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.

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.)

Workflows

• basic_peptide_identification_with_inferenceKNIME Hub
• basic_peptide_identification_with_inferenceOpenMS
• basic_peptide_identification_with_inferenceKNIME Hub

Links

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Developers