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XTandemAdapter

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: Overrides 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_config.xml'. [xml,opt.]

Output Ports

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

Popular Predecessors

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.)

Workflows

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:

v4.7

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

Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Plugin version: 2.7.0.202109131426

On NodePit since: 2022-12-06

Last update: 2024-11-09

KNIME versions: From v3.6 to v4.7

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