Parameters parsed for public submission#

We automatically retrieve the parameters used for a specific worklow run in the parameter file submitted next to the result. The parsing depends on the tool and are described below. If you have any suggestions or concerns related to how we parse these parameters, please let us know by creating a GitHub issue.

DISCLAIMER: When submitting parameter files, please be aware that your dataset may contain identifiable information through embedded file paths. These paths can reveal personal usernames, system architecture, project names, and directory structures associated with e.g.

The FASTA database location

The RAW data location

Installation paths for the tools being used

Such metadata can inadvertently disclose sensitive or institution-specific information. We recommend reviewing and sanitizing any file paths prior to submission to ensure compliance with your organization’s data privacy policies and to protect personal or institutional identifiers.

A single-table overview of the parsing methodology of supported tools can be found here.

General comments on the parameters that are retrieved by ProteoBench#

The parameters that are retrieved from the parameter files are the following:

Parameter	Description
software_name	Name of the software tool.
software_version	Version of the software tool used to generate the run.
search_engine	Name of the search engine used for MS-based identification. Often the same as the software name, but is relevant for data analysis workflows that allow multiple search engines to be used (e.g. quantms).
search_engine_version	Version of the search engine.
ident_fdr_psm	Target or obtained FDR at PSM level.
ident_fdr_peptide	Target or obtained FDR at peptide level
ident_fdr_protein	Target or obtained FDR at protein level
enable_match_between_runs	TRUE if match between run is enabled.
precursor_mass_tolerance	Precursor mass tolerance used for identification (in the format [-20 ppm, 20 ppm]).
fragment_mass_tolerance	Fragment mass tolerance used for identification (in the format [-50 ppm, 50 ppm]).
enzyme	Enzyme used for digesting peptides.
allowed_miscleavages	Number of maximum missed cleavages allowed per peptide.
min_peptide_length	Minimum peptide length considered in the analysis.
max_peptide_length	Maximum peptide length considered in the analysis.
fixed_mods	List of fixed modifications (PTMs) considered in the analysis.
variable_mods	List of variable modifications (PTMs) considered in the analysis.
max_mods	Maximum number of modifications per peptide considered in the analysis.
min_precursor_charge	Minimum precursor charge considered in the analysis.
max_precursor_charge	Maximum precursor charge considered in the analysis.
quantification_method	Quantification method. This applies to software tools that offer different strategies for quantification.
protein_inference	Protein inference method.
predictors_library	Library used for the analysis in DIA. With the current module, we do not support experimentally generated libraries, but some software tools allow use of different in-silico-generated libraries.
scan_window	Scan window settings.

Tool-specific information#

AlphaDIA#

Parsed parameter file: log.txt Example here.

Parameter	Parsed value
software_name	AlphaDIA (fixed)
software_version	Parsed from log file header
search_engine	AlphaDIA (fixed)
search_engine_version	Not parsed as no difference with software_version
ident_fdr_psm	fdr setting in fdr section of the config
ident_fdr_peptide	Not parsed as not an option
ident_fdr_protein	fdr setting in fdr section of the config
enable_match_between_runs	Set to true if MBR step enabled, else False
precursor_mass_tolerance	target_ms1_tolerance setting in search section of the config
fragment_mass_tolerance	target_ms2_tolerance setting in search section of the config
enzyme	enzyme setting in library_prediction section of the config
allowed_miscleavages	missed_cleavages setting in library_prediction section of the config
min_peptide_length	Minimum value in precursor_len setting in library_prediction section of the config
max_peptide_length	Maximum value in precursor_len setting in library_prediction section of the config
min_precursor_mz	Minimum value in precursor_mz setting in library_prediction section of the config
max_precursor_mz	Maximum value in precursor_mz setting in library_prediction section of the config
min_fragment_mz	Minimum value in fragment_mz setting in library_prediction section of the config
max_fragment_mz	Maximum value in fragment_mz setting in library_prediction section of the config
fixed_mods	fixed_modifications setting in library_prediction section of the config
variable_mods	variable_modifications setting in library_prediction section of the config
max_mods	max_var_mod_num setting in library_prediction section of the config
min_precursor_charge	Minimum value in precursor_charge setting in library_prediction section of the config
max_precursor_charge	Maximum value in precursor_charge setting in library_prediction section of the config
quantification_method	DirectLFQ (fixed)
protein_inference	inference_strategy in fdr section of the config
predictors_library	AlphaPeptDeep (fixed)
scan_window	Not parsed

AlphaPept#

Parsed parameter file: .yaml Example here.

Parameter	Parsed value
software_name	AlphaPept (fixed)
software_version	version in summary section of the config
search_engine	AlphaPept (fixed)
search_engine_version	version in summary section of the config
ident_fdr_psm	peptide_fdr in search section of the config
ident_fdr_peptide	Not parsed as not an option
ident_fdr_protein	protein_fdr in search section of the config
enable_match_between_runs	True if match is enabled in workflow section of the config, else False
precursor_mass_tolerance	prec_tol in search section of the config
fragment_mass_tolerance	frag_tol in search section of the config
enzyme	protease in fasta section of the config
allowed_miscleavages	n_missed_cleavages in fasta section of the config
min_peptide_length	pep_length_min in fasta section of the config
max_peptide_length	pep_length_max in fasta section of the config
fixed_mods	mods_fixed & mods_fixed_terminal & mods_fixed_terminal_prot in fasta section of the config
variable_mods	mods_variable & mods_variable_terminal & mods_variable_terminal_prot in fasta section of the config
max_mods	n_modifications_max in fasta section of the config
min_precursor_charge	iso_charge_min in features section of the config
max_precursor_charge	iso_charge_max in features section of the config
quantification_method	Not parsed
protein_inference	Not parsed
predictors_library	Not parsed as not applicable
scan_window	Not parsed

DIA-NN#

Parsed parameter file: log.txt Example here. DIA-NN parameters are parsed either from the command line string found in the log file or, if the –cfg flag is used (meaning a custom configuration file was used, which we do not have access to), the parameters are parsed from the free text underneath the command line string. For robust parameter parsing, we recommend not using the –cfg flag.

Parameter	Parsed value
software_name	DIA-NN (fixed)
software_version	Parsed from log file header
search_engine	DIA-NN (fixed)
search_engine_version	Parsed from log file header
ident_fdr_psm	No –cfg: value set for –qvalue –cfg: parsed from line Output will be filtered at X FDR
ident_fdr_peptide	Not parsed as not an option
ident_fdr_protein	Not parsed as not an option
enable_match_between_runs	No –cfg: True if –reanalyse is set, else false –cfg: True if reanalyse them (version <1.8) or MBR enabled (version >1.8) is mentioned
precursor_mass_tolerance	Value set for –mass-acc-ms1. If this parameter is not set, it means tolerance optimization will be performed. In that case,as well as if –cfg is set, the value will be parsed from the first occurence of the line Recommended MS1 mass accuracy setting: X ppm
fragment_mass_tolerance	Value set for –mass-acc. If this parameter is not set, it means tolerance optimization will be performed. In that case, as well as if –cfg is set, the value will be parsed from line Optimised mass accuracy: X ppm
enzyme	No –cfg: value set for –cut –cfg: parsed from line In silico digest will involve cuts at X but excluding cuts at X
allowed_miscleavages	No –cfg: value set for –missed-cleavages –cfg: parsed from line Maximum number of missed cleavages set to X
min_peptide_length	No –cfg: value set for –min-pep-len (if not provided, default = 7) –cfg: parsed from the line Min peptide length set to X
max_peptide_length	No –cfg: value set for –max-pep-len (if not provided, default = 30) –cfg: parsed from the line Max peptide length set to X
fixed_mods	No –cfg: value set for –mod –cfg: parsed from the lines X enabled as a fixed modification and **Modification X with mass delta X at X will be considered as fixed
variable_mods	No –cfg: value set for –var-mod –cfg: parsed form line Modification X with mass delta X at X will be considered as variable
max_mods	No –cfg: value set for var-mods –cfg: parsed from line Maximum number of variable modifications set to X
min_precursor_charge	No –cfg: value set for min-pr-charge (if not provided, default = 1) –cfg: parsed from line Min precursor charge set to X
max_precursor_charge	No –cfg: value set for max-pr-charge (if not provided, default = 4) –cfg: parsed from line Max precursor charge set to X
min_precursor_mz	No –cfg: value set for min-pr-mz (if not provided, default = 300) –cfg: parsed from line Min precursor m/z set to X
max_precursor_mz	No –cfg: value set for max-pr-mz (if not provided, default = 1800) –cfg: parsed from line Max precursor m/z set to X
min_fragment_mz	No –cfg: value set for min-fr-mz (if not provided, default = 200) –cfg: parsed from line Min fragment m/z set to X
max_fragment_mz	No –cfg: value set for max-fr-mz (if not provided, default = 1800) –cfg: parsed from line Min fragment m/z set to X
quantification_method	No –cfg: either Legacy (if –direct-quant set), QuantUMS high-accuracy if –high-acc set or QuantUMS high-precision (default) –cfg: parsed from line X quantification mode
protein_inference	No –cfg: value set for –pg-level or no-prot-inf, with the mapping {0: Isoforms, 1: Protein_names, 2: Genes} –cfg: parsed from line Implicit protein grouping: X
predictors_library	No –cfg: either DIA-NN if –predictor is set, or User defined if –lib is set to a path
scan_window	Parsed from line Scan window radius set to X

FragPipe#

Parsed parameter file: .workflow Example here.

Parameter	Parsed value
software_name	Either FragPipe or FragPipe (DIA-NN quant), depending on input
software_version	Parsed from header
search_engine	MSFragger (fixed)
search_engine_version	Parsed either from header or from MSFragger binary path
ident_fdr_psm	If not DIA-NN quant, parsed from phi-report.filter if DIA-NN quant, parsed from diann.q-value
ident_fdr_peptide	If not DIA-NN quant, parsed from phi-report.filter if DIA-NN quant, not parsed
ident_fdr_protein	If not DIA-NN quant, parsed from phi-report.filter if DIA-NN quant, parsed from diann.q-value
enable_match_between_runs	If not DIA-NN quant, parsed from ionquant.mbr if DIA-NN quant, parsed by checking if –reanalyse is present in diann.fragpipe.cmd-opts
precursor_mass_tolerance	Parsed from msfragger.precursor_mass_lower and msfragger.precursor_mass_upper
fragment_mass_tolerance	Parsed from msfragger.fragment_mass_tolerance
enzyme	Parsed from msfragger.search_enzyme_name_1 and msfragger.search_enzyme_name_2
allowed_miscleavages	Parsed from msfragger.allowed_missed_cleavage_1
min_peptide_length	Parsed from msfragger.digest_min_length
max_peptide_length	Parsed from msfragger.digest_max_length
fixed_mods	Parsed from msfragger.table.fix-mods
variable_mods	Parsed from msfragger.table.var-mods
max_mods	Parsed from msfragger.max_variable_mods_per_peptide
min_precursor_charge	FragPipe uses charge state information from data, if present. So this value is set to 1 by default, but overwritten using msfragger.misc.fragger.precursor-charge-lo if msfragger.override_charge is set to True
max_precursor_charge	FragPipe uses charge state information from data, if present. So this value is set to None by default, but overwritten using msfragger.misc.fragger.precursor-charge-lo if msfragger.override_charge is set to True
quantification_method	If not DIA-NN quant, not parsed (TODO) if DIA-NN quant, parsed from diann.quantification-strategy
min_precursor_mz	Calculated by dividing the minimum peptide mass set for digestion (msfragger.misc.fragger.digest-mass-lo) by the maximum precursor charge
max_precursor_mz	Calculated by dividing the maximum peptide mass set for digestion (msfragger.misc.fragger.digest-mass-hi) by the minimum precursor charge
min_fragment_mz	Not parsed
max_fragment_mz	Not parsed
protein_inference	Parsed from protein-prophet.cmd-opts
predictors_library	Not parsed
scan_window	Not parsed

i2MassChroQ#

Parsed parameter file: Project parameters.tsv Example here.

Parameter	Parsed value
software_name	i2MassChroQ (fixed)
software_version	Parsed from i2MassChroQ_VERSION
search_engine	Parsed from AnalysisSoftware_name
search_engine_version	Parsed from AnalysisSoftware_version
ident_fdr_psm	Parsed from psm_fdr
ident_fdr_peptide	Parsed from peptide_fdr
ident_fdr_protein	Parsed from protein_fdr
enable_match_between_runs	Parsed from mcq_mbr
precursor_mass_tolerance	Parsed from either sage_precursor_tol or spectrum, parent monoisotopic mass error minus/plus, depending on search engine used
fragment_mass_tolerance	Parsed from either sage_fragment_tol or spectrum, fragment monoisotopic mass error minus/plus, depending on search engine used
enzyme	If Sage is used: parsed from sage_database_enzyme_cleave_at, sage_data_enzyme_restrict, sage_database_enzyme_c_terminal if X!Tandem is used: parsed from protein, cleavage site
allowed_miscleavages	Parsed from either sage_database_enzyme_missed_cleavages or scoring, maximum missed cleavage sites, depending on search engine used
min_peptide_length	Not parsed if X!Tandem is used parsed from sage_database_enzyme_min_len if Sage is used
max_peptide_length	Not parsed if X!Tandem is used parsed from sage_database_enzyme_max_len if Sage is used
fixed_mods	Parsed from either sage_database_static_mods or residue, modification mass**, depending on search engine used
variable_mods	Parsed from either sage_database_variable_mods or residue, potential modification mass, depending on search engine used
max_mods	Not parsed if X!Tandem is used parsed from sage_database_max_variable_mods if Sage is used
min_precursor_charge	Not parsed if X!Tandem is used parsed from sage_precursor_charge if Sage is used
max_precursor_charge	Parsed from either sage_precursor_charge or spectrum, maximum parent charge, depending on search engine used
quantification_method	Not parsed
protein_inference	Not parsed
predictors_library	Not parsed
scan_window	Not parsed

MaxQuant#

Parsed parameter file: mqpar.xml Example here.

Parameter	Parsed value
software_name	MaxQuant (fixed)
software_version	Parsed from maxQuantVersion
search_engine	Andromeda (fixed)
search_engine_version	Not parsed
ident_fdr_psm	Parsed from peptideFdr*
ident_fdr_peptide	Not parsed
ident_fdr_protein	Parsed from proteinFdr
enable_match_between_runs	Parsed from matchBetweenRuns
precursor_mass_tolerance	Parsed from mainSearchTol
fragment_mass_tolerance	Parsed from MatchTolerance
enzyme	Parsed from <enzymes><string>
allowed_miscleavages	Parsed from maxMissedCleavages
min_peptide_length	Parsed from minPepLen (version < 2.6) or minPeptideLength (version >= 2.6)
max_peptide_length	Not parsed if not DIA, otherwise parsed from maxPeptideLengthForUnspecificSearch
fixed_mods	Parsed from fixedModifications
variable_mods	Parsed from variableModifications
max_mods	Parsed from maxNmods
min_precursor_charge	Not parsed
max_precursor_charge	Parsed from maxCharge
min_precursor_mz	Not parsed
max_precursor_mz	Calculated by dividing the maximum peptide mass set (maxPeptideMass) by the minimum precursor charge
min_fragment_mz	Not parsed
max_fragment_mz	Not parsed
quantification_method	Not parsed
protein_inference	Not parsed
predictors_library	Not parsed
scan_window	Not parsed

*This may seem incorrect. However, when the setting PSM FDR is changed in the GUI, this affects the peptideFdr setting in the mqpar.xml.
There does not seem to be a peptide FDR setting in the GUI.

MSAID*#

Parsed parameter file: experiment_details.csv Example here.

Parameter	Parsed value
software_name	MSAID (default)
software_version	Not parsed
search_engine	Parsed from Algorithm
search_engine_version	Parsed from Algorithm
ident_fdr_psm	0.01 (fixed)
ident_fdr_peptide	0.01 (fixed)
ident_fdr_protein	0.01 (fixed)
enable_match_between_runs	True if Quan in all file or MBR is found in quantification_method
precursor_mass_tolerance	Not parsed
fragment_mass_tolerance	Parsed from Fragment Mass Tolerance
enzyme	Parsed from Enzyme
allowed_miscleavages	Parsed from Max. Missed Cleavage Sites
min_peptide_length	Parsed from Min. Peptide Length
max_peptide_length	Parsed from Max. Peptide Length
fixed_mods	Parsed from Static Modifications
variable_mods	Parsed from Variable Modifications
max_mods	Parsed from Maximum Number of Modifications
min_precursor_charge	Parsed from Min. Peptide Charge
max_precursor_charge	Parsed from Max. Peptide Charge
min_precursor_mz	Not parsed
max_precursor_mz	Not parsed
min_fragment_mz	Not parsed
max_fragment_mz	Not parsed
quantification_method	Parsed from Quantification Type
protein_inference	Not parsed
predictors_library	Not parsed
scan_window	Not parsed

*ProteoBench’s compatibility with MSAID output is still a work in progress.

MSAngel#

Parsed parameter file: .json Example here.

Parameter	Parsed value
software_name	MSAngel (fixed)
software_version	Parsed from msAngelVersion
search_engine	Parsed from searchEnginesWithForms
search_engine_version	Not parsed
ident_fdr_psm	Parsed from psmExpectedFdr
ident_fdr_peptide	Not parsed
ident_fdr_protein	Not parsed
enable_match_between_runs	True (fixed)
precursor_mass_tolerance	Parsed from TOL and TOLU in the paramMap section if Mascot is used Parsed from precursorTolerance and precursorAccuracyType in the paramMap section if X!Tandem is used
fragment_mass_tolerance	Not parsed if Mascot is used Parsed from fragmentIonMZTolerance and fragmentAccuraccyType in the paramMap section if X!Tandem is used
enzyme	Parsed from CLE in the paramMap section if Mascot is used Parsed from enzymes in digestionParameters in the paramMap section if X!Tandem is used
allowed_miscleavages	Parsed from PFA in the paramMap section if Mascot is used Parsed from nMissedCleavages in digestionParameters in the paramMap section if X!Tandem is used
min_peptide_length	Not parsed
max_peptide_length	Not parsed
fixed_mods	Parsed from MODS in the paramMap section if Masscot is used Parsed from fixedModifications in modificationParameters in the paramMap section if X!Tandem is used
variable_mods	Parsed from IT_MODS in the paramMap section if Masscot is used Parsed from variableModifications in modificationParameters in the paramMap section if X!Tandem is used. Special parsing of the data section if proteinQuickAcetyl and/or quickPyrolidone are toggled
max_mods	Not parsed
min_precursor_charge	Not parsed
max_precursor_charge	Not parsed
quantification_method	Not parsed
protein_inference	Not parsed
predictors_library	Not parsed
scan_window	Not parsed

PEAKS#

Parsed parameter file: parameters.txt Example here.

Parameter	Parsed value
software_name	PEAKS (fixed)
software_version	Parsed from line PEAKS Version: X
search_engine	PEAKS (fixed)
search_engine_version	Parsed from line PEAKS Version: X
ident_fdr_psm	Parsed from either PSM FDR: X or Precusor FDR: X
ident_fdr_peptide	Parsed from line Peptide FDR: X
ident_fdr_protein	Parsed from line Protein Group FDR: X
enable_match_between_runs	Parsed from line Match Between Run: X
precursor_mass_tolerance	Parsed from line Precursor Mass Error Tolerance: X
fragment_mass_tolerance	Parsed from line Fragment Mass Error Tolerance: X
enzyme	Parsed from line Enzyme: X
allowed_miscleavages	Parsed from line Max Missed Cleavage: X
min_peptide_length	Parsed from line Peptide Length between: X or Peptide Length Range: X
max_peptide_length	Parsed from line Peptide Length between: X or Peptide Length Range: X
fixed_mods	Parsed as the elements between Fixed Modifications: and Variable Modifications
variable_mods	Parsed as the elements between Variable Modifications: and Database:
max_mods	Parsed from line Max Variable PTM per Peptide: X
min_precursor_charge	Parsed from line Precursor Charge between: X or Precursors Charge between: X
max_precursor_charge	Parsed from line Precursor Charge between: X or Precursors Charge between: X
min_precursor_mz	Parsed from line Precursor M/Z between: (DIA)
max_precursor_mz	Parsed from line Precursor M/Z between: (DIA)
min_fragment_mz	Parsed from line Fragment M/Z between: (DIA)
max_fragment_mz	Parsed from line Fragment M/Z between: (DIA)
quantification_method	Parsed from line LFQ Method: X
protein_inference	Not parsed
predictors_library	Not parsed
scan_window	Not parsed

ProlineStudio#

Parsed parameter file: .xlsx Example here.

Parameter	Parsed value
software_name	ProlineStudio (fixed)
software_version	If there is a Dataset statistics and infos sheet, it is parsed from version, otherwise not parsed
search_engine	Parsed from software_name on Search settings and infos sheet
search_engine_version	Parsed from software_version on Search settings and infos sheet
ident_fdr_psm	Parsed from psm_filter_expected_fdr on Import and filters sheet
ident_fdr_peptide	Not parsed
ident_fdr_protein	Not parsed
enable_match_between_runs	Set to true if cross assignment is present in the rows of the Quant config sheet, else False
precursor_mass_tolerance	Parsed from peptide_mass_error_tolerance on Search settings and infos sheet
fragment_mass_tolerance	Parsed from fragment_mass_error_tolerance on Search settings and infos sheet
enzyme	Parsed from enzymes on Search settings and infos sheet
allowed_miscleavages	Parsed from max_missed_cleavages on Search settings and infos sheet
min_peptide_length	Parsed from psm_filter_2 on Import and filters sheet
max_peptide_length	Not parsed
fixed_mods	Parsed from fixed_ptms on Search settings and infos sheet
variable_mods	Parsed from variable_ptms on Search settings and infos sheet
max_mods	Not parsed
min_precursor_charge	Parsed as the minimal charge state found in peptide_charge_states on Search settings and infos sheet
max_precursor_charge	Parsed as the maximal charge state found in peptide_charge_states on Search settings and infos sheet
quantification_method	Not parsed
protein_inference	Not parsed
predictors_library	Not parsed
scan_window	Not parsed

QuantMS#

QuantMS requires three files to be uploaded: a json file, a yml file with version information and an optional sdrf file. Example json here. Example yml here. Example sdrf here.

Parameter	Parsed value
software_name	quantms (fixed)
software_version	Parsed as the bigbio or nf-core/quantms version from the yml file
search_engine	Parsed as a list of all the search engines found under the keys in the yml file that start with SEARCHENGINE
search_engine_version	Parsed as a list of the versions of all the search engines under the keys in the yml file that start with SEARCHENGINE
ident_fdr_psm	Parsed from psm_level_fdr_cutoff from the json file
ident_fdr_peptide	Not parsed
ident_fdr_protein	Parsed from protein_level_fdr_cutoff from the json file
enable_match_between_runs	Not parsed
precursor_mass_tolerance	Parsed from precursor_mass_tolerance from the json file
fragment_mass_tolerance	Parsed from fragment_mass_tolerance from the json file
enzyme	Parsed from enzyme from the json file
allowed_miscleavages	Parsed from allowed_missed_cleavages from the json file
min_peptide_length	Parsed from min_peptide_length from the json file
max_peptide_length	Parsed from max_peptide_length from the json file
fixed_mods	Parsed from fixed_mods from the json file
variable_mods	Parsed from variable_mods from the json file
max_mods	Parsed from max_mods from the json file
min_precursor_charge	Parsed from min_precursor_charge from the json file
max_precursor_charge	Parsed from max_precursor_charge from the json file
quantification_method	Parsed from quantification_method from the json file
protein_inference	Parsed from protein_inference_method from the json file
predictors_library	Not parsed
scan_window	Not parsed

Sage#