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

Overrides 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 separate 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 .

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.)

Workflows

• 00-test_workflowKNIME Hub
• 01-MaCProQCKNIME Hub
• 02-PIA_and_quantKNIME Hub
• Determine_peak_lengthsKNIME Hub
• Labelfree with Protein QuantificationKNIME Hub
• Show all 15 workflows

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