MS2Rescore Configuration (SchemaStore) JSON Schema

Type	object
File match	`ms2rescore.json` `ms2rescore.toml` `.-ms2rescore.json` `.-ms2rescore.toml` `.-ms2rescore-config.json` `.-ms2rescore-config.toml`
Schema URL	https://catalog.lintel.tools/schemas/schemastore/ms2rescore-configuration/latest.json
Source	https://raw.githubusercontent.com/compomics/ms2rescore/main/ms2rescore/package_data/config_schema.json

Validate with Lintel

npx @lintel/lintel check

Type: object

Properties

ms2rescore object required

General MS²Rescore settings.

26 nested properties

psm_file string | null | string[] required

Path to file with peptide-spectrum matches.

feature_generators object

Feature generators and their configurations.

Default:

{
  "basic": {},
  "ms2pip": {
    "model": "HCD",
    "ms2_tolerance": 0.02
  },
  "deeplc": {},
  "maxquant": {}
}

rescoring_engine object

Rescoring engine to use and its configuration. Leave empty to skip rescoring and write features to file.

Default:

{
  "mokapot": {}
}

config_file string | null

Path to configuration file

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 string | null

Path to spectrum file or directory with spectrum files

output_path string | null

Path and root name for output files

log_level string

Logging level

Values: "debug" "info" "warning" "error" "critical"

id_decoy_pattern string | null

Regex pattern used to identify the decoy PSMs in identification file.

Default: null

spectrum_id_pattern string | null

Regex pattern to extract index or scan number from spectrum file. Requires at least one capturing group.

Default: "(.*)"

format=regex

psm_id_pattern string | null

Regex pattern to extract index or scan number from PSM file. Requires at least one capturing group.

Default: "(.*)"

format=regex

psm_id_rt_pattern string | null

Regex pattern to extract retention time from PSM identifier. Requires at least one capturing group.

Default: null

format=regex

psm_id_im_pattern string | null

Regex pattern to extract ion mobility from PSM identifier. Requires at least one capturing group.

Default: null

format=regex

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

Default: 10

min=1

max_psm_rank_output number

Maximum rank of PSMs to return after rescoring, before final FDR calculation

Default: 1

min=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.

Default:

{}

processes number

Number of parallel processes to use; -1 for all available

Default: -1

min=-1multipleOf=1

rename_to_usi boolean

Convert spectrum IDs to their universal spectrum identifier

fasta_file string | null

Path to FASTA file with protein sequences to use for protein inference

write_flashlfq boolean | null

Write results to a FlashLFQ-compatible file

Default: false

write_report boolean | null

Write an HTML report with various QC metrics and charts

Default: true

disable_update_check boolean | null

Disable the automatic update check

Default: false

profile boolean | null

Write a txt report using cProfile for profiling

Default: false