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SpectraMerger

Allows to add up several spectra.

pot. predecessor tools $ \longrightarrow $ SpectraMerger $ \longrightarrow $ 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.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976

Usage:
  SpectraMerger <options>

This tool has algoritm parameters that are not shown here! Please check the ini file for a detailed descripti
on 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: 'block_method' valid: 'precurso
                            r_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.
Have a look at the OpenMS documentation for more information.

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+SpectraMergerMerges spectra (each MS level separately), increasing S/N ratios.
version1.11.1 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_methodblock_method Method of merging which should be used.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
testfalse Enables the test mode (needed for internal use only)true,false
+++algorithmAlgorithm section for merging spectra
mz_binning_width0.0001 Max m/z distance of two peaks to be merged.0:∞
mz_binning_width_unitDa Unit in which the distance between two peaks is given.Da,ppm
sort_blocksRT_ascending Sort blocks by before merging them (useful for precursor order)RT_ascending, RT_descending
++++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 Maximum RT size of the block in seconds (0.0 = no size restriction).0:100000000000
++++precursor_method
mz_tolerance0.0001 Max m/z distance of the precursor entries of two spectra to be merged in [Da].0:∞
rt_tolerance5 Max RT distance of the precursor entries of two spectra to be merged in [s].0:∞

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5