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OpenMS
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Identifies peptides in MS/MS spectra via the search engine X! Tandem.
pot. predecessor tools | → XTandemAdapter → | 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).
X!Tandem has a build-in adventitious cleavage rule for Asp|Pro (Aspartate/D | Proline/P), which it allows as cutting site for all enzymes. Furthermore, it treats any occurence of 'X' as stop codon (and thus as cleavage site). The resulting peptide will be non- or semi-tryptic.
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_advanced).
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_config.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 parameters in
, out
, database
and xtandem_executable
are taken from this adapter.
XTandem_residue_mass.bioml.xml
file (which defines modified AA masses) as provided in OpenMS/share/OpenMS/CHEMISTRY/
. To use it, specify the full path (which will depend on your system!) to this bioml.xml file within the XTandem_default_config.xml
config file (see above). Within this config file, modify the path in the following line to match your system's configuration. default_config_file
parameter to XTandemAdapter. For more details, see https://www.thegpm.org/TANDEM/api/pmrmf.html.
The command line parameters of this tool are:
INI file documentation of this tool: