The most important element of a fermo_core run is the parameters.json file, which specifies all files and run parameters. This file is also generated in the background if fermo gui is being used.

The parameters.json file follows this json-schema and an example can be found here.

fermo_core automatically checks the user-provided parameters file and fails with an error message if the formatting is incorrect.

Specifications parameters.json

The parameters.json file is separated in three parts:

• files: references to input files, paths, and locations
• core_modules: modules that are generally applicable and only require a peaktable and MS/MS information (enabled by default)
• additional_modules: modules requiring specific input files (disabled by default)

Detailed information on modules and functions of parameters can be found on the Modules pages.

files (mandatory)

Nota bene: If a filetype is not provided, the corresponding parameter entry must be omitted.

peaktable (mandatory)

Key	Possible Values	Required
filepath	(the filepath)	True
format	mzmine3	True
polarity	positive, negative	True

msms (optional)

Nota bene: By default, fragment peaks with an intensity lower than 0.01 are removed. To disable filtering, set rel_int_from to 0.0

Key	Possible Values	Required	Default
filepath	(the filepath)	True	N/A
format	mgf	True	N/A
rel_int_from	0.0-1.0	False	0.01

phenotype (optional)

Key	Possible Values	Required
filepath	(the filepath)	True
format	qualitative, quantitative-percentage, quantitative-concentration	True

group_metadata (optional)

Key	Possible Values	Required
filepath	(the filepath)	True
format	fermo	True

spectral_library (optional)

Key	Possible Values	Required
filepath	(the filepath)	True
format	mgf	True

ms2query_results (optional)

Key	Possible Values	Required	Default
filepath	(the filepath)	True	N/A
score_cutoff	0.0-1.0	False	0.7

as_results (optional)

Key	Possible Values	Required	Default
directory_path	(the directory path)	True	N/A
similarity_cutoff	0.0-1.0	False	0.7

core_modules (optional)

adduct_annotation (optional)

Key	Possible Values	Required	Default
activate_module	true, false	True	true
mass_dev_ppm	0-100.0	False	10.0

neutral_loss_annotation (optional)

Key	Possible Values	Required	Default
activate_module	true, false	True	true
mass_dev_ppm	0-100.0	False	10.0
nonbiological	true, false	False	false

fragment_annotation (optional)

Key	Possible Values	Required	Default
activate_module	true, false	True	true
mass_dev_ppm	0-100.0	False	10.0

spec_sim_networking (optional)

modified_cosine (optional)

Key	Possible Values	Required	Default
activate_module	true, false	True	true
msms_min_frag_nr	>=1	False	5
fragment_tol	>0	False	0.1
score_cutoff	0.0-1.0	False	0.7
max_nr_links	>=1	False	10
maximum_runtime	>=0	False	0 (unlimited)

ms2deepscore (optional)

Key	Possible Values	Required	Default
activate_module	true, false	True	true
msms_min_frag_nr	>=1	False	5
score_cutoff	0.0-1.0	False	0.8
max_nr_links	>=1	False	10
maximum_runtime	>=0	False	0 (unlimited)

additional_modules (optional)

feature_filtering (optional)

Key	Possible Values	Required	Default
activate_module	true, false	True	false
filter_rel_int_range_min	0.0-1.0	False	0.0
filter_rel_int_range_max	0.0-1.0	False	1.0
filter_rel_area_range_min	0.0-1.0	False	0.0
filter_rel_area_range_max	0.0-1.0	False	1.0

blank_assignment (optional)

Key	Possible Values	Required	Default
activate_module	true, false	True	false
factor	>=1	False	10
algorithm	mean, median, maximum	False	mean
value	height, area	False	area

group_factor_assignment (optional)

Key	Possible Values	Required	Default
activate_module	true, false	True	false
algorithm	mean, median, maximum	False	mean
value	height, area	False	area

phenotype_assignment (optional)

qualitative (optional)

Key	Possible Values	Required	Default
activate_module	true, false	True	false
factor	>=1	False	10
algorithm	minmax, median, mean	False	minmax
value	height, area	False	area

quantitative-percentage (optional)

Key	Possible Values	Required	Default
activate_module	true, false	True	false
sample_avg	mean, median	False	mean
value	area	False	area
algorithm	pearson	False	pearson
p_val_cutoff	0.0-1.0	False	0.05
coeff_cutoff	0.0-1.0	False	0.7

quantitative-concentration (optional)

Key	Possible Values	Required	Default
activate_module	true, false	True	false
sample_avg	mean, median	False	mean
value	area	False	area
algorithm	pearson	False	pearson
p_val_cutoff	0.0-1.0	False	0.05
coeff_cutoff	0.0-1.0	False	0.7

spectral_library_matching (optional)

modified_cosine (optional)

Key	Possible Values	Required	Default
activate_module	true, false	True	false
min_nr_matched_peaks	>=1	False	5
fragment_tol	>0	False	0.1
score_cutoff	0.0-1.0	False	0.7
max_precursor_mass_diff	>=1	False	600
maximum_runtime	>=0	False	0 (unlimited)

ms2deepscore (optional)

Key	Possible Values	Required	Default
activate_module	true, false	True	false
score_cutoff	0.0-1.0	False	0.8
max_precursor_mass_diff	>=1	False	600
maximum_runtime	>=0	False	0 (unlimited)

as_kcb_matching (optional)

modified_cosine (optional)

Key	Possible Values	Required	Default
activate_module	true, false	True	false
min_nr_matched_peaks	>=1	False	5
fragment_tol	>0	False	0.1
score_cutoff	0.0-1.0	False	0.5
max_precursor_mass_diff	>=1	False	600
maximum_runtime	>=0	False	0 (unlimited)

ms2deepscore (optional)

Key	Possible Values	Required	Default
activate_module	true, false	True	false
score_cutoff	0.0-1.0	False	0.7
max_precursor_mass_diff	>=1	False	600
maximum_runtime	>=0	False	0 (unlimited)