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MSGFPlusAdapter

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

pot. predecessor tools → MSGFPlusAdapter → 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.
At the time of writing, MS-GF+ can be downloaded from https://github.com/MSGFPlus/msgfplus/releases.

The following MS-GF+ version is required: MS-GF+ 2019/07/03. Older versions will not work properly, giving an error: [Error] Invalid parameter: -maxMissedCleavages.

Input spectra for MS-GF+ have to be centroided; profile spectra will raise an error in the adapter.

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_advanced).

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.

An optional MSGF+ configuration file can be added via '-conf' parameter. See https://github.com/MSGFPlus/msgfplus/blob/master/docs/examples/MSGFPlus_Params.txt for an example and consult the MSGF+ documentation for further details. Parameters specified in the configuration file are ignored by MS-GF+ if they are also specified on the command line. This adapter passes all flags which you can set on the command line, so use the configuration file only for parameters which are not available here (this includes fixed/variable modifications, which are passed on the commandline via -mod <file>). Thus, be very careful that your settings in '-conf' actually take effect (try running again without '-conf' file and test if the results change).

Note
This adapter supports 15N labeling by specifying the 20 AA modifications 'Label:15N(x)' as fixed modifications.

The command line parameters of this tool are:

INI file documentation of this tool: