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PeakPickerHiRes

Generic Workflow Nodes for KNIME: OpenMS version 2.4.0.201810261314 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Finds mass spectrometric peaks in profile mass spectra.

Web Documentation for PeakPickerHiRes

Options

version
Version of the tool that generated this parameters file.
processOption
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
log
Name of log file (created only when specified)
debug
Sets the debug level
threads
Sets the number of threads allowed to be used by the TOPP tool
no_progress
Disables progress logging to command line
force
Overwrite tool specific checks.
test
Enables the test mode (needed for internal use only)
signal_to_noise
Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)
spacing_difference_gap
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.
spacing_difference
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.
missing
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.
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.
report_FWHM
Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak.
report_FWHM_unit
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).
max_intensity
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.
auto_max_stdev_factor
parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev
auto_max_percentile
parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile
auto_mode
method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method
win_len
window length in Thomson
bin_count
number of bins for intensity values
min_required_elements
minimum number of elements required in a window (otherwise it is considered sparse)
noise_for_empty_window
noise value used for sparse windows
write_log_messages
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]

Views

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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