TOFCalibration

Options

version

Version of the tool that generated this parameters file.

peak_data

set this flag, if you have peak data, not raw data (the picking parameters are accessible only from the INI 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)

signal_to_noise

Minimal signal to noise ratio for a peak to be picked.

centroid_percentage

Percentage of the maximum height that the raw data points must exceed to be taken into account for the calculation of the centroid. If it is 1 the centroid position corresponds to the position of the highest intensity.

peak_width

Approximate fwhm of the peaks.

estimate_peak_width

Flag if the average peak width shall be estimated. Attention: when this flag is set, the peak_width is ignored.

fwhm_lower_bound_factor

Factor that calculates the minimal fwhm value from the peak_width. All peaks with width smaller than fwhm_bound_factor * peak_width are discarded.

fwhm_upper_bound_factor

Factor that calculates the maximal fwhm value from the peak_width. All peaks with width greater than fwhm_upper_bound_factor * peak_width are discarded.

optimization

If the peak parameters position, intensity and left/right widthshall be optimized set optimization to one_dimensional or two_dimensional.

peak_bound

Minimal peak intensity.

peak_bound_ms2_level

Minimal peak intensity for MS/MS peaks.

correlation

minimal correlation of a peak and the raw signal. If a peak has a lower correlation it is skipped.

noise_level

noise level for the search of the peak endpoints.

search_radius

search radius for the search of the maximum in the signal after a maximum in the cwt was found

spacing

Spacing of the CWT. Note that the accuracy of the picked peak's centroid position depends in the Raw data spacing, i.e., 50% of raw peak distance at most.

iterations

maximal number of iterations for the fitting step

position

penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized

left_width

penalty term for the fitting of the left width:If the left width differs too much from the initial one during the fitting it can be penalized.

right_width

penalty term for the fitting of the right width:If the right width differs too much from the initial one during the fitting it can be penalized.

height

penalty term for the fitting of the intensity (only used in 2D Optimization):If it gets negative during the fitting it can be penalized.

tolerance_mz

mz tolerance for cluster construction

max_peak_distance

maximal peak distance in mz in a cluster

deconvolution

If you want heavily overlapping peaks to be separated set this value to "true"

asym_threshold

If the symmetry of a peak is smaller than asym_thresholds it is assumed that it consists of more than one peak and the deconvolution procedure is started.

left_width

1/left_width is the initial value for the left width of the peaks found in the deconvolution step.

right_width

1/right_width is the initial value for the right width of the peaks found in the deconvolution step.

scaling

Initial scaling of the cwt used in the separation of heavily overlapping peaks. The initial value is used for charge 1, for higher charges it is adapted to scaling/charge.

fwhm_threshold

If the FWHM of a peak is higher than 'fwhm_thresholds' it is assumed that it consists of more than one peak and the deconvolution procedure is started.

eps_abs

if the absolute error gets smaller than this value the fitting is stopped.

eps_rel

if the relative error gets smaller than this value the fitting is stopped.

max_iteration

maximal number of iterations for the fitting step

position

penalty term for the fitting of the peak position:If the position changes more than 0.5Da during the fitting it can be penalized as well as discrepancies of the peptide mass rule.

height

penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized.

left_width

penalty term for the fitting of the left width:If the left width gets too broad or negative during the fitting it can be penalized.

right_width

penalty term for the fitting of the right width:If the right width gets too broad or negative during the fitting it can be penalized.

max_intensity

maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will not be added to the histogram. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime).

auto_max_stdev_factor

parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev

auto_max_percentile

parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile

auto_mode

method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method

win_len

window length in Thomson

bin_count

number of bins for intensity values

stdev_mp

multiplier for stdev

min_required_elements

minimum number of elements required in a window (otherwise it is considered sparse)

noise_for_empty_window

noise value used for sparse windows

Views

TOFCalibration Std Output

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

TOFCalibration Error Output

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