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Table 5 RPN2 and DDOST slightly accumulate in endogenous VAPB immunoprecipitates upon proteasome inhibition

From: VAPB/ALS8 interacts with FFAT-like proteins including the p97 cofactor FAF1 and the ASNA1 ATPase

Protein name UniProt ID MW (Da) SILAC ratio L/Ha
L + MG 2 hr H + MG 2 hr L + MG 6 hr H + MG 6 hr
RPN2 P04844 69,284 1.11 ± 0.02 (4) 0.88 ± 0.00 (2) 1.30 ± 0.10 (4) 0.96 ± 0.02 (6)
DDOST P39656 50,801 - - 1.12 ± 0.00 (2) 0.64 ± 0.00 (1)
  1. aLight- (L) or heavy-labeled (H) cells were treated with MG132 (MG) 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. 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. The numbers in parenthesis represent the number of spectra analyzed for each sample.