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InternalCalibration

Generic Workflow Nodes for KNIME: OpenMS version 2.6.0.202009301213 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Applies an internal mass recalibration.

Web Documentation for InternalCalibration

Options

version
Version of the tool that generated this parameters file.
ppm_match_tolerance
Finding calibrants in raw data uses this tolerance (for lock masses and ID's).
ms_level
Target MS levels to apply the transformation onto. Does not affect calibrant collection.
RT_chunking
RT window (one-sided, i.e. left->center, or center->right) around an MS scan in which calibrants are collected to build a model. Set to -1 to use ALL calibrants for all scans, i.e. a global model.
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
Overrides tool-specific checks
test
Enables the test mode (needed for internal use only)
lock_require_mono
Require all lock masses to be monoisotopic, i.e. not the iso1, iso2 etc ('charge' column is used to determine the spacing). Peaks which are not mono-isotopic are not used.
lock_require_iso
Require all lock masses to have at least the +1 isotope. Peaks without isotope pattern are not used.
model_type
Type of function to be fitted to the calibration points.
enabled
Apply RANSAC to calibration points to remove outliers before fitting a model.
threshold
Threshold for accepting inliers (instrument precision (not accuracy!) as ppm^2 distance)
pc_inliers
Minimum percentage (of available data) of inliers (<threshold away from model) to accept the model.
iter
Maximal # iterations.
median
The median ppm error of calibrated masses must be smaller than this threshold.
MAD
The median absolute deviation of the ppm error of calibrated masses must be smaller than this threshold.

Input Ports

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Input peak file [mzML]
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Path to the Rscript executable (default: 'Rscript'). [,opt.]
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Identifications or features whose peptide ID's serve as calibration masses. [idXML,featureXML,opt.]
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Input file containing reference m/z values (text file with each line as: m/z ms-level charge) which occur in all scans. [csv,opt.]

Output Ports

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Output file [mzML]
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Optional output file containing peaks from 'in' which were matched to reference m/z values. Useful to see which peaks were used for calibration. [mzML]
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Optional output file containing lock masses which were NOT found or accepted(!) in data from 'in'. Useful to see which peaks were used for calibration. [mzML]
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Table of model parameters for each spectrum. [csv]
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Plot image of model parameters for each spectrum. [png]
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Table of pre- and post calibration errors. [csv]
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Plot image of pre- and post calibration errors. [png]

Views

InternalCalibration Std Output
The text sent to standard out during the execution of InternalCalibration.
InternalCalibration Error Output
The text sent to standard error during the execution of InternalCalibration. (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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Best Friends (Outgoing)

Installation

To use this node in KNIME, install OpenMS from the following update site:

KNIME 4.2

A zipped version of the software site can be downloaded here.

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