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OpenSwathAssayGenerator

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
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)

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]

Popular Predecessors

Popular Successors

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

Developers

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Installation

To use this node in KNIME, install the extension OpenMS from the below update site following our NodePit Product and Node Installation Guide:

v5.2

A zipped version of the software site can be downloaded here.

Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, ZIB (GKN-Team) and the OpenMS Team

Plugin version: 3.0.0.202307112039

On NodePit since: 2023-12-06

Last update: 2024-07-22

KNIME versions: v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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