calibration:
  mob_range: 0.3
  n_neighbors: 100
  outlier_std: 3
  ppm_range: 20
  rt_range: 0.5
experiment:
  alphapept_version: 0.3.11-dev0
  file_paths:
  - D:/04_hela_testrun/20190402_QX1_SeVW_MA_HeLa_500ng_LC11.raw
  fractions: []
  results_path: D:/04_hela_testrun/results.hdf
  shortnames:
  - 20190402_QX1_SeVW_MA_HeLa_500ng_LC11.raw
fasta:
  AL_swap: false
  KR_swap: false
  database_path: null
  db_size: 200000
  fasta_block: 1000
  fasta_paths:
  - D:/Bruker/contaminants (1).fasta
  - D:/Bruker/human.fasta
  max_isoforms: 1024
  max_length: 27
  min_length: 6
  mods_fixed:
  - cC
  mods_fixed_terminal: []
  mods_fixed_terminal_prot: []
  mods_variable:
  - oxM
  mods_variable_terminal: []
  mods_variable_terminal_prot: []
  num_missed_cleavages: 2
  protease: trypsin
  pseudo_reverse: true
  save_db: true
  spectra_block: 100000
features:
  mass_importance: 100
  max_distance: 0.4
  max_gap: 2
  max_neighbors: 4
  min_hill_length: 3
  ppm_tol: 8
  search_unidentified: false
  smoothing: 1
general:
  align: true
  create_database: true
  feature_finding: true
  find_features: true
  import_raw_data: true
  lfq_quantification: true
  match: false
  n_processes: 60
  ppm: true
  recalibrate_data: true
  score: random_forest
  search_data: true
matching:
  match_between_runs: true
  min_match_d: 3.0
  min_match_p: 0.05
quantification:
  max_lfq: true
  mode: int_sum
raw:
  most_abundant: 400
  use_profile_ms1: false
search:
  calibrate: true
  calibration_std: 3
  m_offset: 30
  m_tol: 30
  min_frag_hits: 7
  parallel: true
  peptide_fdr: 0.01
  ppm: true
  protein_fdr: 0.01
  recalibration_min: 100