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OpenSwathChromatogramExtractor

Extracts chromatograms (XICs) from a file containing spectra.

potential predecessor tools $ \longrightarrow $ OpenSwathChromatogramExtractor $ \longrightarrow $ potential successor tools
FileFilter OpenSwathAnalyzer

This module extracts ion traces (extracted ion chromatograms or XICs) from a file containing spectra. The masses at which the chromatograms should be extracted are stored in a TraML file and the result is stored in a mzML file holding chromatograms. This tool is designed to extract chromatogams from SWATH (data independent acquisition) data (see ref[1]), thus it will extract the masses found in the product ion section of the TraML transitions, returning as many chromatograms as input transitions were provided.

For SWATH data, the "is_swath" flag which will check the precursor isolation window of the first scan and assume all scans in that file were recorded with this precursor window (thus making it necessary to provide one input file per SWATH window). The module will then only extract transitions whose precursors fall into the corresponding isolation window.

For the extraction method, two convolution functions are available: top-hat and bartlett. While top-hat will just sum up the signal within a quadratic window, bartlett will weigh the signal in the center of the window more than the signal on the edge.

[1] Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L, Bonner R, Aebersold R.
Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis.
Mol Cell Proteomics. 2012 Jun;11(6):O111.016717.

The command line parameters of this tool are:

OpenSwathChromatogramExtractor -- Extract chromatograms (XIC) from a MS2 map file.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976

Usage:
  OpenSwathChromatogramExtractor <options>

Options (mandatory options marked with '*'):
  -in <files>*                      Input files separated by blank (valid formats: 'mzML')
  -tr <file>*                       Transition file ('TraML' or 'csv') (valid formats: 'csv', 'traML')
  -rt_norm <file>                   RT normalization file (how to map the RTs of this run to the ones stored 
                                    in the library) (valid formats: 'trafoXML')
  -out <file>*                      Output file (valid formats: 'mzML')
  -min_upper_edge_dist <double>     Minimal distance to the edge to still consider a precursor, in Thomson 
                                    (default: '0')
  -extraction_window <double>       Extraction window used (in Thomson, to use ppm see -ppm flag) (default: 
                                    '0.05' min: '0')
  -rt_extraction_window <double>    Only extract RT around this value (-1 means extract over the whole range,
                                    a value of 500 means to extract around +/- 500 s of the expected elution
                                    ). (default: '-1')
  -is_swath                         Set this flag if the data is SWATH data
  -ppm                              Extraction_window is in ppm
  -extraction_function <name>       Function used to extract the signal (default: 'tophat' valid: 'tophat', 
                                    'bartlett')

Options to control the modeling of retention time transformations from data:
  -model:type <name>                Type of model (default: 'linear' valid: 'linear', 'b_spline', 'interpolat
                                    ed')
  -model:symmetric_regression       Only for 'linear' model: Perform linear regression on 'y - x' vs. 'y + 
                                    x', instead of on 'y' vs. 'x'.
  -model:num_breakpoints <number>   Only for 'b_spline' model: Number of breakpoints of the cubic spline in 
                                    the smoothing step. The breakpoints are spaced uniformly on the retention
                                    time interval. More breakpoints mean less smoothing. Reduce this number
                                    if the transformation has an unexpected shape. (default: '5' min: '2')
  -model:interpolation_type <name>  Only for 'interpolated' model: Type of interpolation to apply. (default: 
                                    'cspline')

                                    
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)

The algorithm parameters for the Analyzer filter are:

Legend:
required parameter
advanced parameter
+OpenSwathChromatogramExtractorExtract chromatograms (XIC) from a MS2 map file.
version1.11.1 Version of the tool that generated this parameters file.
++1Instance '1' section for 'OpenSwathChromatogramExtractor'
in[] Input files separated by blankinput file*.mzML
tr transition file ('TraML' or 'csv')input file*.csv,*.traML
rt_norm RT normalization file (how to map the RTs of this run to the ones stored in the library)input file*.trafoXML
out output fileoutput file*.mzML
min_upper_edge_dist0 Minimal distance to the edge to still consider a precursor, in Thomson
extraction_window0.05 Extraction window used (in Thomson, to use ppm see -ppm flag)0:∞
rt_extraction_window-1 Only extract RT around this value (-1 means extract over the whole range, a value of 500 means to extract around +/- 500 s of the expected elution).
is_swathfalse Set this flag if the data is SWATH datatrue,false
ppmfalse extraction_window is in ppmtrue,false
extraction_functiontophat Function used to extract the signaltophat,bartlett
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
+++modelOptions to control the modeling of retention time transformations from data
typelinear Type of modellinear,b_spline,interpolated
symmetric_regressionfalse Only for 'linear' model: Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'.true,false
num_breakpoints5 Only for 'b_spline' model: Number of breakpoints of the cubic spline in the smoothing step. The breakpoints are spaced uniformly on the retention time interval. More breakpoints mean less smoothing. Reduce this number if the transformation has an unexpected shape.2:∞
interpolation_typecspline Only for 'interpolated' model: Type of interpolation to apply.

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