Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Macros Groups Pages
OMSSAAdapter

Identifies peptides in MS/MS spectra via OMSSA (Open Mass Spectrometry Search Algorithm).

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

OMSSA must be installed on the system to be able to use the OMSSAAdapter. See pubchem.ncbi.nlm.nih.gov/omssa/ for further information on how to download and install OMSSA on your system. You might find that the latest OMSSA version does not run on your system (to test this, run omssacl in your OMMSA/bin/ directory and see if it crashes). If you encounter an error message, try another OMSSA version

Sequence databases in FASTA format must be converted into the NCBI format before OMSSA can read them. Therefore, use the program formatdb of the NCBI-tools suite (see ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.13/ for a working version). The latest NCBI BLAST distribution does not contain the formatdb executable any longer!). Use formatdb -i SwissProt_TargetAndDecoy.fasta -o to create additional files, which will be used by OMSSA. The database option of the OMSSAAdapter should contain the name of the psq file , e.g., 'SwissProt_TargetAndDecoy.fasta.psq'. The '.psq' suffix can also be omitted, e.g. 'SwissProt_TargetAndDecoy.fasta' and will be added automatically. This makes it easy to specify a common TOPPAS input node (using only the FASTA suffix) for many adapters.

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 options that specify the protease specificity (e) are directly taken from OMSSA. A complete list of available proteases can be found by executing omssacl -el.

This wrapper has been tested successfully with OMSSA, version 2.x.

Note
OMSSA search is much faster when the database (.psq files etc.) is accessed locally, rather than over a network share (we measured 10x speed increase in some cases).

The command line parameters of this tool are:

Improvement:
modes to read OMSSA output data and save in idXML format (Andreas)

OpenMS / TOPP release 1.9.0 Documentation generated on Sun Oct 27 2013 01:11:36 using doxygen 1.8.4