Legend:

required parameter

advanced parameter

+IDMassAccuracyCalculates a distribution of the mass error from given mass spectra and IDs.

version1.10.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'IDMassAccuracy'

in[] Input mzML file list, containing the spectra.input file*.mzML

id_in[] Input idXML file list, containing the identifications.input file*.idXML

precursor_out Output file which contains the deviations from the precursorsoutput file*.csv

precursor_columns[MassDifference] Columns which will be written to the output fileMassDifference

precursor_error_ppmfalse If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da.true,false

fragment_out Output file which contains the fragment ion m/z deviationsoutput file*.csv

fragment_columns[MassDifference] Columns which will be written to the output fileMassDifference

fragment_error_ppmfalse If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da.true,false

fragment_mass_tolerance0.5 Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions.

separator character which should be used to separate the columns in the output files

number_of_bins100 Number of bins that should be used to calculate the histograms for the fitting.10:∞

generate_gnuplot_scriptsfalse If this option is set to true, the distributions and the fits are used to generate a gnuplot script, that can be used to generate plots. The options 'precursor_out' and 'fragment_out' must be set to take this effect.true,false

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue,false

testfalse Enables the test mode (needed for internal use only)true,false