PhosphoScoring

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

Web Documentation for PhosphoScoring

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 Ports

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Input file with MS/MS spectra [mzML]
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Identification input file which contains a search against a concatenated sequence database [idXML]

Output Ports

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Identification output annotated with phosphorylation scores [idXML]

Views

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.)

Workflows

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Further Links

Developers

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