Identifies peptides in MS/MS spectra via XTandem.
pot. predecessor tools | ![]() ![]() | 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 last known version to work is 2009-04-01. We encountered problems with later versions (namely 2010-01-01).
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 docu of X!Tandem for further information about settings.
This adapter supports relative database filenames, which (when not found in the current working directory) is looked up in the directories specified by 'OpenMS.ini:id_db_dir' (see TOPP for Advanced Users).
The major part of the setting can be directly adjusted using the "default_input.xml" of X!Tandem. Parameters set by this wrapper overwrite the default settings given in the "default_input.xml", even those parameters not set explicitly, but defaulting to a value. An example of such a "default_input.xml" is contained in the "bin" folder of the X!Tandem installation. The parameter "default_input_file" must point to a valid file. "Masterfiles" for "default_input.xml" parameter importing other xml input files are not recommended, use at own risk.
The command line parameters of this tool are:
INI file documentation of this tool:
OpenMS / TOPP release 1.11.1 | Documentation generated on Mon Dec 23 2013 22:47:51 using doxygen 1.8.5 |