IconOpenSwathAssayGenerator0 ×

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

Generates assays according to different models for a specific TraML

Web Documentation for OpenSwathAssayGenerator

Options

version
Version of the tool that generated this parameters file.
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
enable_identification_specific_losses
set this flag if specific neutral losses for identification fragment ions should be allowed
enable_identification_unspecific_losses
set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for identification fragment ions should be allowed
enable_identification_ms2_precursors
set this flag if MS2-level precursor ions for identification should be allowed to enable extraction of the precursor signal from the fragment ion data (MS2-level). This may help in identification if the MS1 signal is weak.
enable_ms1_uis_scoring
set this flag if MS1-UIS assays for UIS scoring should be generated
enable_ms2_uis_scoring
set this flag if MS2-UIS assays for UIS scoring should be generated
max_num_alternative_localizations
maximum number of site-localization permutations
enable_reannotation
set this flag if reannotation of 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
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]
Tab separated file containing the SWATH windows for exclusion of fragment ions falling into the precursor isolation window: lower_offset upper_offset \newline 400 425 \newline ... Note that the first line is a header and will be skipped. [txt,opt.]

Output Ports

output file [traML]

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.)

Update Site

To use this node in KNIME, install Generic Workflow Nodes for KNIME: OpenMS from the following update site:

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