IDMapper

Options

version

Version of the tool that generated this parameters file.

rt_tolerance

RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features. Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value.

mz_tolerance

m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features. Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value.

mz_measure

Unit of 'mz_tolerance'.

mz_reference

Source of m/z values for peptide identifications. If 'precursor', the precursor-m/z from the idXML is used. If 'peptide', masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches. ('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)

ignore_charge

For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature.

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)

use_centroid_rt

Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces.

use_centroid_mz

Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces. (If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)

use_subelements

Match using RT and m/z of sub-features instead of consensus RT and m/z. A consensus feature matches if any of its sub-features matches.

annotate_ids_with_subelements

Store the map index of the sub-feature in the peptide ID.

Views

IDMapper Std Output

The text sent to standard out during the execution of IDMapper.

IDMapper Error Output

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

Workflows

• 00-test_workflowKNIME Hub
• 01-MaCProQCKNIME Hub
• 02-download_and_analyze_raw_fileKNIME Hub
• 02-PIA_and_quantKNIME Hub
• Identification_quantification_with_inference_isobaric_epifany_MSstatsTMTOpenMS
• Show all 18 workflows

Links

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Developers