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OpenSwathDecoyGenerator

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

Generates decoys according to different models for a specific TraML

Web Documentation for OpenSwathDecoyGenerator

Options

version
Version of the tool that generated this parameters file.
method
decoy generation method ('shuffle','pseudo-reverse','reverse','shift')
decoy_tag
decoy tag
mz_threshold
MZ threshold in Thomson for fragment ion annotation
exclude_similar
set this flag if decoy assays with similarity of the peptide sequence to the target assays higher than the identity_threshold should be excluded. If similarity_threshold is over 0, decoy assays with an absolute difference of the decoy and target product mz smaller than similarity_threshold are further excluded.
similarity_threshold
Similarity threshold for absolute difference of the product mz of target and decoy assays for exclusion in Dalton. Suggested value: 0.05
append
set this flag if non-decoy TraML should be appended to the output.
remove_CNterm_mods
set this flag to remove decoy peptides with C/N terminal modifications (may be necessary depending on the decoy generation method).
remove_unannotated
set this flag if target assays with unannotated ions should be ignored from decoy generation.
identity_threshold
shuffle: identity threshold for the shuffle algorithm
max_attempts
shuffle: maximum attempts to lower the sequence identity between target and decoy for the shuffle algorithm
mz_shift
shift: MZ shift in Thomson for shift decoy method
precursor_mass_shift
Mass shift to apply to the precursor ion
allowed_fragment_types
allowed fragment types
allowed_fragment_charges
allowed fragment charge states
enable_detection_specific_losses
set this flag if specific neutral losses for detection fragment ions should be allowed
enable_detection_unspecific_losses
set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed
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)

Input Ports

input file ('traML') [traML]

Output Ports

output file [traML]

Views

OpenSwathDecoyGenerator Std Output
The text sent to standard out during the execution of OpenSwathDecoyGenerator.
OpenSwathDecoyGenerator Error Output
The text sent to standard error during the execution of OpenSwathDecoyGenerator. (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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Update Site

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