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MascotAdapterOnline

Identifies peptides in MS/MS spectra via Mascot.

pot. predecessor tools $ \longrightarrow $ MascotAdapterOnline $ \longrightarrow $ 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 communicates with the Mascot server over the network and is not needed to be called from same machine.

It support Mascot security features and has also proxy server support. This minimal version of Mascot support by this wrapper is version 2.2.x. Mascot 2.3 works as well, but has not been tested extensively.

Note
Some Mascot server instances seem to fail without reporting back an error message. Thus, try to run the search on another Mascot server or change/validate search parameters (e.g., using modifications in the INI file, which are unknown to Mascot, but known to OpenMS might be a problem).
Be aware that Mascot returns incomplete/incorrect protein assignments for most identified peptides (why ever that is). Thus we do not forward any protein assignments, only peptide sequences. You should run PeptideIndexer after this tool to get correct assignments. You can use the flag 'keep_protein_links' to override this behavior.

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


OpenMS / TOPP release 1.11.1 Documentation generated on Mon Dec 23 2013 22:47:51 using doxygen 1.8.5