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MascotAdapter

Identifies peptides in MS/MS spectra via Mascot.

pot. predecessor tools → MascotAdapter → pot. successor tools
any signal-/preprocessing tool
(in mzML format)
IDFilter or
any protein/peptide processing tool

This wrapper application serves for getting peptide identifications for MS/MS spectra. It uses a local installation of the Mascot server to generate the identifications. A second wrapper (MascotAdapterOnline) is available which is able to perform identifications by communicating with a Mascot server over the network. So, it is not necessary to execute MascotAdapterOnline on the same machine as Mascot.

The minimal version of Mascot supported with this server is 2.1.

This wrapper can be executed in three different modes:

  1. The whole process of ProteinIdentification via Mascot is executed. Inputfile is a mzData file containing the MS/MS spectra for which the identifications are to be found. The results are written as a idXML output file. This mode is selected by default.

  2. Only the first part of the ProteinIdentification process is performed. This means that the MS/MS data is transformed into Mascot Generic Format (mgf) which can be used directly with Mascot. Being in the cgi directory of the Mascot directory calling a Mascot process should look like the following:

    ./nph-mascot.exe 1 -commandline -f outputfilename < inputfilename

    Consult your Mascot reference manual for further details.

    This mode is selected by the -mascot_in option in the command line.

  3. Only the second part of the ProteinIdentification process is performed. This means that the outputfile of the Mascot server is translated into idXML.

    This mode is selected by the -mascot_out option in the command line.


If your Mascot server is installed on the same computer as the TOPP applications the MascotAdapter can be executed in mode 1. Otherwise the Mascot engine has to be executed manually assisted by mode 2 and mode 3. The ProteinIdentification steps then look like:

  • execute MascotAdapter in mode 2
    ./MascotAdapter -in mzDataFile -out mascotGenericFormatFile -mascot_in
  • copy mascotGenericFormatFile to your Mascot server
  • call your Mascot server process:
    ./nph-mascot.exe 1 -commandline -f mascotOutFile < mascotGenericFormatFile
  • call the script to export your outfile in mascot xml
    ./export_dat.pl do_export=1 export_format=XML file=mascotOutFile _sigthreshold=0
    _showsubset=1 show_same_sets=1 show_unassigned=0 prot_score=0 pep_exp_z=0 pep_score=0
    pep_homol=0 pep_ident=0 pep_seq=1 show_header=1 show_queries=1 pep_rank=0 > mascotXMLFile
  • copy mascotXMLFile to the server on which the TOPP applications are installed
  • execute MascotAdapter in mode 3
    ./MascotAdapter -in mascotXMLFile -out IdXMLFile -mascot_out

For mode 1 you have to specify the directory in which the Mascot server is installed. This is done by setting the option mascot_dir in the ini file. Furthermore you have to specify a folder in which the user has write permissions. This is done by setting the option temp_data_directory in the ini file. Two temporary files will be created in this directory during execution but deleted at the end of execution.

Note
Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

INI file documentation of this tool:

You can specify the Mascot parameters precursor_mass_tolerance (the peptide mass tolerance), peak_mass_tolerance (the MS/MS tolerance), taxonomy (restriction to a certain subset of the database), modifications, variable_modifications, charges (the possible charge variants), db (database where the peptides are searched in), hits (number of hits), cleavage (the cleavage enzyme), missed_cleavages (number of missed cleavages) and mass_type (Monoisotopic or Average) via the ini file.


Known problems with Mascot server execution:

  • getting error message: "FATAL_ERROR: M00327 The ms-monitor daemon/service is not running, please start it."

  • Possible explanations:
    • Your ms-monitor is really not running => consult your Mascot reference manual for details about starting the Mascot server.
    • (Suppose you have Mascot installed in directory mascot.) mascot/data/mascot.control is not writable for the current user. This has to be changed. Otherwise you will not be able to use the Mascot server via the shell and receive the above error message.
      => Change write permissions of the file mascot/data/mascot.control such that the current user has write permissions to it.
Todo
This adapter is using antiquated internal methods and needs to be updated! E.g. use MascotGenericFile.h instead of MascotInfile.h....