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DatabaseSuitability

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

Computes a suitability score for a database which was used for a peptide identification search. Also reports the quality of LC-MS spectra.

Options

version
Version of the tool that generated this parameters 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)
no_rerank
Use this flag if you want to disable re-ranking. Cases, where a de novo peptide scores just higher than the database peptide, are overlooked and counted as a de novo hit. This might underestimate the database quality.
reranking_cutoff_percentile
Swap a top-scoring deNovo hit with a lower scoring DB hit if their xcorr score difference is in the given percentile of all score differences between the first two decoy hits of a PSM. The lower the value the lower the decoy cut-off will be. Therefore it will be harder for a lower scoring DB hit to be re-ranked to the top.
FDR
Filter peptide hits based on this q-value. (e.g., 0.05 = 5 % FDR)

Input Ports

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Input idXML file from peptide search with combined database with added de novo peptide. PeptideIndexer is needed, FDR is forbidden. [idXML]
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Input MzML file used for the peptide identification [mzML]
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Input idXML file containing de novo peptides (unfiltered) [idXML]

Output Ports

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Optional tsv output containing database suitability information as well as spectral quality. [tsv]

Views

DatabaseSuitability Std Output
The text sent to standard out during the execution of DatabaseSuitability.
DatabaseSuitability Error Output
The text sent to standard error during the execution of DatabaseSuitability. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

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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