FeatureFinderLFQ

Options

version

Version of the tool that generated this parameters file.

write_hills

Force writing of hills file even if no output path was provided

mini

Minimum intensity threshold

minmz

Minimum m/z value

maxmz

Maximum m/z value

htol

Mass accuracy in ppm for combining peaks into hills

itol

Mass accuracy in ppm for isotopic patterns

hvf

Hill valley factor for splitting hills

ivf

Isotope valley factor for splitting isotope patterns

minlh

Minimum number of scans for a hill

pasefmini

Minimum combined intensity for PASEF/TIMS clusters after m/zion-mobility centroiding.

pasefminlh

Minimum number of raw points per PASEF/TIMS cluster during centroiding.

cmin

Minimum charge state

cmax

Maximum charge state

iuse

Number of isotopes for intensity calculation (0=mono only, -1=all, 1=mono+first, etc.)

nm

Negative mode (affects neutral mass calculation)

tof

Enable TOF-specific intensity filtering

profile

Enable profile mode processing (centroid spectra using PeakPickerHiRes)

paseftol

Ion mobility accuracy (in the same units as the ion-mobility array) for linking peaks into hills and grouping isotopes (0 = disable IM-based gating).

use_hill_calib

Enable automatic hill mass tolerance calibration

ignore_iso_calib

Disable automatic isotope mass error calibration

hrttol

Maximum allowed RT difference (in seconds) between monoisotopic hill apex and isotope hill apex when assembling isotope patterns (0 disables RT gating).

convex_hulls

Representation of feature convex hulls in the output FeatureMap. 'bounding_box' stores a single RTm/z bounding box per feature (smaller featureXML, no per-trace detail), whereas 'mass_traces' stores one convex hull per contributing hill using all mass-trace points (larger featureXML, preserves detailed trace shape).

faims_merge_features

For FAIMS data with multiple compensation voltages: Merge features representing the same analyte detected at different CV values into a single feature. Only features with DIFFERENT FAIMS CV values are merged (same CV = different analytes). Has no effect on non-FAIMS data.

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)

Views

FeatureFinderLFQ Std Output

The text sent to standard out during the execution of FeatureFinderLFQ.

FeatureFinderLFQ Error Output

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

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