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MSGFPlusAdapter

Adapter for the MS-GF+ protein identification (database search) engine.

pot. predecessor tools $ \longrightarrow $ MSGFPlusAdapter $ \longrightarrow $ pot. successor tools
PeakPickerHiRes
(or another centroiding tool)
IDFilter or
any protein/peptide processing tool

MS-GF+ must be installed before this wrapper can be used. Please make sure that Java and MS-GF+ are working.
The following MS-GF+ version is required: MS-GF+ Beta (v10089) (7/31/2014). At the time of writing, it could be downloaded from http://omics.pnl.gov/software/ms-gf. Older versions will not work properly.

Input spectra for MS-GF+ have to be centroided; profile spectra are ignored.

The first time MS-GF+ is applied to a database (FASTA file), it will index the file contents and generate a number of auxiliary files in the same directory as the database (e.g. for "db.fasta": "db.canno", "db.cnlap", "db.csarr" and "db.cseq" will be generated). It is advisable to keep these files for future MS-GF+ searches, to save the indexing step.

Note
When a new database is used for the first time, make sure to run only one MS-GF+ search against it! Otherwise one process will start the indexing and the others will crash due to incomplete index files. After a database has been indexed, multiple MS-GF+ processes can use it in parallel.

This adapter supports relative database filenames, which (when not found in the current working directory) are looked up in the directories specified by 'OpenMS.ini:id_db_dir' (see TOPP for Advanced Users).

The adapter works in three steps to generate an idXML file: First MS-GF+ is run on the input MS data and the sequence database, producing an mzIdentML (.mzid) output file containing the search results. This file is then converted to a text file (.tsv) using MS-GF+' "MzIDToTsv" tool. Finally, the .tsv file is parsed and a result in idXML format is generated.

The command line parameters of this tool are:

INI file documentation of this tool:


OpenMS / TOPP release 2.0.0 Documentation generated on Thu Jul 28 2016 00:37:34 using doxygen 1.8.11