OMSSA Viewer

OMSSA Viewer is a simple, lightweight viewer of OMSSA MS/MS result files (omx files). The input is the omx file itself and (if available) two files containing details about the amino acid modification that was used by OMSSA in the identification process: mods.xml and usermods.xml. Both of these are located in the OMSSA installation directory. If you don't have these files available you will still be able to use OMSSA Viewer, but no modifications will be shown.

After selecting the files, OMSSA Viewer uses the omssa-parser to parse the omx file into an object model that is then used to extract the information to present to the user. OMSSA Viewer has three separate panels: (i) the Spectra Files panel, (ii) the Spectrum panel, and (iii) the Identification panel. The Spectra files panel contains the basic details about each spectrum file: the filename, the precursor m/z and charge, and if it's identified or not. Selecting a row in this table, automatically updates the two other panels, by displaying all the identification for the given spectrum and by displaying the spectrum itself. Clicking on a column header will automatically sort the table on the values in the given column.

For the spectra identified by OMSSA, the ion coverage is shown. Both on the spectra and in the modified sequence column in the identification table. By selecting two peaks in the spectrum panel the distance between the peaks is shown. If this distance has a mass equal to an amino acid the given amino acid is also displayed.

The information in each of the three tables can be exported to tab delimited text files. This is done via the Export menu. It is also possible to export the spectra as individual dta files.

If you want to submit your OMSSA data to the online PRIDE repository check out the PRIDE Converter.

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