OpenMS
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CometAdapter

Identifies peptides in MS/MS spectra via Comet.

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

Comet must be installed/downloaded before this wrapper can be used. OpenMS installers ship with Comet.

Warning
We recommend to use Comet 2019.01 rev. 5 or later, due to a serious "empty result" bug in earlier versions (which occurs frequently on Windows; Linux seems not/less affected).

Comet settings not exposed by this adapter can be directly adjusted using a param file, which can be generated using comet -p. By default, All (!) parameters available explicitly via this param file will take precedence over the wrapper parameters.

Parameter names have been changed to match names found in other search engine adapters, however some are Comet specific. For a detailed description of all available parameters check the Comet documentation at http://comet-ms.sourceforge.net/parameters/parameters_201601/ The default parameters are set for a high resolution instrument.

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: