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ProteinInference

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

Protein inference based on an aggregation of the scores of the identified peptides.

Web Documentation for ProteinInference

Options

version
Version of the tool that generated this parameters file.
merge_runs
If your idXML contains multiple runs, merge them beforehand?
annotate_indist_groups
If you want to annotate indistinguishable protein groups, either for reporting or for group based quant. later. Only works with a single ID run in the 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)
annotate_origin
If true, adds a map_index MetaValue to the PeptideIDs to annotate the IDRun they came from.
allow_disagreeing_settings
Force merging of disagreeing runs. Use at your own risk.
min_peptides_per_protein
Minimal number of peptides needed for a protein identification. If set to zero, unmatched proteins get a score of -Infinity. If bigger than zero, proteins with less peptides are filtered and evidences removed from the PSMs. PSMs that do not reference any proteins anymore are removed but the spectrum info is kept.
score_aggregation_method
How to aggregate scores of peptides matching to the same protein?
treat_charge_variants_separately
If this is set, different charge variants of the same peptide sequence count as individual evidences.
treat_modification_variants_separately
If this is set, different modification variants of the same peptide sequence count as individual evidences.
use_shared_peptides
If this is set, shared peptides are used as evidences.
skip_count_annotation
If this is true, peptide counts won't be annotated at the proteins.

Input Ports

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input file(s) [idXML]

Output Ports

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output file [idXML]

Views

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

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

KNIME 4.3

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

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Developers

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