Table 2

TRC complex subunits slightly accumulate in endogenous VAPB immunoprecipitates upon proteasome inhibition
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
ASNA1 O43681 38,793 1.31 ± 0.08 (31) 0.79 ± 0.07 (27) 1.42 ± 0.10 (32) 0.87 ± 0.06 (35)
BAG6 P46379 119,409 1.47 ± 0.18 (36) 0.77 ± 0.11 (36) 1.43 ± 0.19 (52) 0.94 ± 0.10 (43)
GET4 Q7L5D6 36,504 1.39 ± 0.11 (8) 0.73 ± 0.06 (11) 1.30 ± 0.08 (9) 0.84 ± 0.03 (13)
UBL4A P11441 17,777 1.50 ± 0.10 (7) 0.74 ± 0.04 (9) 1.51 ± 0.15 (7) 0.89 ± 0.04 (10)

aLight- (L) and 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.

Baron et al.

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

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