AdditiveSeries

Computes an additive series to quantify a peptide in a set of samples.

pot. predecessor tools	$\longrightarrow$ AdditiveSeries $\longrightarrow$	pot. successor tools
FeatureFinderCentroided		-
IDMapper

This module computes an additive series for an absolute quantification of a peptide in a set of samples. The output consists of a GNUplot script which can be used to visualize the results and some XML output for further processing.

In this version, the application computes the additive series as a ratio of the intensities of two different peptides. One of these peptides serves as internal standard for calibration.

The command line parameters of this tool are:

AdditiveSeries -- Computes an additive series to quantify a peptide in a set of samples.
Version: 2.3.0 Jan  9 2018, 17:46:23, Revision: 38ae115

Usage:
  AdditiveSeries <options>

Options (mandatory options marked with '*'):
  -in <files>*                       Input files separated by blanks (valid formats: 'featureXML')
  -out <file>*                       Output XML file containg regression line and confidence interval (valid 
                                     formats: 'XML')
  -mz_tolerance <tol>                Tolerance in m/z dimension (default: '1')
  -rt_tolerance <tol>                Tolerance in RT dimension (default: '1')
  -concentrations <concentrations>*  List of spiked concentrations
                                     
  -feature_rt <rt>                   RT position of the feature (default: '-1')
  -feature_mz <mz>                   M/z position of the feature (default: '-1')
  -standard_rt <rt>                  RT position of the standard (default: '-1')
  -standard_mz <mz>                  M/z position of the standard (default: '-1')
                                     

GNUplot options:
  -plot:write_gnuplot_output         Flag that activates the GNUplot output
  -plot:out_gp <name>                Base file name (3 files with different extensions are created)

                                     
Common TOPP options:
  -ini <file>                        Use the given TOPP INI file
  -threads <n>                       Sets the number of threads allowed to be used by the TOPP tool (default:
                                     '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

+AdditiveSeriesComputes an additive series to quantify a peptide in a set of samples.

version2.3.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'AdditiveSeries'

in[] input files separated by blanksinput file*.featureXML

out output XML file containg regression line and confidence intervaloutput file*.XML

mz_tolerance1 Tolerance in m/z dimension

rt_tolerance1 Tolerance in RT dimension

concentrations[] List of spiked concentrations

feature_rt-1 RT position of the feature

feature_mz-1 m/z position of the feature

standard_rt-1 RT position of the standard

standard_mz-1 m/z position of the standard

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

+++plotGNUplot options

write_gnuplot_outputfalse Flag that activates the GNUplot outputtrue,false

out_gp base file name (3 files with different extensions are created)