Protein functions often rely on protein–protein interactions. Hence, knowledge about the protein interaction network is essential for an understanding of protein functions and plant physiology. A major challenge of the postgenomic era is the mapping of protein–protein interaction networks. This chapter describes a mass spectrometry-based label-free quantification approach to identify in vivo protein interaction networks. The procedure starts with the extraction of intact protein complexes from transgenic plants expressing the protein of interest fused to a GFP-Tag (bait-GFP), as well as plants expressing a free GFP as background control. Enrichment of the GFP-tagged protein together with its interaction partners, as well as the free GFP, is performed by immunoaffinity purification. The pull-down quality can be evaluated by simple gel-based techniques. In parallel, the captured proteins are trypsin-digested and relatively quantified by label-free mass spectrometry-based quantification. The relative quantification approach largely relies on the normalization of protein abundances of background-binding proteins, which occur in both bait-GFP and free GFP pull-downs. Therefore, relative quantification of the protein pull-down is superior over methods that solely rely on protein identifications and removal of often copurified high-abundance proteins from the bait-GFP pull-downs, which might remove real interaction partners. A further strength of this method is that it can be applied to any soluble GFP-tagged protein.
CITATION STYLE
Née, G., Tilak, P., & Finkemeier, I. (2020). A Versatile Workflow for the Identification of Protein–Protein Interactions Using GFP-Trap Beads and Mass Spectrometry-Based Label-Free Quantification. In Methods in Molecular Biology (Vol. 2139, pp. 257–271). Humana Press Inc. https://doi.org/10.1007/978-1-0716-0528-8_19
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