| OpenMS 2.5.0

SpectraMerger

Allows to add up several spectra.

pot. predecessor tools | SpectraMerger | pot. successor tools
any tool operating on MS peak data (in mzML format) | any tool operating on MS peak data (in mzML format)

Experimental classes:
  This TOPP-tool is not well tested and not all features might be properly implemented and tested!

This tool can add several consecutive scans, increasing S/N ratio (for MS1 and above) or merge scans which stem from similar precursors (for MS2 and above).

In any case, the number of scans will be reduced.

The command line parameters of this tool are:

    SpectraMerger -- Merges spectra (each MS level separately), increasing S/N ratios.

    Full documentation: http://www.openms.de/documentation/TOPP_SpectraMerger.html

    Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

    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:

      SpectraMerger <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 mzML file. (valid formats: 'mzML')

      -out <file>*              Output mzML file with merged spectra. (valid formats: 'mzML')

      -merging_method <method>  Method of merging which should be used. (default: 'average_gaussian' valid: 'aver

                                age_gaussian', 'average_tophat', 'precursor_method', 'block_method')

    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 merging spectra

    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.

    For more information, please consult the online documentation for this tool:

      - http://www.openms.de/documentation/TOPP_SpectraMerger.html

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+SpectraMerger Merges spectra (each MS level separately), increasing S/N ratios.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'SpectraMerger'
in Input mzML file.input file*.mzML
out Output mzML file with merged spectra.output file*.mzML
merging_method average_gaussian Method of merging which should be used.average_gaussian,average_tophat,precursor_method,block_method
log Name of log file (created only when specified)
debug 0 Sets the debug level
threads 1 Sets the number of threads allowed to be used by the TOPP tool
no_progress false Disables progress logging to command line true,false
force false Overwrite tool specific checks.true,false
test false Enables the test mode (needed for internal use only)true,false
+++algorithm Algorithm section for merging spectra
mz_binning_width 5.0 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.0.0:∞
mz_binning_width_unit ppm Unit in which the distance between two data points or peaks is given.Da,ppm
sort_blocks RT_ascending Sort blocks by before merging them (useful for precursor order)RT_ascending, RT_descending
++++average_gaussian
spectrum_type automatic Spectrum type of the MS level to be averaged profile,centroid,automatic
ms_level 1 Average spectra of this level. All other spectra remain unchanged.1:∞
rt_FWHM 5.0 FWHM of Gauss curve in seconds to be averaged over.0.0:1.0e11
cutoff 0.01 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.0.0:1.0
++++average_tophat
spectrum_type automatic Spectrum type of the MS level to be averaged profile,centroid,automatic
ms_level 1 Average spectra of this level. All other spectra remain unchanged.1:∞
rt_range 5.0 RT range to be averaged over, i.e. +/-(RT range)/2 from each spectrum.0.0:1.0e11
rt_unit scans Unit for RT range.scans,seconds
++++block_method
ms_levels[1] Merge spectra of this level. All spectra with other MS levels remain untouched.1:∞
rt_block_size 5 Maximum number of scans to be summed up.1:∞
rt_max_length 0.0 Maximum RT size of the block in seconds (0.0 = no size restriction).0.0:1.0e11
++++precursor_method
mz_tolerance 1.0e-04 Max m/z distance of the precursor entries of two spectra to be merged in [Da].0.0:∞
rt_tolerance 5.0 Max RT distance of the precursor entries of two spectra to be merged in [s].0.0:∞