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 ).