OpenSwathAssayGenerator

Options

version

Version of the tool that generated this parameters file.

in_type

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

min_transitions

minimal number of transitions

max_transitions

maximal number of transitions

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

precursor_mz_threshold

MZ threshold in Thomson for precursor ion selection

precursor_lower_mz_limit

lower MZ limit for precursor ions

precursor_upper_mz_limit

upper MZ limit for precursor ions

product_mz_threshold

MZ threshold in Thomson for fragment ion annotation

product_lower_mz_limit

lower MZ limit for fragment ions

product_upper_mz_limit

upper MZ limit for fragment ions

enable_ipf

IPF: set this flag if identification transitions should be generated for IPF. Note: Requires setting 'unimod_file'.

max_num_alternative_localizations

IPF: maximum number of site-localization permutations

disable_identification_ms2_precursors

IPF: set this flag if MS2-level precursor ions for identification should not be allowed for extraction of the precursor signal from the fragment ion data (MS2-level).

disable_identification_specific_losses

IPF: set this flag if specific neutral losses for identification fragment ions should not be allowed

enable_identification_unspecific_losses

IPF: set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for identification fragment ions should be allowed

enable_swath_specifity

IPF: set this flag if identification transitions without precursor specificity (i.e. across whole precursor isolation window instead of precursor MZ) should be generated.

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

OpenSwathAssayGenerator Std Output

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

OpenSwathAssayGenerator Error Output

The text sent to standard error during the execution of OpenSwathAssayGenerator. (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