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MascotAdapterOnline

Identifies peptides in MS/MS spectra via Mascot.

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

This wrapper application generates peptide identifications for MS/MS spectra using the search engine Mascot. It communicates with the Mascot server over the network (i.e. it does not have to run on the server itself).

The adapter supports Mascot security features as well as proxy connections. Mascot versions 2.2.x up to 2.4.1 are supported and have been successfully tested (to varying degrees).

Bug:
Running the adapter on Mascot 2.4 (possibly also other versions) produces the following error messages, which should be ignored:
MascotRemoteQuery: An error occurred (requestId=11): Request aborted (QT Error Code: 7)
MascotRemoteQuery: An error occurred (requestId=12): Request aborted (QT Error Code: 7)
Note
Some Mascot server instances seem to fail without reporting back an error message. In such cases, try to run the search on another Mascot server or change/validate the search parameters (e.g. using modifications that are known to Mascot and can thus be set in the INI file, but which are unknown to Mascot, might pose a problem).
Mascot returns incomplete/incorrect protein assignments for most identified peptides (due to protein-level grouping/filtering). Thus, the protein associations are therefore not included in the output of this adapter, only the peptide sequences. PeptideIndexer should be run after this tool to get correct assignments.
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:

For the parameters of the algorithm section see the algorithms documentation:
Mascot_server
Mascot_parameters