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OpenSwathAssayGenerator

Generic Workflow Nodes for KNIME: OpenMS version 2.4.0.201810261314 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.
in_type
Input file type -- default: determined from file extension or content
out_type
Output 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
Overwrite tool specific checks.
test
Enables the test mode (needed for internal use only)

Input Ports

Input file [tsv,mrm,pqp,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.]
(Modified) Unimod XML file (http://www.unimod.org/xml/unimod.xml) describing residue modifiability [xml,opt.]

Output Ports

Output file [tsv,pqp,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.)

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Update Site

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

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