NovorAdapter

Performs de novo sequencing of peptides from MS/MS data with Novor.

Options

version: Version of the tool that generated this parameters file.
enzyme: Digestion enzyme - currently only Trypsin is supported
fragmentation: Fragmentation method
massAnalyzer: MassAnalyzer e.g. (Oritrap CID-Trap, CID-FT, HCD-FT; QTof CID-TOF)
fragment_mass_tolerance: Fragmentation error tolerance (Da)
precursor_mass_tolerance: Precursor error tolerance (ppm or Da)
precursor_error_units: Unit of precursor mass tolerance
variable_modifications: Variable modifications
fixed_modifications: Fixed modifications
forbiddenResidues: Forbidden Resiudes
java_memory: Maximum Java heap size (in MB)
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)

: novor.jar [,opt.]
: MzML Input file [mzML]
: File to introduce customized algorithm parameters for advanced users (otional .novor file) [novor,opt.]
: The Java executable. Usually Java is on the system PATH. If Java is not found, use this parameter to specify the full path to Java [,opt.]

NovorAdapter Std Output: The text sent to standard out during the execution of NovorAdapter.
NovorAdapter Error Output: The text sent to standard error during the execution of NovorAdapter. (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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To use this node in KNIME, install the extension OpenMSThirdparty from the below update site following our NodePit Product and Node Installation Guide:

v5.3

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

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

Plugin version: 3.2.0.202409181756

On NodePit since: 2024-07-11

Last update: 2024-11-15

KNIME versions: Since v5.1

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