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 before this wrapper can be used. This wrapper has been successfully tested with version 2016.01.2, 2016.01.3 and 2017.01.0beta of 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.

To cite Comet use: Eng, Jimmy K. and Jahan, Tahmina A. and Hoopmann, Michael R., Comet: An open-source MS/MS sequence database search tool PROTEOMICS, 13, 1, 2013, 22–24, 10.1002/pmic.201200439

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: