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. Author manuscript; available in PMC: 2017 Jun 1.
Published in final edited form as: Nat Protoc. 2016 Nov 17;11(12):2515–2528. doi: 10.1038/nprot.2016.140

Figure 1.

Figure 1

Schematic outline and workflow of CoPIT. The three individual workflows performed in CoPIT are shown. Experimental Protocol: Experimental protocols were optimized for high bait and interactor recovery by adjusting cell lysis-, Co-IP and elution conditions. Data analysis: Resulting Raw-data are searched with ProLuCID and uniformly filtered to a peptide FDR of ≤ 0.5 %. Signal-to-noise discrimination is carried out by including different negative controls, such as experiments from CFTR null cells, and significantly regulated interactions are identified using a counting statistics. Network comparison: Protein IDs and results are stored in a relational database, which contains also further ontological information. The Radial Topology Viewer visualizes ranking, functional annotation and connectivity of interactors in the resulting networks as well as differences between conditions.