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: /home/caro/proteobench_benchmarkruns/files/database.hdf
  fasta_paths:
  - /home/caro/proteobench_benchmarkruns/files/BenchmarkFASTAModule2_DDA.fasta
  file_paths:
  - /home/caro/proteobench_benchmarkruns/files/LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.raw
  - /home/caro/proteobench_benchmarkruns/files/LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.raw
  - /home/caro/proteobench_benchmarkruns/files/LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.raw
  - /home/caro/proteobench_benchmarkruns/files/LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.raw
  - /home/caro/proteobench_benchmarkruns/files/LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.raw
  - /home/caro/proteobench_benchmarkruns/files/LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.raw
  fraction:
  - 1
  - 1
  - 1
  - 1
  - 1
  - 1
  matching_group:
  - 1
  - 1
  - 1
  - 2
  - 2
  - 2
  results_path: /home/caro/proteobench_benchmarkruns/files/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: ada3155a45419abed7c74afd393d1842
  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: 10
  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): 458437
    fragment_ions (n in table): 2150730
    fwhm (feature_table, median): 0.12623177777778238
    fwhm (peptide_fdr, median): 0.2032451464646492
    fwhm (protein_fdr, median): 0.203714848484843
    id_rate (0.01): 0.14
    identifications (n in table): 85428
    ms1_int_max_apex (feature_table, median): 844654.0
    ms1_int_max_apex (peptide_fdr, median): 2374019.5
    ms1_int_max_apex (protein_fdr, median): 2407873.0
    ms1_int_max_area (feature_table, median): 112547.37615274914
    ms1_int_max_area (peptide_fdr, median): 510248.49676599936
    ms1_int_max_area (protein_fdr, median): 519029.5606510069
    ms1_int_sum_apex (feature_table, median): 1396117.0101404912
    ms1_int_sum_apex (peptide_fdr, median): 4729989.405690981
    ms1_int_sum_apex (protein_fdr, median): 4822193.11272228
    ms1_int_sum_area (feature_table, median): 179186.34458981827
    ms1_int_sum_area (peptide_fdr, median): 1014987.3377366597
    ms1_int_sum_area (protein_fdr, median): 1036931.8765817771
    peptide_fdr (n in table): 34422
    prec_offset_ppm (peptide_fdr, median): -5.812257768411655e-07
    prec_offset_ppm (protein_fdr, median): -5.771318569713912e-07
    prec_offset_raw_ppm (peptide_fdr, median): 0.4531383514404297
    prec_offset_raw_ppm (protein_fdr, median): 0.46119949221611023
    precursor (protein_fdr, n unique): 32519
    protein (protein_fdr, n unique): 5280
    protein_group (protein_fdr, n unique): 5280
    rt_length (feature_table, median): 0.26126634343434674
    rt_tail (feature_table, median): 1.1590909090909585
    second_search (n in table): 136192
    sequence (protein_fdr, n unique): 29513
    sequence_naked (protein_fdr, n unique): 28737
  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): 666369
    fragment_ions (n in table): 2939704
    fwhm (feature_table, median): 0.10678636363637395
    fwhm (peptide_fdr, median): 0.20217320202020517
    fwhm (protein_fdr, median): 0.20254152525252778
    id_rate (0.01): 0.2
    identifications (n in table): 99007
    ms1_int_max_apex (feature_table, median): 1091019.0
    ms1_int_max_apex (peptide_fdr, median): 2916977.5
    ms1_int_max_apex (protein_fdr, median): 2954417.0
    ms1_int_max_area (feature_table, median): 124483.75116599361
    ms1_int_max_area (peptide_fdr, median): 611186.4142525045
    ms1_int_max_area (protein_fdr, median): 619854.8065012506
    ms1_int_sum_apex (feature_table, median): 1846733.9274262264
    ms1_int_sum_apex (peptide_fdr, median): 5757393.723020615
    ms1_int_sum_apex (protein_fdr, median): 5862276.552633831
    ms1_int_sum_area (feature_table, median): 202082.9838195806
    ms1_int_sum_area (peptide_fdr, median): 1191883.977580161
    ms1_int_sum_area (protein_fdr, median): 1214429.4640993562
    peptide_fdr (n in table): 35588
    prec_offset_ppm (peptide_fdr, median): -5.755019856223953e-07
    prec_offset_ppm (protein_fdr, median): -5.777245632998529e-07
    prec_offset_raw_ppm (peptide_fdr, median): 0.40055418014526367
    prec_offset_raw_ppm (protein_fdr, median): 0.40880027413368225
    precursor (protein_fdr, n unique): 33898
    protein (protein_fdr, n unique): 5327
    protein_group (protein_fdr, n unique): 5327
    rt_length (feature_table, median): 0.22284888888888332
    rt_tail (feature_table, median): 1.1521739130434867
    second_search (n in table): 185343
    sequence (protein_fdr, n unique): 30290
    sequence_naked (protein_fdr, n unique): 29419
  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): 723754
    fragment_ions (n in table): 3201650
    fwhm (feature_table, median): 0.18050616161616517
    fwhm (peptide_fdr, median): 0.23388363636363607
    fwhm (protein_fdr, median): 0.2343590404040441
    id_rate (0.01): 0.22
    identifications (n in table): 110311
    ms1_int_max_apex (feature_table, median): 1226170.0
    ms1_int_max_apex (peptide_fdr, median): 2881614.0
    ms1_int_max_apex (protein_fdr, median): 2923455.0
    ms1_int_max_area (feature_table, median): 214662.9903085017
    ms1_int_max_area (peptide_fdr, median): 711488.9897834923
    ms1_int_max_area (protein_fdr, median): 724731.9376764955
    ms1_int_sum_apex (feature_table, median): 2024339.101863
    ms1_int_sum_apex (peptide_fdr, median): 5659498.222839747
    ms1_int_sum_apex (protein_fdr, median): 5768203.412702423
    ms1_int_sum_area (feature_table, median): 348704.6126305632
    ms1_int_sum_area (peptide_fdr, median): 1410065.5432067895
    ms1_int_sum_area (protein_fdr, median): 1442401.7607637781
    peptide_fdr (n in table): 37865
    prec_offset_ppm (peptide_fdr, median): -6.264370426833921e-07
    prec_offset_ppm (protein_fdr, median): -6.24713720753789e-07
    prec_offset_raw_ppm (peptide_fdr, median): 0.47069060802459717
    prec_offset_raw_ppm (protein_fdr, median): 0.48330792784690857
    precursor (protein_fdr, n unique): 35892
    protein (protein_fdr, n unique): 5483
    protein_group (protein_fdr, n unique): 5483
    rt_length (feature_table, median): 0.33942324242423894
    rt_tail (feature_table, median): 1.1707317073170755
    second_search (n in table): 202569
    sequence (protein_fdr, n unique): 31778
    sequence_naked (protein_fdr, n unique): 30825
  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): 491853
    fragment_ions (n in table): 2271199
    fwhm (feature_table, median): 0.1479760151515137
    fwhm (peptide_fdr, median): 0.22094711111110854
    fwhm (protein_fdr, median): 0.22153727272727508
    id_rate (0.01): 0.14
    identifications (n in table): 92296
    ms1_int_max_apex (feature_table, median): 761059.0
    ms1_int_max_apex (peptide_fdr, median): 2161794.0
    ms1_int_max_apex (protein_fdr, median): 2190077.0
    ms1_int_max_area (feature_table, median): 113011.02941624864
    ms1_int_max_area (peptide_fdr, median): 505112.2660009996
    ms1_int_max_area (protein_fdr, median): 514001.43757150054
    ms1_int_sum_apex (feature_table, median): 1240894.3861163845
    ms1_int_sum_apex (peptide_fdr, median): 4296122.721922439
    ms1_int_sum_apex (protein_fdr, median): 4377492.597654444
    ms1_int_sum_area (feature_table, median): 178141.18505316257
    ms1_int_sum_area (peptide_fdr, median): 1006845.2499610055
    ms1_int_sum_area (protein_fdr, median): 1026401.9192131486
    peptide_fdr (n in table): 35347
    prec_offset_ppm (peptide_fdr, median): -5.50447509795049e-07
    prec_offset_ppm (protein_fdr, median): -5.484217808771064e-07
    prec_offset_raw_ppm (peptide_fdr, median): 0.4347543716430664
    prec_offset_raw_ppm (protein_fdr, median): 0.44194459915161133
    precursor (protein_fdr, n unique): 33860
    protein (protein_fdr, n unique): 5275
    protein_group (protein_fdr, n unique): 5275
    rt_length (feature_table, median): 0.28941702020201454
    rt_tail (feature_table, median): 1.1818181818181683
    second_search (n in table): 144080
    sequence (protein_fdr, n unique): 30406
    sequence_naked (protein_fdr, n unique): 29432
  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): 569687
    fragment_ions (n in table): 2630306
    fwhm (feature_table, median): 0.1657121616161703
    fwhm (peptide_fdr, median): 0.24262902020201693
    fwhm (protein_fdr, median): 0.24302488888888973
    id_rate (0.01): 0.18
    identifications (n in table): 99055
    ms1_int_max_apex (feature_table, median): 804525.0
    ms1_int_max_apex (peptide_fdr, median): 2298353.0
    ms1_int_max_apex (protein_fdr, median): 2321004.0
    ms1_int_max_area (feature_table, median): 127269.71073899744
    ms1_int_max_area (peptide_fdr, median): 593508.8276389999
    ms1_int_max_area (protein_fdr, median): 601148.3161899998
    ms1_int_sum_apex (feature_table, median): 1320877.302977677
    ms1_int_sum_apex (peptide_fdr, median): 4557197.542799583
    ms1_int_sum_apex (protein_fdr, median): 4626537.227528069
    ms1_int_sum_area (feature_table, median): 202527.9342573708
    ms1_int_sum_area (peptide_fdr, median): 1172984.5695356673
    ms1_int_sum_area (protein_fdr, median): 1195118.2952710881
    peptide_fdr (n in table): 35213
    prec_offset_ppm (peptide_fdr, median): -6.632805025219568e-07
    prec_offset_ppm (protein_fdr, median): -6.611174967474653e-07
    prec_offset_raw_ppm (peptide_fdr, median): 0.49967318773269653
    prec_offset_raw_ppm (protein_fdr, median): 0.5107790231704712
    precursor (protein_fdr, n unique): 33493
    protein (protein_fdr, n unique): 5188
    protein_group (protein_fdr, n unique): 5188
    rt_length (feature_table, median): 0.3026909090909129
    rt_tail (feature_table, median): 1.1500000000000123
    second_search (n in table): 167439
    sequence (protein_fdr, n unique): 29678
    sequence_naked (protein_fdr, n unique): 28649
  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): 676847
    fragment_ions (n in table): 3017189
    fwhm (feature_table, median): 0.1805095959595988
    fwhm (peptide_fdr, median): 0.23600484848485337
    fwhm (protein_fdr, median): 0.2364941818181805
    id_rate (0.01): 0.21
    identifications (n in table): 109341
    ms1_int_max_apex (feature_table, median): 1071251.0
    ms1_int_max_apex (peptide_fdr, median): 2614766.0
    ms1_int_max_apex (protein_fdr, median): 2642725.5
    ms1_int_max_area (feature_table, median): 188128.80485600044
    ms1_int_max_area (peptide_fdr, median): 655869.3731815101
    ms1_int_max_area (protein_fdr, median): 664493.4439869996
    ms1_int_sum_apex (feature_table, median): 1774145.218433667
    ms1_int_sum_apex (peptide_fdr, median): 5197420.725392084
    ms1_int_sum_apex (protein_fdr, median): 5269011.94701099
    ms1_int_sum_area (feature_table, median): 305880.1365647374
    ms1_int_sum_area (peptide_fdr, median): 1303913.004774472
    ms1_int_sum_area (protein_fdr, median): 1326554.278575781
    peptide_fdr (n in table): 37829
    prec_offset_ppm (peptide_fdr, median): -6.289793077485228e-07
    prec_offset_ppm (protein_fdr, median): -6.276279691519449e-07
    prec_offset_raw_ppm (peptide_fdr, median): 0.48770588636398315
    prec_offset_raw_ppm (protein_fdr, median): 0.4970867335796356
    precursor (protein_fdr, n unique): 36105
    protein (protein_fdr, n unique): 5433
    protein_group (protein_fdr, n unique): 5433
    rt_length (feature_table, median): 0.33933919191917994
    rt_tail (feature_table, median): 1.1666666666666436
    second_search (n in table): 192831
    sequence (protein_fdr, n unique): 32012
    sequence_naked (protein_fdr, n unique): 30732
  file_sizes:
    files:
      /home/caro/proteobench_benchmarkruns/files/LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.ms_data.hdf: 2009.5346355438232
      /home/caro/proteobench_benchmarkruns/files/LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.ms_data.hdf: 2361.38653755188
      /home/caro/proteobench_benchmarkruns/files/LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.ms_data.hdf: 2471.495274543762
      /home/caro/proteobench_benchmarkruns/files/LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.ms_data.hdf: 2078.9920015335083
      /home/caro/proteobench_benchmarkruns/files/LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.ms_data.hdf: 2351.5934267044067
      /home/caro/proteobench_benchmarkruns/files/LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.ms_data.hdf: 2404.848916053772
    results: 378.2048988342285
  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: '2024-11-28 11:21:09.053565'
  timing:
    create_database (min): 3.8107236226399738e-06
    feature_finding (min): 2.1712490280469257
    import_raw_data (min): 3.982076096534729
    isobaric_labeling (min): 2.6226043701171875e-06
    protein_grouping (min): 0.06907833417256673
    quantification (min): 3.1225882252057393
    recalibrate_data (min): 1.3998125195503235
    score (min): 3.7959116101264954
    search_data (min): 2.118116835753123
    search_data_2 (min): 0.9526389161745707
    total (min): 17.61150063673655
  version: 0.5.3
workflow:
  align: false
  continue_runs: false
  create_database: true
  find_features: true
  import_raw_data: true
  lfq_quantification: true
  match: false
  recalibrate_data: true
  search_data: true
