ATG4B and infection: As Rab GTPases are involved in endosomal trafficking, and GAPs and GEFs regulate membrane transport, phagocytosis, and control the actin cytoskeleton, enrichment of these functional categories indicates profound reorganization of intracellular trafficking upon infection with Mtb. We identified an enrichment in modified proteins in the category ‘regulation of catabolic processes’ (p=2.39×10−25 in the phosphopeptide dataset; Figure 3C), which includes components of the autophagy machinery such as Atg4b, Rubicon, autophagy kinases (Ulk1, Ulk2), and autophagy receptors (Optineurin, Bnip3l).