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EICExtractor

Extracts EICs from an MS experiment, in order to quantify analytes at a given position

pot. predecessor tools $ \longrightarrow $ EICExtractor $ \longrightarrow $ pot. successor tools
FileConverter statistical tools, e.g., Excel, R, ...

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:

Legend:
required parameter
advanced parameter
+EICExtractorExtracts intensities from dedicates positions in a LC/MS map
version1.11.1 Version of the tool that generated this parameters file.
++1Instance '1' section for 'EICExtractor'
in[] Input raw data fileinput file*.mzML
pos Input config file stating where to find signalinput file*.edta
rt_tol3 RT tolerance in [s] for finding max peak (whole RT range around RT middle)
mz_tol10 m/z tolerance in [ppm] for finding a peak
rt_collect1 # of scans up & down in RT from highest point for ppm estimation in result
out Output quantitation file (summed intensities by master compounds)output file*.txt
out_detail Output quantitation fileoutput file*.txt
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

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