ERPairFinder

Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.

This tool allows to calculate ratios of labeled peptides based on single enhanced resolution scans (also called zoom scans). Zoom scans is a mode of some mass spectrometry instruments to allow scanning at a higher resolution, at the cost of low scan speed. It can be used to determine charge states of precursors on ion-trap or related instruments.

This tool works scan based. Each scan is examined using the IsotopeWavelet (see docs of that class) to fit an isotope distribution based on the averagine model. Known pairs are given by the pair_in input parameter, which allows to search for specific pairs. Light and heavy variant are search for, and the pairs are finally reported with their ratios.

If a pair is available in several scans, the intensities are summed up and the ratio is calculated from the sum of the isotope fits.

Experimental classes:

This software is experimental and might contain bugs!

The command line parameters of this tool are:

ERPairFinder -- Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.
Full documentation: http://www.openms.de/doxygen/release/3.1.0/html/TOPP_ERPairFinder.html
Version: 3.1.0 Oct 18 2023, 10:27:18, Revision: 17a07f8
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:
  ERPairFinder <options>

Options (mandatory options marked with '*'):
  -in <file>*                            Input mzML file containing the ER spectra. (valid formats: 'mzML')
  -pair_in <file>*                       Pair-file in the format: m/z-light m/z-heavy charge rt (valid format
                                         s: 'txt')
  -out <file>*                           Output consensusXML file were the pairs of the feature are written 
                                         into. (valid formats: 'consensusXML')
  -feature_out <file>                    Output featureXML file, only written if given, skipped otherwise. 
                                         (valid formats: 'featureXML')
  -precursor_mass_tolerance <tolerance>  Precursor mass tolerance which is used for the pair finding and the 
                                         matching of the given pair m/z values to the features. (default: 
                                         '0.3') (min: '0.0')
                                         
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 (defa
                                         ult: '1')
  -write_ini <file>                      Writes the default configuration file
  --help                                 Shows options
  --helphelp                             Shows all options (including advanced)

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+ERPairFinderUtil which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.

version3.1.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'ERPairFinder'

in Input mzML file containing the ER spectra.input file*.mzML

pair_in Pair-file in the format: m/z-light m/z-heavy charge rtinput file*.txt

out Output consensusXML file were the pairs of the feature are written into.output file*.consensusXML

feature_out Output featureXML file, only written if given, skipped otherwise.output file*.featureXML

precursor_mass_tolerance0.3 Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features.0.0:∞

RT_tolerance200.0 Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file1.0:∞

max_charge3 Maximal charge state features should be search for.1:∞

intensity_threshold-1.0 Intensity threshold, for the meaning see the documentation of the IsotopeWaveletFeatureFinder documentation.-1.0:∞

max_isotope3 Max isotope of the isotope distribution to be considered2:∞

expansion_range5.0 The range that is used to extend the isotope distribution with null intensity peaks in Th.0.0:∞

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