MRMPairFinder

Util which can be used to evaluate labeled pair ratios on MRM features.

Web Documentation for MRMPairFinder

Options

version
Version of the tool that generated this parameters file.
mass_tolerance
Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features.
RT_tolerance
Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file.
RT_pair_tolerance
Maximal deviation in RT dimension in seconds the two partners of a pair is allowed to have.
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)

Input Ports

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Input featureXML file containing the features of the MRM experiment spectra. [featureXML]
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Pair-file in the format: prec-m/z-light prec-m/z-heavy frag-m/z-light frag-m/z-heavy rt [csv]

Output Ports

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Output consensusXML file were the pairs of the features will be written to. [consensusXML]
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Output featureXML file, only written if given, skipped otherwise. [featureXML]

Popular Predecessors

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Views

MRMPairFinder Std Output
The text sent to standard out during the execution of MRMPairFinder.
MRMPairFinder Error Output
The text sent to standard error during the execution of MRMPairFinder. (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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Further Links

Developers

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