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required parameter
advanced parameter
+OpenSwathDecoyGeneratorGenerates decoys according to different models for a specific TraML
version1.10.0
Version of the tool that generated this parameters file.
++1Instance '1' section for 'OpenSwathDecoyGenerator'
in
input file ('traML')input file*.traML
out
output fileoutput file*.traML
methodshuffle
decoy generation method ('shuffle','pseudo-reverse','reverse','shift')
decoy_tagDECOY_
decoy tag
min_transitions2
minimal number of transitions
max_transitions6
maximal number of transitions
theoreticalfalse
set this flag if only annotated transitions should be used and be corrected to the theoretical mz.true,false
mz_threshold0.8
MZ threshold in Thomson for fragment ion annotation
exclude_similarfalse
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.true,false
similarity_threshold-1
Similarity threshold for absolute difference of the product mz of target and decoy assays for exclusion in Dalton. Suggested value: 0.05
appendfalse
set this flag if non-decoy TraML should be appended to the output.true,false
remove_CNterm_modsfalse
set this flag to remove decoy peptides with C/N terminal modifications (may be necessary depending on the decoy generation method).true,false
identity_threshold0.7
shuffle: identity threshold for the shuffle algorithm
max_attempts10
shuffle: maximum attempts to lower the sequence identity between target and decoy for the shuffle algorithm
mz_shift20
shift: MZ shift in Thomson for shift decoy method
log
Name of log file (created only when specified)
debug0
Sets the debug level
threads1
Sets the number of threads allowed to be used by the TOPP tool
no_progressfalse
Disables progress logging to command linetrue,false
testfalse
Enables the test mode (needed for internal use only)true,false