LCM Proteomics Pipeline

Documentation for Millie’s Proteomics project. This site tracks the processing of LCM samples from initial QC to Differential abundance analysis.

Update Parameter changes (run3) - 13/03/26

Updated data filtering criteria to be more stringent: * Filtering Rule: Proteins must have ≥ 50% non-missing values in at least one condition, ensuring that differential abundance analysis is on robustly detected features.

Pipeline Stages

• 1a. Initial QC
• 1b. DAA marker sense check
• 3. DE plots
• 4. GSEA
• 5. GFAP correlation
• 6a. MSstats limma correlation
• 6b. MSstats limma comparison
• 7. Cell-cell interactions
• 8. PPI network
• 9. Tripartite Astrocyte Signature
• 10. Aβ tryptic peptide correlation