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. An example of that file is contained in the "bin" folder of the X!Tandem installation. The parameters "default_input_file" must point to a valid file. Parameters set by this wrapper overwrite the default settings given in the file.
The command line parameters of this tool are:
OpenMS / TOPP release 1.9.0 | Documentation generated on Sun Oct 27 2013 01:11:37 using doxygen 1.8.4 |