#536 #520 Peaks parsing and additional parameter abundance_normalizat…

…ion_ions

proteobench/io/params/__init__.py

@@ -88,7 +88,8 @@ class ProteoBenchParameters:
     min_precursor_charge: Optional[int] = None  # precursor_charge
     max_precursor_charge: Optional[int] = None
     scan_window: Optional[int] = None  # DIA-specific
-    quantification_method: Optional[str] = None
+    quantification_method: Optional[str] = None  #
     second_pass: Optional[bool] = None  # DIANN specific
-    protein_inference: Optional[str] = None
-    predictors_library: Optional[dict] = None
+    protein_inference: Optional[str] = None  # example occams razor, proteinprophet
+    predictors_library: Optional[dict] = None  # type of model used to generate spectral library
+    abundance_normalization_ions: Optional[str] = None  # tic, median etc.

proteobench/io/params/peaks.py

@@ -161,12 +161,12 @@ def read_peaks_settings(file_path: str) -> ProteoBenchParameters:
     params.scan_window = None
 
     params.quantification_method = extract_value(
-        lines, "Quantification Type:"
+        lines, "LFQ Method:"
     )  # "Quantity MS Level:" or "Protein LFQ Method:" or "Quantity Type:"
     params.second_pass = None
     params.protein_inference = None
     params.predictors_library = None
-    params.abundance_normalization = extract_value(lines, "Normalization Method:")
+    params.abundance_normalization_ions = extract_value(lines, "Normalization Method:")
     return params
 
 

test/params/Peaks_parameters.csv

@@ -19,8 +19,8 @@ max_mods,1
 min_precursor_charge,1
 max_precursor_charge,4
 scan_window,
-quantification_method,Label Free Quantification
+quantification_method,Identification Directed Quantification
 second_pass,
 protein_inference,
 predictors_library,
-abundance_normalization,Use TIC
+abundance_normalization_ions,Use TIC