DatabaseSuitability

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

Web Documentation for DatabaseSuitability

Options

version: Version of the tool that generated this parameters file.
novo_threshold: Minimum score a de novo sequence has to have to be defined as 'correct'. The default of 60 is proven to be a good estimate for sequences generated by Novor.
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)
number_of_subsampled_runs: Controls how many runs should be done for calculating corrected suitability. (0 : number of runs will be estimated automaticly) ATTENTION: For each run a seperate ID-search is performed. This can result in some serious run time.
keep_search_files: Set this flag if you wish to keep the files used by and produced by the internal ID search.
disable_correction: Set this flag to disable the calculation of the corrected suitability.
force: Set this flag to enforce re-ranking when no cross correlation score is present. For re-ranking the default score found at each peptide hit is used. Use with care!

Input Ports

: Input idXML file from a peptide identification search with a combined database. 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]
: Input FASTA file of the database in question [FASTA]
: Input deNovo sequences derived from MzML given in 'in_spec' concatenated to one FASTA entry [FASTA]

Output Ports

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

Popular Predecessors

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Popular Successors

Resampler100 %

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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.)

Workflows

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Developers

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Installation

To use this node in KNIME, install the extension OpenMS from the below update site following our NodePit Product and Node Installation Guide:

v5.2

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

Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, ZIB (GKN-Team) and the OpenMS Team

Plugin version: 3.0.0.202307112039

On NodePit since: 2023-12-06

Last update: 2024-04-26

KNIME versions: v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0

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