Proline workflow

--- Resubmitted on 2026-03-30 16:27:35 UTC ---
Changes detected:
  Row count: 56223 → 56696
  Added columns: ['epsilon_precision_mean', 'epsilon_precision_median', 'log2_empirical_mean', 'log2_empirical_median']
  Removed columns: ['logIntensityMean']
Parameter corrections applied:
  search_engine: 'various' → 'XTandem'
--- PERSISTED_CORRECTIONS ---
CORRECTION:search_engine=XTandem
--- END_PERSISTED_CORRECTIONS ---