generated. IEX: ion-exchange; SEC: size exclusion chromatography.