Extracts EICs from an MS experiment, in order to quantify analytes at a given position
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Use this instead of FeatureFinder, if you have bad features which are not recognized (much noise etc) or if you want to quantify non-peptides.
The EDTA file will specify where to search for signal. Retention time is in seconds [s]. 'int' and 'charge' are ignored but need to be present. However, you MUST specify a 'rank' column. Rows with equal rank are summed up in intensity (e.g. useful if you have charge variants you want to sum up to enhance quantitation robustness). Each rank represents a so called Master Compound, which constists of one or more sub compounds. If you do not require ranks, give each row a unique number, e.g. start numbering from 1 to n.
The intensity reported is the MAXIMUM intensity of all peaks each within the given tolerances for this row's position.
Example:
RT m/z int charge rank 19.2 431.8599024 0 0 1 21 678.7729237 0 0 2 25 660.7629237 0 0 2 59.2 431.8599024 0 0 3
Here, rows 2 and 3 will be summed up, as they have the same rank.
As output, two files in text format are given. The detail file gives RT and m/z deltas from expected to identified signal position etc, the sum file represents the master compounds.
The command line parameters of this tool are:
EICExtractor -- Extracts intensities from dedicates positions in a LC/MS map Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976 Usage: EICExtractor <options> Options (mandatory options marked with '*'): -in <file>* Input raw data file (valid formats: 'mzML') -pos <file>* Input config file stating where to find signal (valid formats: 'edta') -rt_tol RT tolerance in [s] for finding max peak (whole RT range around RT middle) (default: '3') -mz_tol M/z tolerance in [ppm] for finding a peak (default: '10') -rt_collect # of scans up & down in RT from highest point for ppm estimation in result (default: '1') -out <file>* Output quantitation file (summed intensities by master compounds) (valid formats: 'txt ') -out_detail <file>* Output quantitation file (valid formats: 'txt') 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)
INI file documentation of this tool:
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5 |