Antibody Conjugation and Storage Protocol

Antibodies were conjugated to isotopic metal reporters as described previously^{18 (link)}. Following conjugation antibodies were diluted in Candor PBS Antibody Stabilization solution (Candor Bioscience). Antibodies were either stored at 4 °C or lyophilized in 100 mM D-( + )-Trehalose dehydrate (Sigma-Aldrich) with ultrapure distilled H₂O for storage at −20 °C. Before staining, lyophilized antibodies were reconstituted in a buffer of Tris (Thermo Fisher Scientific), sodium azide (Sigma-Aldrich), ultrapure water (Thermo Fisher Scientific) and antibody stabilizer (Candor Bioscience) to a concentration of 0.05 mg ml⁻¹. The antibodies, metal reporters and staining concentrations are listed in Extended Data Table 2. A limitation of this study is that we did not have an antibody for labeling bacteria due to the inherent difficulty of antibody-based detection of Mtb in FFPE tissue.