InternalCalibration

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

: Input peak file [mzML]
: Path to the Rscript executable (default: 'Rscript'). [,opt.]
: Identifications or features whose peptide ID's serve as calibration masses. [idXML,featureXML,opt.]
: 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

: Output file [mzML]
: 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]
: 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]
: Table of model parameters for each spectrum. [csv]
: Plot image of model parameters for each spectrum. [png]
: Table of pre- and post calibration errors. [csv]
: Plot image of pre- and post calibration errors. [png]

Popular Predecessors

Popular Successors

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.)

Workflows

test-real-life-edge-casesKNIME Hub

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.

Installation

To use this node in KNIME, install the extension OpenMS from the below update site following our NodePit Product and Node Installation Guide:

v5.2

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

Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, ZIB (GKN-Team) and the OpenMS Team

Plugin version: 3.0.0.202307112039

On NodePit since: 2023-12-06

Last update: 2024-04-24

KNIME versions: v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.

Try NodePit Runner!