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MSstatsConverter

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

Converter to input for MSstats

Web Documentation for MSstatsConverter

Options

version
Version of the tool that generated this parameters file.
method
Method used in the experiment(label free [LFQ], isobaric labeling [ISO]))
msstats_bioreplicate
Which column in the condition table should be used for MSstats 'BioReplicate'
msstats_condition
Which column in the condition table should be used for MSstats 'Condition'
msstats_mixture
Which column in the condition table should be used for MSstats 'Mixture'
labeled_reference_peptides
If set, IsotopeLabelType is 'H', else 'L'
retention_time_summarization_method
How indistinguishable peptidoforms at different retention times should be treated. This is usually necessary for LFQ experiments and therefore defaults to 'max'. In case of TMT/iTRAQ, MSstatsTMT does the aggregation itself later and the parameter always resets to manual (i.e. is unused).
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 consensusXML with peptide intensities [consensusXML]
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Experimental Design file [tsv]
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Overwrite MS file names in consensusXML [mzML,opt.]

Output Ports

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Input CSV file for MSstats. [csv]

Views

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

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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