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OpenSwathAnalyzer

Executes a peak-picking and scoring algorithm on MRM/SRM data.

potential predecessor tools $ \longrightarrow $ OpenSwathAnalyzer $ \longrightarrow $ potential successor tools
OpenSwathChromatogramExtractor OpenSwathFeatureXMLToTSV
MRMMapper OpenSwathConfidenceScoring

The idea of the MRM peak-picker is to analyze a series of chromatograms together with the associated meta information (stored in TraML format) in order to determine likely places of elution of a peptide in MRM/SRM.

The command line parameters of this tool are:

OpenSwathAnalyzer -- Picks peaks and finds features in an SRM experiment.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976

Usage:
  OpenSwathAnalyzer <options>

This tool has algoritm parameters that are not shown here! Please check the ini file for a detailed descripti
on or use the --helphelp option.

Options (mandatory options marked with '*'):
  -in <file>*                    Input file containing the chromatograms. (valid formats: 'mzML')
  -tr <file>*                    Transition file (valid formats: '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: 'featureXML')
  -no-strict                     Run in non-strict mode and allow some chromatograms to not be mapped.
                                 
  -swath_files <files>           [applies only if you have full MS2 spectra maps] Swath files that were used 
                                 to extract the transitions. If present, SWATH specific scoring will be used.
                                 (valid formats: 'mzML')
  -min_upper_edge_dist <double>  [applies only if you have full MS2 spectra maps] Minimal distance to the 
                                 edge to still consider a precursor, in Thomson (only in SWATH) (default:
                                 '0')
                                 
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 following configuration subsections are valid:
 - algorithm   Algorithm parameters section

You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
Have a look at the OpenMS documentation for more information.

The algorithm parameters for the Analyzer filter are:

Legend:
required parameter
advanced parameter
+OpenSwathAnalyzerPicks peaks and finds features in an SRM experiment.
version1.11.1 Version of the tool that generated this parameters file.
++1Instance '1' section for 'OpenSwathAnalyzer'
in input file containing the chromatograms.input file*.mzML
tr transition fileinput file*.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*.featureXML
no-strictfalse run in non-strict mode and allow some chromatograms to not be mapped.true,false
swath_files[] [applies only if you have full MS2 spectra maps] Swath files that were used to extract the transitions. If present, SWATH specific scoring will be used.input file*.mzML
min_upper_edge_dist0 [applies only if you have full MS2 spectra maps] Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)
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.
+++algorithmAlgorithm parameters section
stop_report_after_feature-1 Stop reporting after feature (ordered by quality; -1 means do not stop).
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). For this to work, the TraML input file needs to contain normalized RT values.
rt_normalization_factor1 The normalized RT is expected to be between 0 and 1. If your normalized RT has a different range, pass this here (e.g. it goes from 0 to 100, set this value to 100)
quantification_cutoff0 Cutoff below which peaks should not be used for quantification any more0:∞
write_convex_hullfalse Whether to write out all points of all features into the featureXMLtrue,false
add_up_spectra1 Add up spectra around the peak apex (needs to be a non-even integer)1:∞
spacing_for_spectra_resampling0.005 If spectra are to be added, use this spacing to add them up0:∞
++++TransitionGroupPicker
sgolay_frame_length15 The number of subsequent data points used for smoothing.
This number has to be uneven. If it is not, 1 will be added.
sgolay_polynomial_order3 Order or the polynomial that is fitted.
gauss_width50 Gaussian width in seconds, estimated peak size.
use_gausstrue Use gauss for smoothing (other option is sgolay)
peak_width40 Estimated peak width in seconds.0:∞
signal_to_noise1 Signal to noise.0:∞
sn_win_len1000 Signal to noise window length.
sn_bin_count30 Signal to noise bin count.
stop_after_feature-1 Stop finding after feature (ordered by intensity; -1 means do not stop).
stop_after_intensity_ratio0.0001 Stop after reaching intensity ratio
background_subtractionnone Try to apply a background subtraction to the peak (experimental). The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that.none,smoothed,original
++++DIAScoring
dia_extraction_window0.05 DIA extraction window in Th.0:∞
dia_centroidedfalse Use centroded DIA data.true,false
dia_byseries_intensity_min300 DIA b/y series minimum intensity to consider.0:∞
dia_byseries_ppm_diff10 DIA b/y series minimal difference in ppm to consider.0:∞
dia_nr_isotopes4 DIA nr of isotopes to consider.0:∞
dia_nr_charges4 DIA nr of charges to consider.0:∞
++++EMGScoring
interpolation_step0.2 Sampling rate for the interpolation of the model function.
tolerance_stdev_bounding_box3 Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data.
max_iteration500 Maximum number of iterations using by Levenberg-Marquardt algorithm.
deltaAbsError0.0001 Absolute error used by the Levenberg-Marquardt algorithm.
deltaRelError0.0001 Relative error used by the Levenberg-Marquardt algorithm.
+++++statistics
mean1 Centroid position of the model.
variance1 Variance of the model.
++++Scores
use_shape_scoretrue Use the shape scoretrue,false
use_coelution_scoretrue Use the coelution scoretrue,false
use_rt_scoretrue Use the retention time scoretrue,false
use_library_scoretrue Use the library scoretrue,false
use_elution_model_scoretrue Use the elution model (EMG) scoretrue,false
use_intensity_scoretrue Use the intensity scoretrue,false
use_nr_peaks_scoretrue Use the number of peaks scoretrue,false
use_total_xic_scoretrue Use the total XIC scoretrue,false
use_sn_scoretrue Use the SN (signal to noise) scoretrue,false

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