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.