IDMassAccuracy

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

Note

Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

IDMassAccuracy -- Calculates a distribution of the mass error from given mass spectra and IDs.
Version: 2.3.0 Jan  9 2018, 17:46:23, Revision: 38ae115

Usage:
  IDMassAccuracy <options>

Options (mandatory options marked with '*'):
  -in <file list>*                      Input mzML file list, containing the spectra. (valid formats: 'mzML')
  -id_in <file list>*                   Input idXML file list, containing the identifications. (valid formats
                                        : 'idXML')
  -precursor_out <file>                 Output file which contains the deviations from the precursors (valid 
                                        formats: 'csv')
  -precursor_columns <columns>          Columns which will be written to the output file (default: '[MassDiff
                                        erence]' valid: 'MassDifference')
  -precursor_error_ppm                  If this flag is used, the precursor mass tolerances are estimated in 
                                        ppm instead of Da.
  -fragment_out <file>                  Output file which contains the fragment ion m/z deviations (valid 
                                        formats: 'csv')
  -fragment_columns <columns>           Columns which will be written to the output file (default: '[MassDiff
                                        erence]' valid: 'MassDifference')
  -fragment_error_ppm                   If this flag is used, the fragment mass tolerances are estimated in 
                                        ppm instead of Da.
  -fragment_mass_tolerance <tolerance>  Maximal fragment mass tolerance which is allowed for MS/MS spectra, 
                                        used for the calculation of matching ions. (default: '0.5')
  -separator <character>                Character which should be used to separate the columns in the output 
                                        files (default: ' ')
                                        
Common UTIL options:
  -ini <file>                           Use the given TOPP INI file
  -threads <n>                          Sets the number of threads allowed to be used by the TOPP tool (defau
                                        lt: '1')
  -write_ini <file>                     Writes the default configuration file
  --help                                Shows options
  --helphelp                            Shows all options (including advanced)

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

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

version2.3.0 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

forcefalse Overwrite tool specific checks.true,false

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

Given a number of peak maps and for each of the maps an idXML file which contains peptide identifications the theoretical masses of the identifications and the peaks of the spectra are compared. This can be done for precursor information stored in the spectra as well as for fragment information.

The result is a distribution of errors of experimental vs. theoretical masses. Having such distributions given the search parameters of the sequence database search can be adjusted to speed-up the identification process and to get a higher performance.