config_schema.md

MS²Rescore configuration

Properties

• ms2rescore (object): General MS²Rescore settings. Cannot contain additional properties.
  • feature_generators (object): Feature generators and their configurations. Default: {"basic": {}, "ms2pip": {"model": "HCD", "ms2_tolerance": 0.02}, "deeplc": {}, "maxquant": {}}.
    • .*: Refer to #/definitions/feature_generator.
    • basic: Refer to #/definitions/basic.
    • ms2pip: Refer to #/definitions/ms2pip.
    • deeplc: Refer to #/definitions/deeplc.
    • maxquant: Refer to #/definitions/maxquant.
    • ionmob: Refer to #/definitions/ionmob.
    • im2deep: Refer to #/definitions/im2deep.
  • rescoring_engine (object): Rescoring engine to use and its configuration. Leave empty to skip rescoring and write features to file. Default: {"mokapot": {}}.
    • .*: Refer to #/definitions/rescoring_engine.
    • percolator: Refer to #/definitions/percolator.
    • mokapot: Refer to #/definitions/mokapot.
  • config_file: Path to configuration file.
    • One of
      • string
      • null
  • psm_file: Path to file with peptide-spectrum matches.
    • One of
      • string
      • null
      • array
        • Items (string)
  • psm_file_type (string): PSM file type. By default inferred from file extension. Default: "infer".
  • psm_reader_kwargs (object): Keyword arguments passed to the PSM reader. Default: {}.
  • spectrum_path: Path to spectrum file or directory with spectrum files.
    • One of
      • string
      • null
  • output_path: Path and root name for output files.
    • One of
      • string
      • null
  • log_level (string): Logging level. Must be one of: ["debug", "info", "warning", "error", "critical"].
  • id_decoy_pattern: Regex pattern used to identify the decoy PSMs in identification file. Default: null.
    • One of
      • string
      • null
  • spectrum_id_pattern: Regex pattern to extract index or scan number from spectrum file. Requires at least one capturing group. Default: "(.*)".
    • One of
      • string
      • null
  • psm_id_pattern: Regex pattern to extract index or scan number from PSM file. Requires at least one capturing group. Default: "(.*)".
    • One of
      • string
      • null
  • psm_id_rt_pattern: Regex pattern to extract retention time from PSM identifier. Requires at least one capturing group. Default: null.
    • One of
      • string
      • null
  • psm_id_im_pattern: Regex pattern to extract ion mobility from PSM identifier. Requires at least one capturing group. Default: null.
    • One of
      • string
      • null
  • lower_score_is_better (boolean): Bool indicating if lower score is better. Default: false.
  • max_psm_rank_input (number): Maximum rank of PSMs to use as input for rescoring. Minimum: 1. Default: 10.
  • max_psm_rank_output (number): Maximum rank of PSMs to return after rescoring, before final FDR calculation. Minimum: 1. Default: 1.
  • modification_mapping (object): Mapping of modification labels to each replacement label. Default: {}.
  • fixed_modifications (object): Mapping of amino acids with fixed modifications to the modification name. Can contain additional properties. Default: {}.
  • processes (number): Number of parallel processes to use; -1 for all available. Minimum: -1. Default: -1.
  • rename_to_usi (boolean): Convert spectrum IDs to their universal spectrum identifier.
  • fasta_file: Path to FASTA file with protein sequences to use for protein inference.
    • One of
      • string
      • null
  • write_flashlfq: Write results to a FlashLFQ-compatible file. Default: false.
    • One of
      • boolean
      • null
  • write_report: Write an HTML report with various QC metrics and charts. Default: true.
    • One of
      • boolean
      • null
  • disable_update_check: Disable the automatic update check. Default: false.
    • One of
      • boolean
      • null
  • profile: Write a txt report using cProfile for profiling. Default: false.
    • One of
      • boolean
      • null

Definitions

• feature_generator (object): Feature generator configuration. Can contain additional properties.
• rescoring_engine (object): Rescoring engine configuration. Can contain additional properties.
• basic (object): Basic feature generator configuration. Can contain additional properties. Refer to #/definitions/feature_generator.
• ms2pip (object): MS²PIP feature generator configuration. Can contain additional properties. Refer to #/definitions/feature_generator.
  • model (string): MS²PIP model to use (see MS²PIP documentation). Default: "HCD".
  • ms2_tolerance (number): MS2 error tolerance in Da. Minimum: 0. Default: 0.02.
• deeplc (object): DeepLC feature generator configuration. Can contain additional properties. Refer to #/definitions/feature_generator.
  • calibration_set_size: Calibration set size. Default: 0.15.
    • One of
      • integer
      • number
• maxquant (object): MaxQuant feature generator configuration. Can contain additional properties. Refer to #/definitions/feature_generator.
• ionmob (object): Ion mobility feature generator configuration using Ionmob. Can contain additional properties. Refer to #/definitions/feature_generator.
  • ionmob_model (string): Path to Ionmob model directory. Default: "GRUPredictor".
  • reference_dataset (string): Path to Ionmob reference dataset file. Default: "Meier_unimod.parquet".
  • tokenizer (string): Path to tokenizer json file. Default: "tokenizer.json".
• im2deep (object): Ion mobility feature generator configuration using IM2Deep. Can contain additional properties. Refer to #/definitions/feature_generator.
  • reference_dataset (string): Path to IM2Deep reference dataset file. Default: "Meier_unimod.parquet".
• mokapot (object): Mokapot rescoring engine configuration. Additional properties are passed to the Mokapot brew function. Can contain additional properties. Refer to #/definitions/rescoring_engine.
  • train_fdr (number): FDR threshold for training Mokapot. Minimum: 0. Maximum: 1. Default: 0.01.
  • write_weights (boolean): Write Mokapot weights to a text file. Default: false.
  • write_txt (boolean): Write Mokapot results to a text file. Default: false.
• percolator (object): Percolator rescoring engine configuration. Can contain additional properties. Refer to #/definitions/rescoring_engine.
  • init-weights: Weights file for scoring function. Default: false.
    • One of
      • string
      • null