proteomics-database-search-skill

Plan, run, resume, audit, and report proteomics database searches on Linux with FragPipe/MSFragger and compatible validation or quantification tools. Use for DDA or DIA, label-free or isobaric workflows, total proteome or PTM-enriched data, protein/peptide/PTM identification, targeted protein or residue checks, SSH/tmux execution, FASTA preparation, FDR review, quantification, and publication-ready tables, figures, and source-data packages. Includes PTM-specific branches without assuming any particular protein, gene, modification, organism, or sample design.