calibration:
  calib_mob_range: 0.3
  calib_mz_range: 2000
  calib_n_neighbors: 100
  calib_rt_range: 0.5
  outlier_std: 3
experiment:
  database_path: C:\Users\brvpuyve\Downloads\Temp\database.hdf
  fasta_paths:
  - C:\Users\brvpuyve\Downloads\Temp\ProteoBenchFASTA_DDAQuantification.fasta
  file_paths:
  - C:\Users\brvpuyve\Downloads\Temp\LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.raw
  - C:\Users\brvpuyve\Downloads\Temp\LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.raw
  - C:\Users\brvpuyve\Downloads\Temp\LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.raw
  - C:\Users\brvpuyve\Downloads\Temp\LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.raw
  - C:\Users\brvpuyve\Downloads\Temp\LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.raw
  - C:\Users\brvpuyve\Downloads\Temp\LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.raw
  fraction:
  - 1
  - 1
  - 1
  - 1
  - 1
  - 1
  matching_group:
  - 0
  - 0
  - 0
  - 0
  - 0
  - 0
  results_path: C:\Users\brvpuyve\Downloads\Temp\results.hdf
  sample_group:
  - LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01
  - LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02
  - LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03
  - LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01
  - LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02
  - LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03
  shortnames:
  - LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01
  - LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02
  - LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03
  - LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01
  - LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02
  - LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03
failed:
  calibrate_hdf: []
  find_features: []
  raw_conversion: []
  score_hdf: []
  search_db: []
  search_db_2: []
fasta:
  AL_swap: false
  KR_swap: false
  fasta_block: 1000
  fasta_size_max: 100
  isoforms_max: 1024
  mods_fixed:
  - cC
  mods_fixed_terminal: []
  mods_fixed_terminal_prot: []
  mods_variable:
  - oxM
  mods_variable_terminal: []
  mods_variable_terminal_prot:
  - a<^
  n_missed_cleavages: 2
  n_modifications_max: 3
  pep_length_max: 27
  pep_length_min: 7
  protease: trypsin
  pseudo_reverse: true
  save_db: true
  spectra_block: 100000
features:
  centroid_tol: 8
  hill_check_large: 40
  hill_length_min: 3
  hill_nboot: 150
  hill_nboot_max: 300
  hill_smoothing: 1
  hill_split_level: 1.3
  iso_charge_max: 6
  iso_charge_min: 1
  iso_corr_min: 0.6
  iso_mass_range: 5
  iso_n_seeds: 100
  iso_split_level: 1.3
  map_mob_range: 0.3
  map_mz_range: 1.5
  map_n_neighbors: 5
  map_rt_range: 0.5
  max_gap: 2
  search_unidentified: false
general:
  modfile_hash: 72252eb041669ea9b826e49f54a4ac50
  n_processes: 60
matching:
  match_d_min: 3
  match_group_tol: 0
  match_p_min: 0.05
quantification:
  lfq_ratio_min: 1
  max_lfq: true
  mode: ms1_int_sum_apex
raw:
  n_most_abundant: 400
  use_profile_ms1: false
score:
  method: random_forest
  ml_ini_score: generic_score
search:
  calibrate: true
  calibration_std_frag: 5
  calibration_std_prec: 5
  frag_tol: 50
  min_frag_hits: 7
  parallel: true
  peptide_fdr: 0.01
  ppm: true
  prec_tol: 20
  protein_fdr: 0.01
  recalibration_min: 100
  top_n: 10
summary:
  LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01:
    acquisition_date_time: '2021-02-15T21:12:15.1229978Z'
    feature_cluster_mapping (n in table): 438670
    feature_table (n in table): 165602
    feature_table_idx (n in table): 37641628
    features (n in table): 267813
    first_search (n in table): 635632
    fragment_ions (n in table): 2312997
    fwhm (feature_table, median): 0.12623177777778238
    fwhm (peptide_fdr, median): 0.20208830303029401
    fwhm (protein_fdr, median): 0.2025355353535332
    id_rate (0.01): 0.16
    identifications (n in table): 90981
    ms1_int_max_apex (feature_table, median): 844654.0
    ms1_int_max_apex (peptide_fdr, median): 2273632.0
    ms1_int_max_apex (protein_fdr, median): 2304614.0
    ms1_int_max_area (feature_table, median): 112547.37615274914
    ms1_int_max_area (peptide_fdr, median): 484557.32276800583
    ms1_int_max_area (protein_fdr, median): 493301.83788349706
    ms1_int_sum_apex (feature_table, median): 1396117.0101404912
    ms1_int_sum_apex (peptide_fdr, median): 4496778.870991005
    ms1_int_sum_apex (protein_fdr, median): 4583759.557745095
    ms1_int_sum_area (feature_table, median): 179186.34458981827
    ms1_int_sum_area (peptide_fdr, median): 956869.7792948312
    ms1_int_sum_area (protein_fdr, median): 979738.3449531642
    peptide_fdr (n in table): 35795
    prec_offset_ppm (peptide_fdr, median): -6.052271146472776e-07
    prec_offset_ppm (protein_fdr, median): -6.02911427449726e-07
    prec_offset_raw_ppm (peptide_fdr, median): 0.44225263595581055
    prec_offset_raw_ppm (protein_fdr, median): 0.44900578260421753
    precursor (protein_fdr, n unique): 33924
    protein (protein_fdr, n unique): 5367
    protein_group (protein_fdr, n unique): 5367
    rt_length (feature_table, median): 0.26126634343434674
    rt_tail (feature_table, median): 1.1590909090909585
    second_search (n in table): 148872
    sequence (protein_fdr, n unique): 30753
    sequence_naked (protein_fdr, n unique): 29914
  LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02:
    acquisition_date_time: '2021-02-17T05:58:09.9313599Z'
    feature_cluster_mapping (n in table): 490116
    feature_table (n in table): 182019
    feature_table_idx (n in table): 36934614
    features (n in table): 269330
    first_search (n in table): 893522
    fragment_ions (n in table): 3199026
    fwhm (feature_table, median): 0.10678636363637395
    fwhm (peptide_fdr, median): 0.2011151515151539
    fwhm (protein_fdr, median): 0.20139032323231731
    id_rate (0.01): 0.23
    identifications (n in table): 105517
    ms1_int_max_apex (feature_table, median): 1091019.0
    ms1_int_max_apex (peptide_fdr, median): 2839125.0
    ms1_int_max_apex (protein_fdr, median): 2876709.0
    ms1_int_max_area (feature_table, median): 124483.75116599361
    ms1_int_max_area (peptide_fdr, median): 589175.744904999
    ms1_int_max_area (protein_fdr, median): 597666.0553645004
    ms1_int_sum_apex (feature_table, median): 1846733.9274262264
    ms1_int_sum_apex (peptide_fdr, median): 5597615.855935995
    ms1_int_sum_apex (protein_fdr, median): 5689677.366075407
    ms1_int_sum_area (feature_table, median): 202082.9838195806
    ms1_int_sum_area (peptide_fdr, median): 1148336.8068355822
    ms1_int_sum_area (protein_fdr, median): 1170854.0747940163
    peptide_fdr (n in table): 36729
    prec_offset_ppm (peptide_fdr, median): -6.048238674338791e-07
    prec_offset_ppm (protein_fdr, median): -6.025984475854784e-07
    prec_offset_raw_ppm (peptide_fdr, median): 0.3991774320602417
    prec_offset_raw_ppm (protein_fdr, median): 0.41016653180122375
    precursor (protein_fdr, n unique): 35096
    protein (protein_fdr, n unique): 5409
    protein_group (protein_fdr, n unique): 5409
    rt_length (feature_table, median): 0.22284888888888332
    rt_tail (feature_table, median): 1.1521739130434867
    second_search (n in table): 204898
    sequence (protein_fdr, n unique): 31329
    sequence_naked (protein_fdr, n unique): 30390
  LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03:
    acquisition_date_time: '2021-02-18T22:31:16.2898136Z'
    feature_cluster_mapping (n in table): 388797
    feature_table (n in table): 144932
    feature_table_idx (n in table): 36996665
    features (n in table): 298727
    first_search (n in table): 973119
    fragment_ions (n in table): 3549521
    fwhm (feature_table, median): 0.18050616161616517
    fwhm (peptide_fdr, median): 0.23311627272727975
    fwhm (protein_fdr, median): 0.23369251515151745
    id_rate (0.01): 0.25
    identifications (n in table): 117190
    ms1_int_max_apex (feature_table, median): 1226170.0
    ms1_int_max_apex (peptide_fdr, median): 2826276.5
    ms1_int_max_apex (protein_fdr, median): 2859976.0
    ms1_int_max_area (feature_table, median): 214662.9903085017
    ms1_int_max_area (peptide_fdr, median): 692528.6751607563
    ms1_int_max_area (protein_fdr, median): 704040.9440294983
    ms1_int_sum_apex (feature_table, median): 2024339.101863
    ms1_int_sum_apex (peptide_fdr, median): 5549321.360277159
    ms1_int_sum_apex (protein_fdr, median): 5651442.535956388
    ms1_int_sum_area (feature_table, median): 348704.6126305632
    ms1_int_sum_area (peptide_fdr, median): 1372812.082967498
    ms1_int_sum_area (protein_fdr, median): 1404424.144023391
    peptide_fdr (n in table): 38612
    prec_offset_ppm (peptide_fdr, median): -6.595390686925384e-07
    prec_offset_ppm (protein_fdr, median): -6.53330630484561e-07
    prec_offset_raw_ppm (peptide_fdr, median): 0.47568827867507935
    prec_offset_raw_ppm (protein_fdr, median): 0.48990026116371155
    precursor (protein_fdr, n unique): 36653
    protein (protein_fdr, n unique): 5558
    protein_group (protein_fdr, n unique): 5558
    rt_length (feature_table, median): 0.33942324242423894
    rt_tail (feature_table, median): 1.1707317073170755
    second_search (n in table): 229084
    sequence (protein_fdr, n unique): 32442
    sequence_naked (protein_fdr, n unique): 31457
  LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01:
    acquisition_date_time: '2021-02-16T00:35:33.4711979Z'
    feature_cluster_mapping (n in table): 422957
    feature_table (n in table): 159696
    feature_table_idx (n in table): 38266599
    features (n in table): 282141
    first_search (n in table): 672020
    fragment_ions (n in table): 2510772
    fwhm (feature_table, median): 0.1479760151515137
    fwhm (peptide_fdr, median): 0.219749212121215
    fwhm (protein_fdr, median): 0.22024804545455368
    id_rate (0.01): 0.17
    identifications (n in table): 98472
    ms1_int_max_apex (feature_table, median): 761059.0
    ms1_int_max_apex (peptide_fdr, median): 2073018.5
    ms1_int_max_apex (protein_fdr, median): 2101175.0
    ms1_int_max_area (feature_table, median): 113011.02941624864
    ms1_int_max_area (peptide_fdr, median): 483058.4607649953
    ms1_int_max_area (protein_fdr, median): 492229.547006755
    ms1_int_sum_apex (feature_table, median): 1240894.3861163845
    ms1_int_sum_apex (peptide_fdr, median): 4105860.882662309
    ms1_int_sum_apex (protein_fdr, median): 4187200.891414035
    ms1_int_sum_area (feature_table, median): 178141.18505316257
    ms1_int_sum_area (peptide_fdr, median): 958272.0831294714
    ms1_int_sum_area (protein_fdr, median): 977601.7056275478
    peptide_fdr (n in table): 37096
    prec_offset_ppm (peptide_fdr, median): -5.913145741942571e-07
    prec_offset_ppm (protein_fdr, median): -5.858927352164756e-07
    prec_offset_raw_ppm (peptide_fdr, median): 0.4260919690132141
    prec_offset_raw_ppm (protein_fdr, median): 0.43663710355758667
    precursor (protein_fdr, n unique): 35585
    protein (protein_fdr, n unique): 5426
    protein_group (protein_fdr, n unique): 5426
    rt_length (feature_table, median): 0.28941702020201454
    rt_tail (feature_table, median): 1.1818181818181683
    second_search (n in table): 162755
    sequence (protein_fdr, n unique): 31946
    sequence_naked (protein_fdr, n unique): 30887
  LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02:
    acquisition_date_time: '2021-02-17T17:08:43.6657345Z'
    feature_cluster_mapping (n in table): 420122
    feature_table (n in table): 160015
    feature_table_idx (n in table): 43445155
    features (n in table): 297720
    first_search (n in table): 786902
    fragment_ions (n in table): 2873708
    fwhm (feature_table, median): 0.1657121616161703
    fwhm (peptide_fdr, median): 0.24140575757575888
    fwhm (protein_fdr, median): 0.24174927272726876
    id_rate (0.01): 0.21
    identifications (n in table): 105480
    ms1_int_max_apex (feature_table, median): 804525.0
    ms1_int_max_apex (peptide_fdr, median): 2225401.0
    ms1_int_max_apex (protein_fdr, median): 2253193.0
    ms1_int_max_area (feature_table, median): 127269.71073899744
    ms1_int_max_area (peptide_fdr, median): 566514.0062360042
    ms1_int_max_area (protein_fdr, median): 576857.8682264979
    ms1_int_sum_apex (feature_table, median): 1320877.302977677
    ms1_int_sum_apex (peptide_fdr, median): 4388791.22311038
    ms1_int_sum_apex (protein_fdr, median): 4464888.972817011
    ms1_int_sum_area (feature_table, median): 202527.9342573708
    ms1_int_sum_area (peptide_fdr, median): 1119135.965077097
    ms1_int_sum_area (protein_fdr, median): 1144168.339804095
    peptide_fdr (n in table): 36006
    prec_offset_ppm (peptide_fdr, median): -6.794110163355072e-07
    prec_offset_ppm (protein_fdr, median): -6.786235644540284e-07
    prec_offset_raw_ppm (peptide_fdr, median): 0.500469446182251
    prec_offset_raw_ppm (protein_fdr, median): 0.5118041634559631
    precursor (protein_fdr, n unique): 34684
    protein (protein_fdr, n unique): 5268
    protein_group (protein_fdr, n unique): 5268
    rt_length (feature_table, median): 0.3026909090909129
    rt_tail (feature_table, median): 1.1500000000000123
    second_search (n in table): 186555
    sequence (protein_fdr, n unique): 30745
    sequence_naked (protein_fdr, n unique): 29667
  LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03:
    acquisition_date_time: '2021-02-19T01:54:34.5516971Z'
    feature_cluster_mapping (n in table): 399472
    feature_table (n in table): 148953
    feature_table_idx (n in table): 37870929
    features (n in table): 303009
    first_search (n in table): 921508
    fragment_ions (n in table): 3423229
    fwhm (feature_table, median): 0.1805095959595988
    fwhm (peptide_fdr, median): 0.23560402525252044
    fwhm (protein_fdr, median): 0.23611414141414855
    id_rate (0.01): 0.24
    identifications (n in table): 117602
    ms1_int_max_apex (feature_table, median): 1071251.0
    ms1_int_max_apex (peptide_fdr, median): 2552542.5
    ms1_int_max_apex (protein_fdr, median): 2581502.0
    ms1_int_max_area (feature_table, median): 188128.80485600044
    ms1_int_max_area (peptide_fdr, median): 634817.0797369969
    ms1_int_max_area (protein_fdr, median): 645529.8847619954
    ms1_int_sum_apex (feature_table, median): 1774145.218433667
    ms1_int_sum_apex (peptide_fdr, median): 5070465.894421345
    ms1_int_sum_apex (protein_fdr, median): 5157643.36399886
    ms1_int_sum_area (feature_table, median): 305880.1365647374
    ms1_int_sum_area (peptide_fdr, median): 1267721.7609596807
    ms1_int_sum_area (protein_fdr, median): 1292018.0960341806
    peptide_fdr (n in table): 38836
    prec_offset_ppm (peptide_fdr, median): -6.617241297135479e-07
    prec_offset_ppm (protein_fdr, median): -6.596175694539852e-07
    prec_offset_raw_ppm (peptide_fdr, median): 0.494691401720047
    prec_offset_raw_ppm (protein_fdr, median): 0.5040476322174072
    precursor (protein_fdr, n unique): 37121
    protein (protein_fdr, n unique): 5527
    protein_group (protein_fdr, n unique): 5527
    rt_length (feature_table, median): 0.33933919191917994
    rt_tail (feature_table, median): 1.1666666666666436
    second_search (n in table): 224401
    sequence (protein_fdr, n unique): 32903
    sequence_naked (protein_fdr, n unique): 31587
  file_sizes:
    files:
      C:\Users\brvpuyve\Downloads\Temp\LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.ms_data.hdf: 2224.1264123916626
      C:\Users\brvpuyve\Downloads\Temp\LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.ms_data.hdf: 2640.982144355774
      C:\Users\brvpuyve\Downloads\Temp\LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.ms_data.hdf: 2777.946752548218
      C:\Users\brvpuyve\Downloads\Temp\LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.ms_data.hdf: 2299.7064819335938
      C:\Users\brvpuyve\Downloads\Temp\LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.ms_data.hdf: 2613.986017227173
      C:\Users\brvpuyve\Downloads\Temp\LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.ms_data.hdf: 2705.722064971924
    results: 501.7833251953125
  processed_files:
  - LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.raw
  - LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.raw
  - LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.raw
  - LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.raw
  - LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.raw
  - LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.raw
  time: '2024-12-16 18:36:18.432084'
  timing:
    align (min): 0.17122435967127483
    create_database (min): 5.6799968441327415
    feature_finding (min): 43.99843482573827
    import_raw_data (min): 5.847387838363647
    isobaric_labeling (min): 4.921754201253255e-05
    match (min): 0.9964283307393392
    protein_grouping (min): 0.08870373169581096
    quantification (min): 2.4909319639205934
    recalibrate_data (min): 2.516463879744212
    score (min): 4.52515971660614
    search_data (min): 14.056435489654541
    search_data_2 (min): 4.069904867808024
    total (min): 84.44153785705566
  version: 0.5.0
workflow:
  align: true
  continue_runs: false
  create_database: true
  find_features: true
  import_raw_data: true
  lfq_quantification: true
  match: true
  recalibrate_data: true
  search_data: true
