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. Author manuscript; available in PMC: 2024 Oct 16.
Published in final edited form as: Mol Cell. 2024 May 16;84(10):1948–1963.e11. doi: 10.1016/j.molcel.2024.04.014

Figure 1. Ubiquitome-enrichment proteomics reveals a CTLH E3 substrate.

Figure 1

A) Workflow of the proteomics study indicating the used HEK293 cell systems (1) parental vs MAEA-/- knockout and (2) MAEA-/- + MAEA rescue line (resMAEA-/-) vs MAEA-/-, enrichment of ubiquitylated proteins with Halo-tagged pan-TUBE (TUBEHalo), followed by DDA- or DIA-quantitation and data processing/analysis.

B) Individual volcano plots of the -log10 p-values vs the log2 protein abundance of TUBE-precipitates between parental and two MAEA-/- clones (cl1 and cl8). 5% p-value and 4x cut off are indicated.

C) Individual volcano plots of the -log10 p-values vs the log2 protein abundance of TUBE-precipitates between resMAEA-/- vs MAEA-/-cl8 and between parental vs MAEA-/- cl8. 5% p-value and 4x cut off are indicated.

D) Venn diagrams showing overlapping proteins from 5% p-value and 4x cut off of B and C.

E) TUBEHalo-captured proteins from MAEA-/-cl8 and resMAEA-/- cell lines were precipitated with Halo-resin (TUBE: pellet) and analyzed by immunoblot analysis. Vinculin serves as protein input control.