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XTandemAdapter

Generic Workflow Nodes for KNIME: OpenMS version 2.4.0.201810261314 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Annotates MS/MS spectra using X! Tandem.

Web Documentation for XTandemAdapter

Options

version
Version of the tool that generated this parameters file.
ignore_adapter_param
Set this to use the configuration given in 'default_config_file' exclusively, ignoring other parameters (apart from 'in', 'out', 'database', 'xtandem_executable') set via this adapter.
precursor_mass_tolerance
Precursor mass tolerance
fragment_mass_tolerance
Fragment mass error
precursor_error_units
Parent monoisotopic mass error units
fragment_error_units
Fragment monoisotopic mass error units
max_precursor_charge
Maximum precursor charge ('0' to use X! Tandem default)
no_isotope_error
By default, misassignment to the first and second isotopic 13C peak are also considered. Set this flag to disable.
fixed_modifications
Fixed modifications, specified using Unimod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'
variable_modifications
Variable modifications, specified using Unimod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'
minimum_fragment_mz
Minimum fragment m/z
enzyme
The enzyme used for peptide digestion.
missed_cleavages
Number of possible cleavage sites missed by the enzyme
semi_cleavage
Require only peptide end to have a valid cleavage site, not both.
output_results
Which hits should be reported. All, valid ones (passing the E-Value threshold), or stochastic (failing the threshold)
max_valid_expect
Maximal E-Value of a hit to be reported (only evaluated if 'output_result' is 'valid' or 'stochastic')
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 containing MS2 spectra [mzML]
FASTA file or pro file. Non-existing relative file-names are looked up via'OpenMS.ini:id_db_dir' [FASTA]
Default X! Tandem configuration file. All parameters of this adapter take precedence over the file - use it for parameters not available here. A template file can be found at 'OpenMS/share/CHEMISTRY/XTandem_default_input.xml'. [xml,opt.]

Output Ports

Output file containing search results [idXML,Inactive]
Raw output file directly from X! Tandem. Either 'out' or 'xml_out' are required. They can be used together. [xml,Inactive]

Views

XTandemAdapter Std Output
The text sent to standard out during the execution of XTandemAdapter.
XTandemAdapter Error Output
The text sent to standard error during the execution of XTandemAdapter. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

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

KNIME 4.0
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