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Usual known mass spectrometry contaminants and reversed sequences were also searched. Andromeda searches were performed choosing trypsin as specific enzyme with a maximum number of two missed cleavages. Possible modifications included carbamidomethylation (Cys, fixed), oxidation (Met, variable) and N-terminal acetylation (variable). The mass tolerance in MS was set to 20 parts per million (ppm) for the first search then 6 ppm for the main search and 10 ppm for the MS/MS. Maximum peptide charge was set to 7 and 5 amino acids were required as minimum peptide length. The ''match between runs'' feature was used between conditions with a maximal retention time window of 1 min. One unique peptide to the protein group was required for the protein identification. A false discovery rate (FDR) cutoff of, Then the samples were diluted to 1 M urea with 100 mM Tris pH 7.5, and Sequencing Grade Modified Trypsin was added to the sample at a ratio of 50:1 for 16 h at 37 C. A second incubation, 2008. ,
Large SCVs have semi-spherical to spherical shapes and a lumen can be clearly distinguished between the bacteria and the SCV membrane by standard light microscopy. Statistical analyses of microscopic acquisitions were performed using GraphPad Prism. t tests were used to evaluate the significance of the results, referred like *, **, ***, **** for p values < 0.05, < 0.01, < 0.001, and < 0.0001, respectively. Statistical details of experiments can be found in the figure legends. The statistical analysis of the proteomics data was performed as follows: Three biological replicates were acquired per condition. To highlight significantly differentially abundant proteins between two conditions, differential analyses were conducted through the following data analysis pipeline: (1) deleting the reverse and potential contaminant proteins; (2) keeping only proteins with at least two quantified values in one of the two compared fractions to limit misidentifications and ensure a minimum of replicability; (3) log2-transformation of the remaining LFQ intensities of proteins, QUANTIFICATION AND STATISTICAL ANALYSIS Following image acquisition, fixed samples and time-lapse images were analyzed using Fiji, Imaris or CellProfiler. The number of infected cells was assessed using CellProfiler automatic segmentation. LAMP1 recruitment around intracellular salmonellae was measured using Imaris analyses of 3D confocal images, p.4, 2005. ,
, The proteins associated with an adjusted p value inferior to an FDR level of 1% have been considered as significantly differentially abundant proteins. Finally, the proteins of interest are therefore the proteins that emerge from this statistical analysis supplemented by those being quantitatively absent from one condition and present in another. The lists and details of the significantly differentially abundant proteins arising from the analyses between the fraction Minf and Mctrl, and between the fraction Minf and Ninf have been deposited to the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2019) partner repository. To focus on proteins which are not related to DNA/RNA, nucleus, mitochondria or ribosome