ProteinResolver

protein inference

Web Documentation for ProteinResolver

Options

version
Version of the tool that generated this parameters file.
in_path
Path to idXMLs or consensusXMLs files. Ignored if 'in' is given.
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)
missed_cleavages
Number of allowed missed cleavages
min_length
Minimum length of peptide
enzyme
Digestion enzyme
experiment
Identifier for the experimental design.
file
Identifier for the file name.
separator
Separator, which should be used to split a row into columns

Input Ports

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Input database file [fasta]
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Input file(s) holding experimental data [idXML,consensusXML,opt.]
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Text file containing the experimental design. See documentation for specific format requirements [txt,opt.]

Output Ports

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output file. Contains all protein groups [csv]
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output file. Contains one peptide per line and all proteins which contain that peptide [csv]
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output file. Contains one protein per line [csv]
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output file for additional info [csv]

Popular Predecessors

Popular Successors

Views

ProteinResolver Std Output
The text sent to standard out during the execution of ProteinResolver.
ProteinResolver Error Output
The text sent to standard error during the execution of ProteinResolver. (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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Links

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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: 2024-04-24
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

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