PhosphoScoring

Scores potential phosphorylation sites in order to localize the most probable sites.

Options

version: Version of the tool that generated this parameters file.
fragment_mass_tolerance: Fragment mass tolerance for spectrum comparisons
fragment_mass_unit: Unit of fragment mass tolerance
max_peptide_length: Restrict scoring to peptides with a length no greater than this value ('0' for 'no restriction')
max_num_perm: Maximum number of permutations a sequence can have to be processed ('0' for 'no restriction')
unambiguous_score: Score to use for unambiguous assignments, where all sites on a peptide are phosphorylated. (Note: If a peptide is not phosphorylated at all, its score is set to '-1'.)
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 file with MS/MS spectra [mzML]
: Identification input file which contains a search against a concatenated sequence database [idXML]

PhosphoScoring Std Output: The text sent to standard out during the execution of PhosphoScoring.
PhosphoScoring Error Output: The text sent to standard error during the execution of PhosphoScoring. (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 OpenMS from the below update site following our NodePit Product and Node Installation Guide:

v5.4

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: 3.2.0.202411141610

On NodePit since: 2024-12-06

Last update: 2024-12-24

KNIME versions: v5.4, v5.3, 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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