FragPipe v22.0 Analysis Outputs for Phosphoproteomics & Total Proteome of ATG16L1-Deficient Murine Macrophages (Maculins et al., eLife 2021)

This archive contains partial FragPipe v22.0 outputs for both phospho-enriched and total‐proteome TMT analyses of ATG16L1-deficient and wild-type murine macrophages following Shigella flexneri infection, as described in Maculins et al. (eLife 2021;10:e62320, DOI:10.7554/eLife.62320) pubmed.ncbi.nlm.nih.gov. Contents include: Phosphoproteomics (data_ptm/FP_22/): abundance_single-site_None.tsv (quantification of singly‐phosphorylated peptides) abundance_multi-site_None.tsv (quantification of multi‐phosphorylated peptides) FASTA database (p37688_db3_MusNShigella_20250219.fasta) FragPipe workflow config, MSFragger & IonQuant parameter files, and execution log Total Proteome (data_total/FP_22/): p1/psm.tsv and p2/psm.tsv (peptide‐spectrum matches for Plex 1 & 2) Same FASTA database as above Workflow configs and log All searches used strict trypsin digestion, TMT‐16 labeling, ±20 ppm precursor tolerance, 0.6 Da fragments, 1% FDR (peptide & protein), Match Between Runs, MaxLFQ, median normalization, and phosphorylation‐site localization probability ≥ 0.75. These outputs are ready for downstream differential‐expression and PTM analyses (e.g. via the prolfquapp R package).