  
extract_peaks:
  ms_data_type: MS_Chromatogram
  ms_level: 2
  mz_tolerance: 0.3
  precursor_mz_tolerance: 0.3
  chromatogram_boundary_factor: 5
  integration_algorithm: emg_robust

tic_normalize_peaks:  
  peak_group_col="pid",
  amount_col="area_chromatogram",
  tic_col="tic_area",
  sample_wise=True

normalize_peaks:
  peak_group_col: pid
  std_group_col: std_id
  norm_id_column: normalize_by_std_id
  amount_col: area
  sample_wise: true

coeluting_peaks:
  group_id_column: peptide_standard_sequence
  reference_column:  coelution_reference_peak
  dt: 0.1 
  apply_median: false

 
classify_peaks:
  scoring_model: random_forest_classification
  scoring_model_params: 
     classifier_name: srm_peak_classifier
     ext: .predict
     path_to_folder: None

processing_steps:
- extract_peaks
- classify_peaks
- coeluting_peaks
- normalize_peaks

reprocessing_steps:
- classify_peaks
- coeluting_peaks
- normalize_peaks
