0 ×

FeatureFinderSuperHirn

Generic Workflow Nodes for KNIME: OpenMS version 2.5.0.202002201806 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Finds mass spectrometric features in mass spectra.

Web Documentation for FeatureFinderSuperHirn

Options

version
Version of the tool that generated this parameters file.
log
Name of log file (created only when specified)
debug
Sets the debug level
threads
Sets the number of threads allowed to be used by the TOPP tool
no_progress
Disables progress logging to command line
force
Overwrite tool specific checks.
test
Enables the test mode (needed for internal use only)
active
MS1 data centroid data
window_width
Centroid window width
absolute_isotope_mass_precision
Absolute isotope mass precision (Da)
relative_isotope_mass_precision
Relative isotope mass precision
minimal_peak_height
Minimal peak height
min_ms_signal_intensity
Minimal Centroid MS Signal Intensity
precursor_detection_scan_levels
Precursor detection scan levels
max_inter_scan_distance
MS1 max inter scan distance
tr_resolution
MS1 LC retention time resolution
intensity_threshold
FT peak detect MS1 intensity min threshold
max_inter_scan_rt_distance
MS1 max inter scan distance
min_nb_cluster_members
FT peak detect MS1 min nb peak members
detectable_isotope_factor
Detectable isotope factor
intensity_cv
IntensityCV
retention_time_tolerance
MS1 retention time tolerance (minutes)
mz_tolerance
MS1 m/z tolerance (ppm)
active
Activation of MS1 feature merging post processing
tr_resolution
MS1 LC retention time resolution
initial_apex_tr_tolerance
Initial Apex Tr tolerance
feature_merging_tr_tolerance
MS1 feature Tr merging tolerance
intensity_variation_percentage
Percentage of intensity variation between LC border peaks
ppm_tolerance_for_mz_clustering
PPM value for the m/z clustering of merging candidates
start_elution_window
start elution window (minutes)
end_elution_window
end elution window (minutes)
mz_range_min
MS1 feature mz range min
mz_range_max
MS1 feature mz range max
chrg_range_min
MS1 feature CHRG range min
chrg_range_max
MS1 feature CHRG range max

Input Ports

input profile data file [mzML]

Output Ports

output peak file [featureXML]

Views

FeatureFinderSuperHirn Std Output
The text sent to standard out during the execution of FeatureFinderSuperHirn.
FeatureFinderSuperHirn Error Output
The text sent to standard error during the execution of FeatureFinderSuperHirn. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install OpenMS from the following update site:

KNIME 4.1
Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform.

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.