MultiplexResolver

Completes peptide multiplets and resolves conflicts within them.

Web Documentation for MultiplexResolver

Options

version: Version of the tool that generated this parameters file.
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)
labels: Labels used for labelling the samples. [...] specifies the labels for a single sample. For example [][Lys8,Arg10] ... SILAC [][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC [Dimethyl0][Dimethyl6] ... Dimethyl [Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl [ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL
missed_cleavages: Maximum number of missed cleavages due to incomplete digestion. (Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)
mass_tolerance: Mass tolerance in Da for matching the mass shifts in the detected peptide multiplet to the theoretical mass shift pattern.
mz_tolerance: m/z tolerance in ppm for checking if dummy feature vicinity was blacklisted.
rt_tolerance: Retention time tolerance in seconds for checking if dummy feature vicinity was blacklisted.
Arg6: Label:13C(6) | C(-6) 13C(6) | unimod #188
Arg10: Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267
Lys4: Label:2H(4) | H(-4) 2H(4) | unimod #481
Lys6: Label:13C(6) | C(-6) 13C(6) | unimod #188
Lys8: Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259
Leu3: Label:2H(3) | H(-3) 2H(3) | unimod #262
Dimethyl0: Dimethyl | H(4) C(2) | unimod #36
Dimethyl4: Dimethyl:2H(4) | 2H(4) C(2) | unimod #199
Dimethyl6: Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510
Dimethyl8: Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330
ICPL0: ICPL | H(3) C(6) N O | unimod #365
ICPL4: ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687
ICPL6: ICPL:13C(6) | H(3) 13C(6) N O | unimod #364
ICPL10: ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866

Input Ports

: Peptide multiplets with assigned sequence information [consensusXML]
: Optional input containing spectral peaks blacklisted during feature detection. Needed for generation of dummy features. [mzML,opt.]

Output Ports

: Complete peptide multiplets. [consensusXML]
: Optional output containing peptide multiplets without ID annotation or with conflicting quant/ID information. [consensusXML]

Popular Predecessors

Popular Successors

Views

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

Workflows

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Developers

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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: 2024-04-17

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

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