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