Introduction for the whole source 

• Brief overview of the types of materials and general questions 

• Some overview workflow, importance 

• Summary of common research questions addressed through these analyses 

• Notes on sample suitability (context) 

●  Template Workflow (ceramics example) 

 Sampling and Sample Preparation 

• Criteria for choosing ceramics or crusts (visible residues, surface vs. embedded layers) 

• Methods of scraping or powdering residues 

• Pre-treatment protocols (e.g., decalcification, lipid removal, decontamination) 

• Metadata documentation: sample weight, visual characteristics, prior treatments 

○ Data Acquisition and Export 

• Overview of lab instrumentation used Sample submission procedures and chain of custody 

• Run setup, controls, and blank inclusion 

• Exporting raw files and accompanying metadata (e.g., instrument settings, run order) 

○ Data Processing and Quality Control 

• Raw data formats and initial inspection (e.g., .RAW files, chromatograms) 

• Conversion or preprocessing tools 

• Internal QC procedures: blank subtraction, retention time alignment, contamination check 

○ Analysis Tools and Workflow 

• Software tools used (e.g., MaxQuant, MetaMorpheus) 

• Parameter settings and database selection (e.g., species-specific protein DBs, decoy databases) 

• Search engine outputs: identification thresholds, peptide-spectrum matches (PSMs), FDR 

○ Interpretation and Data Structuring 

• Annotation of protein functions and taxonomic origin 

• Filtering and summarizing identified proteins 

• Structuring output tables for integration into SharePoint/ARHUT 

• Standard column headers and metadata fields 

○ Documentation and Reproducibility 

• Versioning and storage of scripts, parameter files, and software versions 

• Linking raw and processed files to sample metadata in SharePoint or ARHUT 

• Description of any manual validation or corrections 

○ Output and Data Archival 

• Exported result formats (.txt, .csv, annotated PDF reports) 

• Deposition of final datasets and metadata in ARHUT 

• Optional: deposition in external proteomics repositories (e.g., PRIDE) with cross-links 

○ Limitations and Considerations 

• Challenges in protein preservation and contamination risks 

• Limitations of taxonomic resolution 

• Notes on sample reusability and destructive nature of analysis