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MassCalculator

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

Calculates masses and mass-to-charge ratios of peptide sequences

Web Documentation for MassCalculator

Options

version
Version of the tool that generated this parameters file.
in_seq
List of peptide sequences (mutually exclusive to 'in')
charge
List of charge states; required if 'in_seq' is given
format
Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)
average_mass
Compute average (instead of monoisotopic) peptide masses
fragment_type
For what type of sequence/fragment the mass should be computed
separator
Field separator for 'table' output format; by default, the 'tab' character is used
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)

Input Ports

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Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq') [tsv,opt.]

Output Ports

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Output file; if empty, output is written to the screen [csv]

Views

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

Best Friends (Incoming)

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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Developers

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