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XTandemAdapter

Identifies peptides in MS/MS spectra via the search engine X! Tandem.

pot. predecessor tools $ \longrightarrow $ XTandemAdapter $ \longrightarrow $ pot. successor tools
any signal-/preprocessing tool
(in mzML format)
IDFilter or
any protein/peptide processing tool

X! Tandem must be installed before this wrapper can be used. This wrapper has been successfully tested with several versions of X! Tandem. The earliest version known to work is "PILEDRIVER" (2015-04-01). The latest is "ALANINE" (2017-02-01).

To speed up computations, FASTA databases can be compressed using the fasta_pro.exe tool of X! Tandem. It is contained in the "bin" folder of the X! Tandem installation. Refer to the documentation of X! Tandem for further information about settings.

This adapter supports relative database filenames. If a database is not found in the current working directory, it is looked up in the directories specified by 'OpenMS.ini:id_db_dir' (see TOPP for Advanced Users).

X! Tandem settings not exposed by this adapter (especially refinement settings) can be directly adjusted using an XML configuration file. By default, all (!) parameters available explicitly via this wrapper take precedence over the XML configuration file. The parameter default_config_file can be used to specify such a custom configuration. An example of a configuration file (named "default_input.xml") is contained in the "bin" folder of the X! Tandem installation and in the OpenMS installation under OpenMS/share/CHEMISTRY/XTandem_default_input.xml. If you want to use the XML configuration file and ignore most of the parameters set via this adapter, use the ignore_adapter_param flag. Then, the config given via default_config_file is used exclusively and only the values for the paramters in, out, database and xtandem_executable are taken from this adapter.

Note
Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

INI file documentation of this tool:


OpenMS / TOPP release 2.2.0 Documentation generated on Sat Oct 14 2017 13:34:19 using doxygen 1.8.13