SpectraMerger

Options

version

Version of the tool that generated this parameters file.

merging_method

Method of merging which should be used.

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)

mz_binning_width

minimum m/z distance for two data points (profile data) or peaks (centroided data) to be considered distinct. Closer data points or peaks will be merged.

mz_binning_width_unit

Unit in which the distance between two data points or peaks is given.

sort_blocks

Sort blocks by <?> before merging them (useful for precursor order)

spectrum_type

Spectrum type of the MS level to be averaged

ms_level

If set to be 0, each MS level will be merged from 1 to max. Otherwise, average spectra of this level. All other spectra remain unchanged.

rt_FWHM

FWHM of Gauss curve in seconds to be averaged over.

cutoff

Intensity cutoff for Gaussian. The Gaussian RT profile decreases from 1 at its apex to 0 at infinity. Spectra for which the intensity of the Gaussian drops below the cutoff do not contribute to the average.

precursor_mass_tol

PPM mass tolerance for precursor mass. If set, MSn (n>2) spectra of precursor masses within the tolerance are averaged.

precursor_max_charge

Possible maximum precursor ion charge. Effective only when average_gaussian:precursor_mass_tol option is active.

spectrum_type

Spectrum type of the MS level to be averaged

ms_level

If set to be 0, each MS level will be merged from 1 to max. Otherwise, average spectra of this level. All other spectra remain unchanged.

rt_range

RT range to be averaged over, i.e. +/-(RT range)/2 from each spectrum.

rt_unit

Unit for RT range.

ms_levels

Merge spectra of this level. All spectra with other MS levels remain untouched.

rt_block_size

Maximum number of scans to be summed up.

rt_max_length

Maximum RT size of the block in seconds (0.0 = no size restriction).

mz_tolerance

Max m/z distance of the precursor entries of two spectra to be merged in [Da].

mass_tolerance

Max mass distance of the precursor entries of two spectra to be merged in [Da]. Active when set to a positive value.

rt_tolerance

Max RT distance of the precursor entries of two spectra to be merged in [s].

Views

SpectraMerger Std Output

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

SpectraMerger Error Output

The text sent to standard error during the execution of SpectraMerger. (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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