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

This adapter is deprecated (and likely removed in OpenMS 3.3). Contact us, if you feel it's irreplaceable.
pot. predecessor tools → XTandemAdapter → pot. successor tools
any signal-/preprocessing tool
(in mzML format)
IDFilter or
any protein/peptide processing tool
@em X!Tandem must be installed before this wrapper can be used.
This wrapper has been successfully tested with several versions of @em X!Tandem.
The earliest version known to work is "PILEDRIVER" (2015-04-01). The latest is "ALANINE" (2017-02-01).

@note @em X!Tandem only support <b>uncompressed mzML files</b> (e.g. no zlib compression or other fancy things like numpress) may be used internally!
This converter only forwards the mzML filename and you will get an error like 'Fatal error: unsupported CODEC used for mzML peak data (CODEC type=zlib compression)'.
If this happens, preprocess the mzML files using OpenMS' @ref TOPP_FileConverter to write a plain mzML which @em X!Tandem understands.

@em 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 @em X!Tandem.
It is contained in the "bin" folder of the @em X!Tandem installation.
Refer to the documentation of @em 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 @subpage TOPP_advanced).

@em 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 @p 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 @em X!Tandem installation and in the %OpenMS installation
under <code>OpenMS/share/CHEMISTRY/XTandem_default_config.xml</code>.
If you want to use the XML configuration file and @em ignore most of the parameters set via this adapter, use the @p ignore_adapter_param flag.
Then, the config given via @p default_config_file is used exclusively and only the values for the parameters @p in, @p out, @p database and @p xtandem_executable are taken from this adapter.

@note This adapter supports <b>15N labeling</b> by using the <tt>XTandem_residue_mass.bioml.xml</tt> file (which defines modified AA masses) as provided in
      <code>OpenMS/share/OpenMS/CHEMISTRY/</code>. To use it, specify the full path (which will depend on your system!) to this bioml.xml file 
      within the <tt>XTandem_default_config.xml</tt> config file (see above).
Within this config file, modify the path in the following line to match your system's configuration.
<note type="input" label="protein, modified residue mass file">/path/to/XTandem_residue_mass.bioml.xml</note>

and pass the config file's filename via the default_config_file parameter to XTandemAdapter. For more details, see
Warning: If the path to XTandem_residue_mass.bioml.xml is invalid, X!Tandem will simply ignore the setting without feedback!
Warning: The resulting peptide sequences in the idXML file will not contain any N15 labeling information because X!Tandem simply received modified AA masses without further information what they mean. Add the 15N modification information by calling the StaticModification tool on the idXML file created by this adapter.

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.
<B>The command line parameters of this tool are:</B>
@verbinclude TOPP_XTandemAdapter.cli
<B>INI file documentation of this tool:</B>
@htmlinclude TOPP_XTandemAdapter.html