Performs an external calibration for tof spectra.

pot. predecessor tools	$\longrightarrow$ TOFCalibration $\longrightarrow$	pot. successor tools
-		InternalCalibration
		PeakPickerWavelet

Given one or more calibrant spectra containing flight times, the instrument's calibration constants and the expected masses the quadratic function $y_i = a + bx_i + cx_i^2$ is fitted, where $x_i$ is the ith flight time. If there are more than one calibrant spectra the coefficients $a$ , $b$ and $c$ are averaged. The fitted function is then used to convert the flight times of the given experiment to m/z-values.

You can choose to calibrate picked or raw data. If you use picked data, set the flag peak_data. If you have raw data an additional peak picking step for the calibrant spectra is needed, the parameters for the peak picker can be set in the ini-file.

The command line parameters of this tool are:

TOFCalibration -- Applies time of flight calibration.
Version: 2.4.0 Oct 29 2018, 15:52:19, Revision: 9690d06
To cite OpenMS:
  Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

Usage:
  TOFCalibration <options>

This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript
ion or use the --helphelp option.

Options (mandatory options marked with '*'):
  -in <file>*              Input peak or raw data file  (valid formats: 'mzML')
  -out <file>*             Output file  (valid formats: 'mzML')
                           
  -ext_calibrants <file>*  Input file containing the external calibrant spectra (peak or raw data)
                           (valid formats: 'mzML')
  -ref_masses <file>*      Input file containing reference masses of the external calibrant spectra (one per 
                           line) (valid formats: 'txt')
  -tof_const <file>*       File containing TOF conversion constants. These can be either two or three constan
                           ts
                           per set, depending on the conversion type. Either one set for all calibrant spect
                           ra
                           (tab separated), or one for each spectrum.
                           For a detailed description, please have a look at the doxygen documentation.(one
                           set, tab separated, per line) (valid formats: 'csv')
  -peak_data               Set this flag, if you have peak data, not raw data (the picking parameters are 
                           accessible only from the INI file).
                           
Common TOPP options:
  -ini <file>              Use the given TOPP INI file
  -threads <n>             Sets the number of threads allowed to be used by the TOPP tool (default: '1')
  -write_ini <file>        Writes the default configuration file
  --help                   Shows options
  --helphelp               Shows all options (including advanced)

The following configuration subsections are valid:
 - algorithm   Algorithm section for peak picking

You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
Have a look at the OpenMS documentation for more information.

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+TOFCalibrationApplies time of flight calibration.

version2.4.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'TOFCalibration'

in input peak or raw data file input file*.mzML

out output file output file*.mzML

ext_calibrants input file containing the external calibrant spectra (peak or raw data)
input file*.mzML

ref_masses input file containing reference masses of the external calibrant spectra (one per line)input file*.txt

tof_const File containing TOF conversion constants. These can be either two or three constants
per set, depending on the conversion type. Either one set for all calibrant spectra
(tab separated), or one for each spectrum.
For a detailed description, please have a look at the doxygen documentation.(one set, tab separated, per line)input file*.csv

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

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue,false

forcefalse Overwrite tool specific checks.true,false

testfalse Enables the test mode (needed for internal use only)true,false

+++algorithmAlgorithm section for peak picking

++++PeakPicker

signal_to_noise1 Minimal signal to noise ratio for a peak to be picked.0:∞

centroid_percentage0.8 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.0:1

peak_width0.15 Approximate fwhm of the peaks.0:∞

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

fwhm_lower_bound_factor0.7 Factor that calculates the minimal fwhm value from the peak_width. All peaks with width smaller than fwhm_bound_factor * peak_width are discarded.0:∞

fwhm_upper_bound_factor20 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.0:∞

optimizationno If the peak parameters position, intensity and left/right widthshall be optimized set optimization to one_dimensional or two_dimensional.no,one_dimensional,two_dimensional

+++++thresholds

peak_bound10 Minimal peak intensity.0:∞

peak_bound_ms2_level10 Minimal peak intensity for MS/MS peaks.0:∞

correlation0.5 minimal correlation of a peak and the raw signal. If a peak has a lower correlation it is skipped.0:1

noise_level0.1 noise level for the search of the peak endpoints.0:∞

search_radius3 search radius for the search of the maximum in the signal after a maximum in the cwt was found0:∞

+++++wavelet_transform

spacing0.001 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.0:∞

+++++optimization

iterations400 maximal number of iterations for the fitting step1:∞

++++++penalties

position0 penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized 0:∞

left_width1 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.0:∞

right_width1 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.0:∞

height1 penalty term for the fitting of the intensity (only used in 2D Optimization):If it gets negative during the fitting it can be penalized.0:∞

++++++2d

tolerance_mz2.2 mz tolerance for cluster construction0:∞

max_peak_distance1.2 maximal peak distance in mz in a cluster0:∞

+++++deconvolution

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

asym_threshold0.3 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.0:∞

left_width2 1/left_width is the initial value for the left width of the peaks found in the deconvolution step.0:∞

right_width2 1/right_width is the initial value for the right width of the peaks found in the deconvolution step.0:∞

scaling0.12 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.0:∞

++++++fitting

fwhm_threshold0.7 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.0:∞

eps_abs9.99999974737875e-06 if the absolute error gets smaller than this value the fitting is stopped.0:∞

eps_rel9.99999974737875e-06 if the relative error gets smaller than this value the fitting is stopped.0:∞

max_iteration10 maximal number of iterations for the fitting step1:∞

+++++++penalties

position0 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.0:∞

height1 penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized.0:∞

left_width0 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.0:∞

right_width0 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.0:∞

+++++SignalToNoiseEstimationParameter

max_intensity-1 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).-1:∞

auto_max_stdev_factor3 parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev0:999

auto_max_percentile95 parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile0:100

auto_mode0 method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method-1:1

win_len200 window length in Thomson1:∞

bin_count30 number of bins for intensity values3:∞

stdev_mp3 multiplier for stdev0.01:999

min_required_elements10 minimum number of elements required in a window (otherwise it is considered sparse)1:∞

noise_for_empty_window1e+20 noise value used for sparse windows