OpenSwathDecoyGenerator

Options

version

Version of the tool that generated this parameters file.

in_type

Input file type -- default: determined from file extension or content

method

Decoy generation method

decoy_tag

decoy tag

min_decoy_fraction

Minimum fraction of decoy / target peptides and proteins

aim_decoy_fraction

Number of decoys the algorithm should generate (if unequal to 1, the algorithm will randomly select N peptides for decoy generation)

shuffle_max_attempts

shuffle: maximum attempts to lower the amino acid sequence identity between target and decoy for the shuffle algorithm

shuffle_sequence_identity_threshold

shuffle: target-decoy amino acid sequence identity threshold for the shuffle algorithm

shift_precursor_mz_shift

shift: precursor ion MZ shift in Thomson for shift decoy method

shift_product_mz_shift

shift: fragment ion MZ shift in Thomson for shift decoy method

product_mz_threshold

MZ threshold in Thomson for fragment ion annotation

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

switchKR

Whether to switch terminal K and R (to achieve different precursor mass)

separate

set this flag if decoys should not be appended to targets.

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)

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.)

Workflows

• OpenSwathKNIME Hub

Links

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Developers