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 allow 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.
The command line parameters of this tool are:
ERPairFinder -- Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans. Version: 2.3.0 Jan 9 2018, 17:46:23, Revision: 38ae115 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') Common UTIL 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:
OpenMS / TOPP release 2.3.0 | Documentation generated on Tue Jan 9 2018 18:22:06 using doxygen 1.8.13 |