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: 1
  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: 20
  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): 41824
    fragment_ions (n in table): 947926
    fwhm (feature_table, median): 0.12623177777778238
    fwhm (peptide_fdr, median): 0.20436363636364518
    fwhm (protein_fdr, median): 0.20482576767675909
    id_rate (0.01): 0.04
    identifications (n in table): 47365
    ms1_int_max_apex (feature_table, median): 844654.0
    ms1_int_max_apex (peptide_fdr, median): 2453168.5
    ms1_int_max_apex (protein_fdr, median): 2482246.0
    ms1_int_max_area (feature_table, median): 112547.37615274914
    ms1_int_max_area (peptide_fdr, median): 533140.8651684956
    ms1_int_max_area (protein_fdr, median): 541410.9861757548
    ms1_int_sum_apex (feature_table, median): 1396117.0101404912
    ms1_int_sum_apex (peptide_fdr, median): 5057190.038073016
    ms1_int_sum_apex (protein_fdr, median): 5121978.871635664
    ms1_int_sum_area (feature_table, median): 179186.34458981827
    ms1_int_sum_area (peptide_fdr, median): 1092538.836434016
    ms1_int_sum_area (protein_fdr, median): 1113280.3546041464
    peptide_fdr (n in table): 22024
    prec_offset_ppm (peptide_fdr, median): -7.462988946826954e-07
    prec_offset_ppm (protein_fdr, median): -7.306819043151336e-07
    prec_offset_raw_ppm (peptide_fdr, median): 0.5188661813735962
    prec_offset_raw_ppm (protein_fdr, median): 0.5258505344390869
    precursor (protein_fdr, n unique): 21422
    protein (protein_fdr, n unique): 4611
    protein_group (protein_fdr, n unique): 4611
    rt_length (feature_table, median): 0.26126634343434674
    rt_tail (feature_table, median): 1.1590909090909585
    second_search (n in table): 59128
    sequence (protein_fdr, n unique): 19496
    sequence_naked (protein_fdr, n unique): 19025
  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): 52495
    fragment_ions (n in table): 1170416
    fwhm (feature_table, median): 0.10678636363637395
    fwhm (peptide_fdr, median): 0.19939043939394097
    fwhm (protein_fdr, median): 0.1998145454545437
    id_rate (0.01): 0.07
    identifications (n in table): 53790
    ms1_int_max_apex (feature_table, median): 1091019.0
    ms1_int_max_apex (peptide_fdr, median): 2870674.0
    ms1_int_max_apex (protein_fdr, median): 2902612.0
    ms1_int_max_area (feature_table, median): 124483.75116599361
    ms1_int_max_area (peptide_fdr, median): 595784.978612754
    ms1_int_max_area (protein_fdr, median): 604300.3560499938
    ms1_int_sum_apex (feature_table, median): 1846733.9274262264
    ms1_int_sum_apex (peptide_fdr, median): 5925836.890681097
    ms1_int_sum_apex (protein_fdr, median): 6022295.553113151
    ms1_int_sum_area (feature_table, median): 202082.9838195806
    ms1_int_sum_area (peptide_fdr, median): 1210587.2620834755
    ms1_int_sum_area (protein_fdr, median): 1230086.6671541005
    peptide_fdr (n in table): 23652
    prec_offset_ppm (peptide_fdr, median): -7.672261972402339e-07
    prec_offset_ppm (protein_fdr, median): -7.596791533615033e-07
    prec_offset_raw_ppm (peptide_fdr, median): 0.5178252458572388
    prec_offset_raw_ppm (protein_fdr, median): 0.5236387252807617
    precursor (protein_fdr, n unique): 22931
    protein (protein_fdr, n unique): 4743
    protein_group (protein_fdr, n unique): 4743
    rt_length (feature_table, median): 0.22284888888888332
    rt_tail (feature_table, median): 1.1521739130434867
    second_search (n in table): 72365
    sequence (protein_fdr, n unique): 20639
    sequence_naked (protein_fdr, n unique): 20077
  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): 75743
    fragment_ions (n in table): 1674053
    fwhm (feature_table, median): 0.18050616161616517
    fwhm (peptide_fdr, median): 0.23732222222221822
    fwhm (protein_fdr, median): 0.23791182828282942
    id_rate (0.01): 0.1
    identifications (n in table): 74927
    ms1_int_max_apex (feature_table, median): 1226170.0
    ms1_int_max_apex (peptide_fdr, median): 2914573.0
    ms1_int_max_apex (protein_fdr, median): 2956881.0
    ms1_int_max_area (feature_table, median): 214662.9903085017
    ms1_int_max_area (peptide_fdr, median): 732771.9799659976
    ms1_int_max_area (protein_fdr, median): 746382.2134822519
    ms1_int_sum_apex (feature_table, median): 2024339.101863
    ms1_int_sum_apex (peptide_fdr, median): 5843493.390942354
    ms1_int_sum_apex (protein_fdr, median): 5955805.576499356
    ms1_int_sum_area (feature_table, median): 348704.6126305632
    ms1_int_sum_area (peptide_fdr, median): 1482798.8537628404
    ms1_int_sum_area (protein_fdr, median): 1516048.6555881118
    peptide_fdr (n in table): 29565
    prec_offset_ppm (peptide_fdr, median): -8.900266834643844e-07
    prec_offset_ppm (protein_fdr, median): -8.72028238063649e-07
    prec_offset_raw_ppm (peptide_fdr, median): 0.5435998439788818
    prec_offset_raw_ppm (protein_fdr, median): 0.5537288784980774
    precursor (protein_fdr, n unique): 28709
    protein (protein_fdr, n unique): 5159
    protein_group (protein_fdr, n unique): 5159
    rt_length (feature_table, median): 0.33942324242423894
    rt_tail (feature_table, median): 1.1707317073170755
    second_search (n in table): 104353
    sequence (protein_fdr, n unique): 25644
    sequence_naked (protein_fdr, n unique): 24922
  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): 62637
    fragment_ions (n in table): 1207650
    fwhm (feature_table, median): 0.1479760151515137
    fwhm (peptide_fdr, median): 0.22749545454544773
    fwhm (protein_fdr, median): 0.22796406060606245
    id_rate (0.01): 0.06
    identifications (n in table): 59356
    ms1_int_max_apex (feature_table, median): 761059.0
    ms1_int_max_apex (peptide_fdr, median): 2279606.0
    ms1_int_max_apex (protein_fdr, median): 2303362.0
    ms1_int_max_area (feature_table, median): 113011.02941624864
    ms1_int_max_area (peptide_fdr, median): 550000.5053600001
    ms1_int_max_area (protein_fdr, median): 559070.945844758
    ms1_int_sum_apex (feature_table, median): 1240894.3861163845
    ms1_int_sum_apex (peptide_fdr, median): 4664993.927350649
    ms1_int_sum_apex (protein_fdr, median): 4732765.313081434
    ms1_int_sum_area (feature_table, median): 178141.18505316257
    ms1_int_sum_area (peptide_fdr, median): 1132462.8537649058
    ms1_int_sum_area (protein_fdr, median): 1152933.826231223
    peptide_fdr (n in table): 26437
    prec_offset_ppm (peptide_fdr, median): -7.934415862109745e-07
    prec_offset_ppm (protein_fdr, median): -7.88281909080979e-07
    prec_offset_raw_ppm (peptide_fdr, median): 0.5356272459030151
    prec_offset_raw_ppm (protein_fdr, median): 0.5397579669952393
    precursor (protein_fdr, n unique): 25732
    protein (protein_fdr, n unique): 4915
    protein_group (protein_fdr, n unique): 4915
    rt_length (feature_table, median): 0.28941702020201454
    rt_tail (feature_table, median): 1.1818181818181683
    second_search (n in table): 75263
    sequence (protein_fdr, n unique): 23020
    sequence_naked (protein_fdr, n unique): 22315
  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): 49384
    fragment_ions (n in table): 1269055
    fwhm (feature_table, median): 0.1657121616161703
    fwhm (peptide_fdr, median): 0.2481048080808108
    fwhm (protein_fdr, median): 0.2485652525252533
    id_rate (0.01): 0.07
    identifications (n in table): 60965
    ms1_int_max_apex (feature_table, median): 804525.0
    ms1_int_max_apex (peptide_fdr, median): 2349665.5
    ms1_int_max_apex (protein_fdr, median): 2386546.0
    ms1_int_max_area (feature_table, median): 127269.71073899744
    ms1_int_max_area (peptide_fdr, median): 624378.7933819995
    ms1_int_max_area (protein_fdr, median): 634252.5118357546
    ms1_int_sum_apex (feature_table, median): 1320877.302977677
    ms1_int_sum_apex (peptide_fdr, median): 4804288.418943534
    ms1_int_sum_apex (protein_fdr, median): 4878935.018290643
    ms1_int_sum_area (feature_table, median): 202527.9342573708
    ms1_int_sum_area (peptide_fdr, median): 1278406.5189456097
    ms1_int_sum_area (protein_fdr, median): 1308271.1514910937
    peptide_fdr (n in table): 25206
    prec_offset_ppm (peptide_fdr, median): -8.124321766445064e-07
    prec_offset_ppm (protein_fdr, median): -8.054915952016017e-07
    prec_offset_raw_ppm (peptide_fdr, median): 0.5742343664169312
    prec_offset_raw_ppm (protein_fdr, median): 0.5818887948989868
    precursor (protein_fdr, n unique): 24505
    protein (protein_fdr, n unique): 4718
    protein_group (protein_fdr, n unique): 4718
    rt_length (feature_table, median): 0.3026909090909129
    rt_tail (feature_table, median): 1.1500000000000123
    second_search (n in table): 79693
    sequence (protein_fdr, n unique): 21867
    sequence_naked (protein_fdr, n unique): 21160
  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): 69618
    fragment_ions (n in table): 1532837
    fwhm (feature_table, median): 0.1805095959595988
    fwhm (peptide_fdr, median): 0.24040692929292717
    fwhm (protein_fdr, median): 0.24095490909090245
    id_rate (0.01): 0.08
    identifications (n in table): 70880
    ms1_int_max_apex (feature_table, median): 1071251.0
    ms1_int_max_apex (peptide_fdr, median): 2712166.0
    ms1_int_max_apex (protein_fdr, median): 2752394.0
    ms1_int_max_area (feature_table, median): 188128.80485600044
    ms1_int_max_area (peptide_fdr, median): 695134.439940746
    ms1_int_max_area (protein_fdr, median): 709889.7031795062
    ms1_int_sum_apex (feature_table, median): 1774145.218433667
    ms1_int_sum_apex (peptide_fdr, median): 5523388.116812809
    ms1_int_sum_apex (protein_fdr, median): 5619325.491420584
    ms1_int_sum_area (feature_table, median): 305880.1365647374
    ms1_int_sum_area (peptide_fdr, median): 1414100.3769893195
    ms1_int_sum_area (protein_fdr, median): 1448946.502272101
    peptide_fdr (n in table): 28506
    prec_offset_ppm (peptide_fdr, median): -8.141323064592143e-07
    prec_offset_ppm (protein_fdr, median): -8.075890605141467e-07
    prec_offset_raw_ppm (peptide_fdr, median): 0.5388190150260925
    prec_offset_raw_ppm (protein_fdr, median): 0.5441269874572754
    precursor (protein_fdr, n unique): 27695
    protein (protein_fdr, n unique): 5044
    protein_group (protein_fdr, n unique): 5044
    rt_length (feature_table, median): 0.33933919191917994
    rt_tail (feature_table, median): 1.1666666666666436
    second_search (n in table): 95675
    sequence (protein_fdr, n unique): 24787
    sequence_naked (protein_fdr, n unique): 23873
  file_sizes:
    files:
      C:\Users\brvpuyve\Downloads\Temp\LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01.ms_data.hdf: 1482.7209396362305
      C:\Users\brvpuyve\Downloads\Temp\LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02.ms_data.hdf: 1574.6031370162964
      C:\Users\brvpuyve\Downloads\Temp\LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03.ms_data.hdf: 1669.5328826904297
      C:\Users\brvpuyve\Downloads\Temp\LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01.ms_data.hdf: 1541.422046661377
      C:\Users\brvpuyve\Downloads\Temp\LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02.ms_data.hdf: 1704.2832050323486
      C:\Users\brvpuyve\Downloads\Temp\LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03.ms_data.hdf: 1652.620460510254
    results: 355.0540895462036
  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: '2024-12-17 09:19:58.588240'
  timing:
    align (min): 0.15146939754486083
    create_database (min): 0.0008828083674112956
    feature_finding (min): 35.39946259260178
    import_raw_data (min): 4.178935511906942
    isobaric_labeling (min): 9.589195251464843e-05
    match (min): 1.0644822478294373
    protein_grouping (min): 0.07890653212865194
    quantification (min): 1.9369409998257956
    recalibrate_data (min): 1.0250500758488974
    score (min): 2.1305446585019427
    search_data (min): 4.390419777234396
    search_data_2 (min): 2.4754672050476074
    total (min): 52.83300926685333
  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
