ProteinInference

Options

version

Version of the tool that generated this parameters file.

merge_runs

If your idXML contains multiple runs, merge them beforehand? Otherwise performs inference separately per run.

protein_fdr

Additionally calculate the target-decoy FDR on protein-level after inference

conservative_fdr

Use (D+1)/(T) instead of (D+1)/(T+D) for reporting protein FDRs.

picked_fdr

Use picked protein FDRs.

picked_decoy_string

If using picked protein FDRs, which decoy string was used? Leave blank for auto-detection.

picked_decoy_prefix

If using picked protein FDRs, was the decoy string a prefix or suffix? Ignored during auto-detection.

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 true, different charge variants of the same peptide sequence count as individual evidences.

treat_modification_variants_separately

If this is true, different modification variants of the same peptide sequence count as individual evidences.

use_shared_peptides

If this is true, shared peptides are used as evidences. Note: shared_peptides are not deleted and potentially resolved in postprocessing as well.

skip_count_annotation

If this is set, peptide counts won't be annotated at the proteins.

annotate_indistinguishable_groups

If this is true, calculates and annotates indistinguishable protein groups.

greedy_group_resolution

If this is true, shared peptides will be associated to best proteins only (i.e. become potentially quantifiable razor peptides).

score_type

PSM score type to use for inference. (default: empty = main score)

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_inferenceKNIME Hub
• basic_peptide_identification_with_inference_and_spectral_countingOpenMS
• labelfree_with_protein_quantificationOpenMS

Links

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Developers