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Generic Workflow Nodes for KNIME: OpenMS version by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Finds mass spectrometric peaks in profile mass spectra.

Web Documentation for PeakPickerHiRes


Version of the tool that generated this parameters file.
Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first
Name of log file (created only when specified)
Sets the debug level
Sets the number of threads allowed to be used by the TOPP tool
Disables progress logging to command line
Overrides tool-specific checks
Enables the test mode (needed for internal use only)
Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)
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.
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.
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.
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.
Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak.
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).
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.
parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev
parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile
method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method
window length in Thomson
number of bins for intensity values
minimum number of elements required in a window (otherwise it is considered sparse)
noise value used for sparse windows
Write out log messages in case of sparse windows or median in rightmost histogram bin

Input Ports

input profile data file [mzML]

Output Ports

output peak file [mzML]


PeakPickerHiRes Std Output
The text sent to standard out during the execution of PeakPickerHiRes.
PeakPickerHiRes Error Output
The text sent to standard error during the execution of PeakPickerHiRes. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

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