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required parameter
advanced parameter
+FeatureFinderSuperHirnFinds mass spectrometric features in mass spectra.
version1.10.0
Version of the tool that generated this parameters file.
++1Instance '1' section for 'FeatureFinderSuperHirn'
in
input profile data file input file*.mzML
out
output peak file 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
+++algorithmAlgorithm parameters section
++++centroiding
activefalse
MS1 data centroid datatrue,false
window_width5
Centroid window width1:∞
absolute_isotope_mass_precision0.01
Absolute isotope mass precision (Da)0:∞
relative_isotope_mass_precision10
Relative isotope mass precision0:∞
minimal_peak_height0
Minimal peak height0:∞
min_ms_signal_intensity50
Minimal Centroid MS Signal Intensity0:∞
++++ms1
precursor_detection_scan_levels[1]
Precursor detection scan levels
max_inter_scan_distance0
MS1 max inter scan distance0:∞
tr_resolution0.01
MS1 LC retention time resolution0:∞
intensity_threshold1000
FT peak detect MS1 intensity min threshold0:∞
max_inter_scan_rt_distance0.1
MS1 max inter scan distance0:∞
min_nb_cluster_members4
FT peak detect MS1 min nb peak members0:∞
detectable_isotope_factor0.05
Detectable isotope factor0:∞
intensity_cv0.9
IntensityCV0:∞
retention_time_tolerance0.5
MS1 retention time tolerance (minutes)0:∞
mz_tolerance0
MS1 m/z tolerance (ppm)0:∞
++++ms1_feature_merger
activetrue
Activation of MS1 feature merging post processingtrue,false
tr_resolution0.01
MS1 LC retention time resolution0:∞
initial_apex_tr_tolerance5
Initial Apex Tr tolerance0:∞
feature_merging_tr_tolerance1
MS1 feature Tr merging tolerance0:∞
intensity_variation_percentage25
Percentage of intensity variation between LC border peaks0:100
ppm_tolerance_for_mz_clustering10
PPM value for the m/z clustering of merging candidates0:∞
++++ms1_feature_selection_options
start_elution_window0
start elution window (minutes)0:∞
end_elution_window180
end elution window (minutes)0:∞
mz_range_min0
MS1 feature mz range min0:∞
mz_range_max2000
MS1 feature mz range max0:∞
chrg_range_min1
MS1 feature CHRG range min0:∞
chrg_range_max5
MS1 feature CHRG range max0:∞