This node is currently not available in KNIME v5.2 — instead we’re showing this page for KNIME v4.7. You can use the version menu in the title bar to permanently switch your preferred version. This will also show the link to the update site.

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

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.

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: 2024-04-20

KNIME versions: From v3.6 to v4.7

Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.

Try NodePit Runner!