OpenMS
2.7.0
|
Extracts EICs from an MS experiment, in order to quantify analytes at a given position
pot. predecessor tools | EICExtractor | 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 input EDTA file specifies where to search for signal in RT and m/z. Retention time is in seconds [s]. A third intensity column is ignored but needs to be present.
Example (replace space separator with <TAB>):
RT positions can also be automatically generated using the 'auto-RT' functionality, which can be enabled by the flag 'auto_rt:enabled'. All EDTA input lines with negative RT and some m/z values are replaced by 'n' other lines, where the m/z value is identical and the RT column is replaced by of the 'n' RT estimates as discovered by the auto-RT functionality. This allows you to specify only the expected m/z positions and let the auto-RT function handle the RT positions. Info: auto-RT positions are only generated once from the FIRST mzML input file. All other mzML input files are expected to have similar RT positions! To debug auto-RT, you can specify an mzML output file (see 'auto_rt:out_debug_TIC' option) which will contain four single spectra which represent:
The intensity reported is the MAXIMUM intensity of all peaks each within the given tolerances for this row's position.
As output, one file in text format is given. It contains the actual RT and m/z positions of the data, as well as RT delta (in [s]) and m/z delta (in ppm) from the expected position as specified in the EDTA file or as found by the auto-RT feature.
RT - expected RT position (in [s]) mz - expected m/z position RTobs - RT position (in [s]) of the quantified entity dRT - RT delta (in [s]) to the input RT value (as specified in input file or as computed by the auto-rt heuristic) mzobs - m/z position of the quantified entity dppm - m/z delta (in parts-per-million) to the input m/z value (as specified in input file) intensity quantification (height of centroided peak); this is an average over multiple scans, thus does usually not correspond to the maximum peak ppm intensity
Each input experiment gives rise to the two RT and mz columns plus additional five columns (starting from RTobs) for each input file.
The command line parameters of this tool are:
EICExtractor -- Extracts intensities from dedicates positions in a LC/MS map Full documentation: http://www.openms.de/doxygen/release/2.7.0/html/TOPP_EICExtractor.html Version: 2.7.0 Sep 13 2021, 20:58:47, Revision: 9110e58 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: EICExtractor <options> Options (mandatory options marked with '*'): -in <file>* Input raw data file (valid formats: 'mzML') -in_header <file> [for Waters data only] Read additional information from _HEADER.TXT. Provide one for each raw input file. (valid formats: 'txt') -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: '3.0') -mz_tol M/z tolerance in [ppm] for finding a peak (default: '10.0') -rt_collect # of scans up & down in RT from highest point for ppm estimation in result (default: '1') Parameters for automatic detection of injection RT peaks (no need to specify them in 'pos' input file): -auto_rt:enabled Automatically detect injection peaks from TIC and quantify all m/z x RT combinations. -out <file>* Output quantitation file (multiple columns for each input compound) (valid formats: 'csv ') 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: