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): 0.20319463636363722
    fwhm (protein_fdr, median): 0.20367609595959024
    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): 2372437.0
    ms1_int_max_apex (protein_fdr, median): 2406920.0
    ms1_int_max_area (feature_table, median): 112547.37615274914
    ms1_int_max_area (peptide_fdr, median): 509721.3294922457
    ms1_int_max_area (protein_fdr, median): 518308.1004917413
    ms1_int_sum_apex (feature_table, median): 1396117.0101404912
    ms1_int_sum_apex (peptide_fdr, median): 4724865.029501634
    ms1_int_sum_apex (protein_fdr, median): 4812021.249112029
    ms1_int_sum_area (feature_table, median): 179186.34458981827
    ms1_int_sum_area (peptide_fdr, median): 1014124.6174816813
    ms1_int_sum_area (protein_fdr, median): 1035755.3624820043
    peptide_fdr (n in table): 34508
    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): 32602
    protein (protein_fdr, n unique): 5283
    protein_group (protein_fdr, n unique): 5283
    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): 29586
    sequence_naked (protein_fdr, n unique): 28804
  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): 0.20217002020203267
    fwhm (protein_fdr, median): 0.20252892424241864
    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): 2916757.0
    ms1_int_max_apex (protein_fdr, median): 2952603.5
    ms1_int_max_area (feature_table, median): 124483.75116599361
    ms1_int_max_area (peptide_fdr, median): 611075.0108599956
    ms1_int_max_area (protein_fdr, median): 619680.8367557491
    ms1_int_sum_apex (feature_table, median): 1846733.9274262264
    ms1_int_sum_apex (peptide_fdr, median): 5756195.737757138
    ms1_int_sum_apex (protein_fdr, median): 5860876.257209161
    ms1_int_sum_area (feature_table, median): 202082.9838195806
    ms1_int_sum_area (peptide_fdr, median): 1191539.0061839
    ms1_int_sum_area (protein_fdr, median): 1213919.172711776
    peptide_fdr (n in table): 35613
    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): 33922
    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): 30312
    sequence_naked (protein_fdr, n unique): 29438
  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): 0.2338004040404087
    fwhm (protein_fdr, median): 0.2343003434343487
    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): 2880170.0
    ms1_int_max_apex (protein_fdr, median): 2921404.5
    ms1_int_max_area (feature_table, median): 214662.9903085017
    ms1_int_max_area (peptide_fdr, median): 711024.8370499912
    ms1_int_max_area (protein_fdr, median): 723874.9025427457
    ms1_int_sum_apex (feature_table, median): 2024339.101863
    ms1_int_sum_apex (peptide_fdr, median): 5654546.207044396
    ms1_int_sum_apex (protein_fdr, median): 5760445.714873301
    ms1_int_sum_area (feature_table, median): 348704.6126305632
    ms1_int_sum_area (peptide_fdr, median): 1408425.2379573083
    ms1_int_sum_area (protein_fdr, median): 1440023.5292953402
    peptide_fdr (n in table): 37951
    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): 35977
    protein (protein_fdr, n unique): 5488
    protein_group (protein_fdr, n unique): 5488
    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): 31854
    sequence_naked (protein_fdr, n unique): 30898
  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): 0.22088186868686677
    fwhm (protein_fdr, median): 0.22148904040404105
    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): 2159670.5
    ms1_int_max_apex (protein_fdr, median): 2188225.5
    ms1_int_max_area (feature_table, median): 113011.02941624864
    ms1_int_max_area (peptide_fdr, median): 504435.4326682488
    ms1_int_max_area (protein_fdr, median): 513093.55553874833
    ms1_int_sum_apex (feature_table, median): 1240894.3861163845
    ms1_int_sum_apex (peptide_fdr, median): 4291499.026837705
    ms1_int_sum_apex (protein_fdr, median): 4372689.437203174
    ms1_int_sum_area (feature_table, median): 178141.18505316257
    ms1_int_sum_area (peptide_fdr, median): 1005236.1298365968
    ms1_int_sum_area (protein_fdr, median): 1025416.7419607153
    peptide_fdr (n in table): 35384
    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): 33897
    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): 30433
    sequence_naked (protein_fdr, n unique): 29456
  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): 0.2425790707070803
    fwhm (protein_fdr, median): 0.24296880808081056
    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): 2297110.0
    ms1_int_max_apex (protein_fdr, median): 2318253.0
    ms1_int_max_area (feature_table, median): 127269.71073899744
    ms1_int_max_area (peptide_fdr, median): 592684.0742149985
    ms1_int_max_area (protein_fdr, median): 600649.4540540025
    ms1_int_sum_apex (feature_table, median): 1320877.302977677
    ms1_int_sum_apex (peptide_fdr, median): 4552402.51152824
    ms1_int_sum_apex (protein_fdr, median): 4622395.023747753
    ms1_int_sum_area (feature_table, median): 202527.9342573708
    ms1_int_sum_area (peptide_fdr, median): 1171050.0062469135
    ms1_int_sum_area (protein_fdr, median): 1193363.3616546162
    peptide_fdr (n in table): 35281
    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): 33557
    protein (protein_fdr, n unique): 5194
    protein_group (protein_fdr, n unique): 5194
    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): 29733
    sequence_naked (protein_fdr, n unique): 28695
  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): 0.23598951515151967
    fwhm (protein_fdr, median): 0.23648994444443971
    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): 2613471.0
    ms1_int_max_apex (protein_fdr, median): 2639121.5
    ms1_int_max_area (feature_table, median): 188128.80485600044
    ms1_int_max_area (peptide_fdr, median): 654981.6802877404
    ms1_int_max_area (protein_fdr, median): 664029.2827320017
    ms1_int_sum_apex (feature_table, median): 1774145.218433667
    ms1_int_sum_apex (peptide_fdr, median): 5190275.11723364
    ms1_int_sum_apex (protein_fdr, median): 5264480.842112646
    ms1_int_sum_area (feature_table, median): 305880.1365647374
    ms1_int_sum_area (peptide_fdr, median): 1302254.9047434772
    ms1_int_sum_area (protein_fdr, median): 1324173.3140765117
    peptide_fdr (n in table): 37930
    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): 36203
    protein (protein_fdr, n unique): 5438
    protein_group (protein_fdr, n unique): 5438
    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): 32088
    sequence_naked (protein_fdr, n unique): 30803
  file_sizes:
    files:
      /home/caro/proteobench_benchmarkruns/files/LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.ms_data.hdf: 2023.2426280975342
      /home/caro/proteobench_benchmarkruns/files/LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.ms_data.hdf: 2375.8078756332397
      /home/caro/proteobench_benchmarkruns/files/LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.ms_data.hdf: 2485.7454509735107
      /home/caro/proteobench_benchmarkruns/files/LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.ms_data.hdf: 2092.8584241867065
      /home/caro/proteobench_benchmarkruns/files/LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.ms_data.hdf: 2365.3818893432617
      /home/caro/proteobench_benchmarkruns/files/LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.ms_data.hdf: 2419.1854753494263
    results: 500.58713817596436
  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 11:59:31.782468'
  timing:
    align (min): 0.07182443141937256
    create_database (min): 4.6173731486002605e-06
    feature_finding (min): 2.2520427465438844
    import_raw_data (min): 4.022175176938375
    isobaric_labeling (min): 3.166993459065755e-06
    match (min): 0.38717082341512044
    protein_grouping (min): 0.0784181276957194
    quantification (min): 11.827545487880707
    recalibrate_data (min): 1.3885747154553731
    score (min): 3.793041702111562
    search_data (min): 2.09965846935908
    search_data_2 (min): 0.9441272457440694
    total (min): 26.864617069562275
  version: 0.5.3
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
