Make fragment calibration configurable

alphadia/constants/default.yaml

@@ -119,6 +119,12 @@ calibration:
   # TODO: remove this parameter
   norm_rt_mode: 'linear'
 
+  # the maximum number of fragments with correlation scores exceeding correlation_threshold to use for calibrating fragment mz (i.e. ms2)
+  max_fragments: 5000
+
+  # the correlation threshold for fragments used to calibrate fragment mz (i.e. ms2)
+  min_correlation: 0.7
+
 search_initial:
   # Number of peak groups identified in the convolution score to classify with target decoy comeptition
   initial_num_candidates: 1

alphadia/workflow/peptidecentric.py

@@ -549,8 +549,11 @@ def filter_dfs(self, precursor_df, fragments_df):
             by="correlation", ascending=False
         )
         # Determine the number of fragments to keep
-        min_fragments, max_fragments = 500, 5000
-        min_correlation = 0.7
+        min_fragments, max_fragments = (
+            500,
+            self.config["calibration"]["max_fragments"],
+        )  # TODO remove min_fragments as it seems to have no effect
+        min_correlation = self.config["calibration"]["min_correlation"]
 
         high_corr_count = (fragments_df_filtered["correlation"] > min_correlation).sum()
         stop_rank = min(max(high_corr_count, min_fragments), max_fragments)