Legend:
required parameter
advanced parameter
+FeatureFinderRawDetermination of peak ratios in LC-MS data
version1.10.0
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.