0 ×


Generic Workflow Nodes for KNIME: OpenMS version 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.


Version of the tool that generated this parameters file.
Name of log file (created only when specified)
Sets the debug level
Sets the number of threads allowed to be used by the TOPP tool
Disables progress logging to command line
Overrides tool-specific checks
Enables the test mode (needed for internal use only)
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.
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.
Filter peptide hits based on this q-value. (e.g., 0.05 = 5 % FDR)

Input Ports

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

Output Ports

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


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.)


To use this node in KNIME, install OpenMS from the following update site:


A zipped version of the software site can be downloaded here.

You don't know what to do with this link? Read our NodePit Product and Node Installation Guide that explains you in detail how to install nodes to your KNIME Analytics Platform.

Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform. Browse NodePit from within KNIME, install nodes with just one click and share your workflows with NodePit Space.


You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.