Identifies peptide features in raw (i.e. profile) LC-MS data.
 
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:
- in [*.mzML] - LC-MS dataset to be analyzed
- ini [*.ini] - file containing all parameters (see discussion below)
standard output:
- out [*.consensusXML] - contains the list of identified peptides
optional output:
- out_clusters [*.consensusXML] - contains the complete set of data points passing the filters - The results of an analysis can be easily visualized within TOPPView. Simply load *.consensusXML and *.featureXML as layers over the original *.mzML. - Parameters in section algorithm: 
- allow_missing_peaks - Low intensity peaks might be missing from the isotopic pattern of some of the peptides. Specify if such peptides should be included in the analysis.
- rt_threshold - Upper bound for the retention time [s] over which a characteristic peptide elutes.
- rt_min - Lower bound for the retentions time [s].
- intensity_cutoff - Lower bound for the intensity of isotopic peaks in a SILAC pattern.
- intensity_correlation - Lower bound for the Pearson correlation coefficient, which measures how well intensity profiles of different isotopic peaks correlate.
- model_deviation - 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 ).