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.

per_spectrum

(only idXML) if set, mapping will be done based on exact matching of originating mzml file and spectrum_ref

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

Overrides 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'?

keep_old_scores

if set, keeps the original scores as user params

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)

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.)

Workflows

• Consensus IDKNIME Hub
• Peptide Identification from MSKNIME Hub
• Protein label-free quantificationKNIME Hub
• Protein label-free quantificationKNIME Hub
• Proteomics_LFQOpenMS
• Show all 6 workflows

Links

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Developers