Allows to add up several spectra.

pot. predecessor tools	→ SpectraMerger →	pot. successor tools
any tool operating on MS peak data (in mzML format)	→ SpectraMerger →	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/doxygen/release/3.0.0/html/TOPP_SpectraMerger.html
Version: 3.0.0 Jul 14 2023, 11:57:33, Revision: be787e9
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: 
                            'average_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/doxygen/release/3.0.0/html/TOPP_SpectraMerger.html

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+SpectraMergerMerges spectra (each MS level separately), increasing S/N ratios.

version3.0.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'SpectraMerger'

in Input mzML file.input file*.mzML

out Output mzML file with merged spectra.output file*.mzML

merging_methodaverage_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)

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 Overrides tool-specific checkstrue, false

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

+++algorithmAlgorithm section for merging spectra

mz_binning_width5.0 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_unitppm Unit in which the distance between two data points or peaks is given.Da, ppm

sort_blocksRT_ascending Sort blocks by before merging them (useful for precursor order)RT_ascending, RT_descending

++++average_gaussian

spectrum_typeautomatic Spectrum type of the MS level to be averagedprofile, centroid, automatic

ms_level1 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.0:∞

rt_FWHM5.0 FWHM of Gauss curve in seconds to be averaged over.0.0:1.0e11

cutoff0.01 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

precursor_mass_tol0.0 PPM mass tolerance for precursor mass. If set, MSn (n>2) spectra of precursor masses within the tolerance are averaged.0.0:∞

precursor_max_charge1 Possible maximum precursor ion charge. Effective only when average_gaussian:precursor_mass_tol option is active.1:∞

++++average_tophat

spectrum_typeautomatic Spectrum type of the MS level to be averagedprofile, centroid, automatic

ms_level1 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.0:∞

rt_range5.0 RT range to be averaged over, i.e. +/-(RT range)/2 from each spectrum.0.0:1.0e11

rt_unitscans 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_size5 Maximum number of scans to be summed up.1:∞

rt_max_length0.0 Maximum RT size of the block in seconds (0.0 = no size restriction).0.0:1.0e11

++++precursor_method

mz_tolerance1.0e-04 Max m/z distance of the precursor entries of two spectra to be merged in [Da].0.0:∞

mass_tolerance0.0 Max mass distance of the precursor entries of two spectra to be merged in [Da]. Active when set to a positive value.0.0:∞

rt_tolerance5.0 Max RT distance of the precursor entries of two spectra to be merged in [s].0.0:∞