Automated Mass Spectrometry Data Pipeline Processor

Create a robust Bash script that automatically processes raw mass spectrometry data files from multiple instrument models (Thermo Fisher, Waters, Agilent). The script must: 1) Detect new .raw and .mzML files in multiple watched directories, 2) Perform automated file conversion using msconvert, 3) Apply standardized peak detection algorithms, 4) Generate comprehensive metadata JSON summaries, 5) Archive processed files with cryptographic checksums, and 6) Log all processing steps with timestamp and error handling.