| OpenMS 2.5.0

LowMemPeakPickerHiRes

A tool for peak detection on streamed profile data (low-memory requirements). Executes the peak picking with high_res algorithm.

pot. predecessor tools | PeakPickerHiRes | pot. successor tools
BaselineFilter | any tool operating on MS peak data (in mzML format)
NoiseFilterGaussian
NoiseFilterSGolay

Reference:
Weisser et al.: An automated pipeline for high-throughput label-free quantitative proteomics (J. Proteome Res., 2013, PMID: 23391308).

The conversion of the "raw" ion count data acquired by the machine into peak lists for further processing is usually called peak picking or centroiding. The choice of the algorithm should mainly depend on the resolution of the data. As the name implies, the high_res algorithm is fit for high resolution (orbitrap or FTICR) data.

Finding the right parameters for the is explained in the TOPP tutorial.

The command line parameters of this tool are:

    LowMemPeakPickerHiRes -- Finds mass spectrometric peaks in profile mass spectra.

    Full documentation: http://www.openms.de/documentation/UTILS_LowMemPeakPickerHiRes.html

    Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

    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:

      LowMemPeakPickerHiRes <options>

    This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript

    ion or use the --helphelp option.

    Options (mandatory options marked with '*'):

      -in <file>*        Input profile data file  (valid formats: 'mzML')

      -out <file>*       Output peak file  (valid formats: 'mzML')

    Common UTIL 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.

    For more information, please consult the online documentation for this tool:

      - http://www.openms.de/documentation/UTILS_LowMemPeakPickerHiRes.html

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+LowMemPeakPickerHiRes Finds mass spectrometric peaks in profile mass spectra.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'LowMemPeakPickerHiRes'
in input profile data file input file*.mzML
out output peak file output file*.mzML
log Name of log file (created only when specified)
debug 0 Sets the debug level
threads 1 Sets the number of threads allowed to be used by the TOPP tool
no_progress false Disables progress logging to command line true,false
force false Overwrite tool specific checks.true,false
test false Enables the test mode (needed for internal use only)true,false
+++algorithm Algorithm parameters section
signal_to_noise 0.0 Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)0.0:∞
spacing_difference_gap 4.0 The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. '0' to disable the constraint. Not applicable to chromatograms.0.0:∞
spacing_difference 1.5 Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points. If this difference is exceeded a missing point is assumed (see parameter 'missing'). A higher value implies a less stringent peak definition, since individual signals within the peak are allowed to be further apart. '0' to disable the constraint. Not applicable to chromatograms.0.0:∞
missing 1 Maximum number of missing points allowed when extending a peak to the left or to the right. A missing data point occurs if the spacing between two subsequent data points exceeds 'spacing_difference * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. Not applicable to chromatograms.0:∞
ms_levels[] List of MS levels for which the peak picking is applied. If empty, auto mode is enabled, all peaks which aren't picked yet will get picked. Other scans are copied to the output without changes.1:∞
report_FWHM false Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak.true,false
report_FWHM_unit relative Unit of FWHM. Either absolute in the unit of input, e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms).relative,absolute
++++SignalToNoise
max_intensity-1 maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N.-1:∞
auto_max_stdev_factor 3.0 parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev 0.0:999.0
auto_max_percentile 95 parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile 0:100
auto_mode 0 method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method-1:1
win_len 200.0 window length in Thomson 1.0:∞
bin_count 30 number of bins for intensity values 3:∞
min_required_elements 10 minimum number of elements required in a window (otherwise it is considered sparse)1:∞
noise_for_empty_window 1.0e20 noise value used for sparse windows
write_log_messages true Write out log messages in case of sparse windows or median in rightmost histogram bin true,false

For the parameters of the algorithm section see the algorithm documentation: PeakPickerHiRes

In the following table you, can find example values of the most important algorithm parameters for different instrument types.
These parameters are not valid for all instruments of that type, but can be used as a starting point for finding suitable parameters.

| Q-TOF | LTQ Orbitrap
signal_to_noise | 2 | 0