Initially, protein-level intensities were normalized to the intensity of bait (DNAJB8) in each TMT channel. We then used a version of the scaled reference approach to combine multiple TMT runs . The bait-normalized integrated TMT reporter ion intensities were averaged for each protein across the three control conditions in each AP-MS run to get a scaling factor. Each bait-normalized protein intensity was then divided by this scaling factor. Storey's modification of the method of Benjamini and Hochberg was used to convert unadjusted p-values to q-values (local false discovery rates) . Unadjusted p-values were ranked in increasing order and the q-value for the ith protein determined from: