OMSSA Advanced Settings

The Open Mass Spectrometry Search Engine (OMSSA) comes with many options for fine tuning the search settings. Note that these settings aim to be used by advanced users only. It is highly recommended to carefully test any changes from the default settings, to document them and report them in any publication/report.

Running OMSSA with the -help option will display all details of the available settings. If you are missing a parameter, please contact the developers.

Spectrum

The Spectrum category groups all settings related to the spectrum preprocessing:

Database

The Database category groups all settings related to the database preprocessing:

Search

The Search category groups all settings related to the search itself:

Iterative Search

The Iterative Search category groups all settings related to the thresholding of the iterative search:

Semi-Enzymatic

The Semi-Enzymatic category groups all settings related to the use of OMSSA in no-enzyme and semi-tryptic searches mode:

Output

The Output category groups all settings related to the file output: