ULK1/2 Restricts the Formation of Inducible SINT-Speckles, Membraneless Organelles Controlling the Threshold of TBK1 Activation

Saul, Vera Vivian; Seibert, Markus; Krüger, Marcus; Jeratsch, Sylvia; Kracht, Michael; Schmitz, Michael Lienhard

Data from two biological replicates (2 ï‚´ 28 raw files of IgG control and anti-Flag-SINITBAD) were analyzed using MaxQuant (v1.5.5.18) (Cox and Mann, 2008) and the implemented Andromeda search engine (Cox et al., 2011) . Protein assignment was accomplished with correlation of fragment spectra with the UniProt human database (July 2016). Common contaminants were excluded from the analysis. Data processing was performed with tryptic specifications and default settings for mass tolerance in MS and MS/MS spectra. The minimal peptide length was set to 7 amino acids by default and the false discovery rate on protein and peptide level was set to 1 %. Prior to further processing of the data, contaminants, reverse entries and proteins that were only identified by a modification site were filtered out. In order to define high confidence interactors, identified proteins were classified according to criteria given in suppl. Fig. 8A . Proteins from all three groups were combined and constitute the SINTBAD interactome.