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FeatureFinderSuperHirn

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]

Popular Predecessors

Popular Successors

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.)

Workflows

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Developers

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Installation

To use this node in KNIME, install the extension OpenMS from the below update site following our NodePit Product and Node Installation Guide:

v3.7

A zipped version of the software site can be downloaded here.

Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Plugin version: 2.4.0.201810261316

On NodePit since: 2018-08-10

Last update: 2024-04-15

KNIME versions: From v3.6 to v4.4

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