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FeatureFinderCentroided

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

Detects two-dimensional features in LC-MS data.

Web Documentation for FeatureFinderCentroided

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)
debug
When debug mode is activated, several files with intermediate results are written to the folder 'debug' (do not use in parallel mode).
bins
Number of bins per dimension (RT and m/z). The higher this value, the more local the intensity significance score is. This parameter should be decreased, if the algorithm is used on small regions of a map.
mz_tolerance
Tolerated m/z deviation of peaks belonging to the same mass trace. It should be larger than the m/z resolution of the instrument. This value must be smaller than that 1/charge_high!
min_spectra
Number of spectra that have to show a similar peak mass in a mass trace.
max_missing
Number of consecutive spectra where a high mass deviation or missing peak is acceptable. This parameter should be well below 'min_spectra'!
slope_bound
The maximum slope of mass trace intensities when extending from the highest peak. This parameter is important to seperate overlapping elution peaks. It should be increased if feature elution profiles fluctuate a lot.
charge_low
Lowest charge to search for.
charge_high
Highest charge to search for.
mz_tolerance
Tolerated m/z deviation from the theoretical isotopic pattern. It should be larger than the m/z resolution of the instrument. This value must be smaller than that 1/charge_high!
intensity_percentage
Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present.
intensity_percentage_optional
Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing.
optional_fit_improvement
Minimal percental improvement of isotope fit to allow leaving out an optional peak.
mass_window_width
Window width in Dalton for precalculation of estimated isotope distributions.
abundance_12C
Rel. abundance of the light carbon. Modify if labeled.
abundance_14N
Rel. abundance of the light nitrogen. Modify if labeled.
min_score
Minimum seed score a peak has to reach to be used as seed. The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score. If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score.
max_iterations
Maximum number of iterations of the fit.
min_score
Feature score threshold for a feature to be reported. The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks.
min_isotope_fit
Minimum isotope fit of the feature before model fitting.
min_trace_score
Trace score threshold. Traces below this threshold are removed after the model fitting. This parameter is important for features that overlap in m/z dimension.
min_rt_span
Minimum RT span in relation to extended area that has to remain after model fitting.
max_rt_span
Maximum RT span in relation to extended area that the model is allowed to have.
rt_shape
Choose model used for RT profile fitting. If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used.
max_intersection
Maximum allowed intersection of features.
reported_mz
The mass type that is reported for features. 'maximum' returns the m/z value of the highest mass trace. 'average' returns the intensity-weighted average m/z value of all contained peaks. 'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model.
rt_tolerance
Allowed RT deviation of seeds from the user-specified seed position.
mz_tolerance
Allowed m/z deviation of seeds from the user-specified seed position.
min_score
Overwrites 'seed:min_score' for user-specified seeds. The cutoff is typically a bit lower in this case.
pseudo_rt_shift
Pseudo RT shift used when .

Input Ports

input file [mzML]
User specified seed list [featureXML,opt.]

Output Ports

output file [featureXML]
Optional output file of MzQuantML. [mzq]

Views

FeatureFinderCentroided Std Output
The text sent to standard out during the execution of FeatureFinderCentroided.
FeatureFinderCentroided Error Output
The text sent to standard error during the execution of FeatureFinderCentroided. (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)

Workflows

Installation

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

KNIME 4.1
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