Peter,
You can use VSpec or BASS to process and calibrate spectra.
http://www.astrosurf.com/vdesnoux/download.html
https://uk.groups.yahoo.com/neo/groups/astrobodger/info
The spectrum you show doesn't look correct....sorry.
What set-up are you using, can you explain the spectrograph design you're using?
Over on the astronomical spectroscopy group, in the files area there's a copy of the design spreadsheet - SimSpec which can be used to define and analyse your design.
https://groups.yahoo.com/neo/groups/...troscopy/files