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)

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.)

Workflows

• Identification_quantification_with_inference_isobaric_epifany_MSstatsTMTOpenMS
• Identification_quantification_with_inference_isobaric_epifany_MSstatsTMTKNIME Hub
• MSstats_statPostProcessing_iPRG2015OpenMS
• MSstats_statPostProcessing_iPRG2015KNIME Hub

Links

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Developers