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FeatureFinderRaw

Identifies peptide features in raw (i.e. profile) LC-MS data.

pot. predecessor tools $ \longrightarrow $ FeatureFinderRaw $ \longrightarrow $ pot. successor tools
FileConverter IDMapper
FileFilter

FeatureFinderRaw is a tool for the identification of peptide features in profile LC-MS data.

Algorithm

The underlying algorithm of the tool is equivalent to that of SILACAnalyzer.

The command line parameters of this tool are:

FeatureFinderRaw -- Determination of peak ratios in LC-MS data
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976

Usage:
  FeatureFinderRaw <options>

This tool has algoritm parameters that are not shown here! Please check the ini file for a detailed descripti
on or use the --helphelp option.

Options (mandatory options marked with '*'):
  -in <file>*        Raw LC-MS data to be analyzed. (Profile data required. Will not work with centroided 
                     data!) (valid formats: 'mzML')
  -out <file>        Set of all identified peptides. The m/z-RT positions correspond to the lightest peptide 
                     in each group. (valid formats: 'featureXML')
                     
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)

The following configuration subsections are valid:
 - algorithm   Parameters for the algorithm.
 - sample      Parameters describing the sample and its labels.

You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
Have a look at the OpenMS documentation for more information.

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+FeatureFinderRawDetermination of peak ratios in LC-MS data
version1.11.1 Version of the tool that generated this parameters file.
++1Instance '1' section for 'FeatureFinderRaw'
in Raw LC-MS data to be analyzed. (Profile data required. Will not work with centroided data!)input file*.mzML
out Set of all identified peptides. The m/z-RT positions correspond to the lightest peptide in each group.output file*.featureXML
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
+++algorithmParameters for the algorithm.
rt_threshold30 Typical retention time [s] over which a characteristic peptide elutes. (This is not an upper bound. Peptides that elute for longer will be reported.)0:∞
rt_min0 Lower bound for the retention time [s].0:∞
intensity_cutoff1000 Lower bound for the intensity of isotopic peaks in a SILAC pattern.0:∞
intensity_correlation0.7 Lower bound for the Pearson correlation coefficient, which measures how well intensity profiles of different isotopic peaks correlate.0:1
model_deviation3 Upper bound on the factor by which the ratios of observed isotopic peaks are allowed to differ from the ratios of the theoretic averagine model, i.e. ( theoretic_ratio / model_deviation ) < observed_ratio < ( theoretic_ratio * model_deviation ).1:∞
+++sampleParameters describing the sample and its labels.
charge2:4 Range of charge states in the sample, i.e. min charge : max charge.
peaks_per_peptide3:5 Range of peaks per peptide in the sample, i.e. min peaks per peptide : max peaks per peptide. For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks.

Parameter Tuning

input:

standard output:

optional output:


OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5