Additional file 4: Table S3.

SILAC mass spectrometry analysis of endogenous VAPB immunoprecipitates from human U2OS cells. Light- or heavy-labeled cells were treated with MG132 for 2 or 6 hr, as indicated. Equal amounts of light- and heavy-labeled extracts were mixed and endogenous VAPB was immunoprecipitated using specific antibodies. The light/heavy SILAC ratios (L/H) determined by mass spectrometry are indicated, as well as the protein coverage. L + MG indicates that the light-labeled samples were treated with MG132. Proteins whose interaction with VAPB is stimulated by proteasome inhibition accumulate in these samples, resulting in L/H ratios higher than 1. H + MG indicates that the heavy-labeled samples were treated with MG132. Protein accumulation in the heavy-labeled samples results in L/H ratios lower than 1. The L/H for proteins that are not affected by proteasome inhibition will be close to 1.

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Baron et al. BMC Biology 2014 12:39   doi:10.1186/1741-7007-12-39