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ConsensusID

Generic Workflow Nodes for KNIME: OpenMS version 2.3.0.201712211252 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Computes a consensus of peptide identifications of several identification engines.

Web Documentation for ConsensusID

Options

version
Version of the tool that generated this parameters file.
rt_delta
[idXML input only] Maximum allowed retention time deviation between identifications belonging to the same spectrum.
mz_delta
[idXML input only] Maximum allowed precursor m/z deviation between identifications belonging to the same spectrum.
algorithm
Algorithm used for consensus scoring. * PEPMatrix: Scoring based on posterior error probabilities (PEPs) and peptide sequence similarities (scored by a substitution matrix). Requires PEPs as scores. * PEPIons: Scoring based on posterior error probabilities (PEPs) and fragment ion similarities ('shared peak count'). Requires PEPs as scores. * best: For each peptide ID, use the best score of any search engine as the consensus score. Requires the same score type in all ID runs. * worst: For each peptide ID, use the worst score of any search engine as the consensus score. Requires the same score type in all ID runs. * average: For each peptide ID, use the average score of all search engines as the consensus. Requires the same score type in all ID runs. * ranks: Calculates a consensus score based on the ranks of peptide IDs in the results of different search engines. The final score is in the range (0, 1], with 1 being the best score. No requirements about score types.
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
Overwrite tool specific checks.
test
Enables the test mode (needed for internal use only)
considered_hits
The number of top hits in each ID run that are considered for consensus scoring ('0' for all hits).
min_support
For each peptide hit from an ID run, the fraction of other ID runs that must support that hit (otherwise it is removed).
count_empty
Count empty ID runs (i.e. those containing no peptide hit for the current spectrum) when calculating 'min_support'?
mass_tolerance
Maximum difference between fragment masses (in Da) for fragments to be considered 'shared' between peptides .
min_shared
The minimal number of 'shared' fragments (between two suggested peptides) that is necessary to evaluate the similarity based on shared peak count (SPC).
matrix
Substitution matrix to use for alignment-based similarity scoring
penalty
Alignment gap penalty (the same value is used for gap opening and extension)

Input Ports

input file [idXML,featureXML,consensusXML]

Output Ports

output file [idXML,featureXML,consensusXML]

Views

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

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Best Friends (Outgoing)

Workflows

Update Site

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