Mass spectrometry of co-immunoprecipitation using Arabidopsis MKIP1-YFP as bait

Arabidopsis thaliana (Arabidopsis) MATURASE K INTERACTING PROTEIN1 (MKIP1) is a plastid-localized, non-canonical member of the starch-branching enzyme family. Here we used co-immunoprecipitation (IP) coupled with proteomics to identify proteins bound to MKIP1 in stably transformed Arabidopsis lines expressing MKIP1 fused to a C-terminal YFP tag in the wild-type (Col-0) background. Untransformed wild-type (Col-0) Arabidopsis plants served as control. Proteins co-precipitating with MKIP1-YFP were purified via anti-GFP beads and identified via shotgun proteomics. We performed three individual experiments each using multiple replicates. Each experiment was separately analysed using MaxQuant.