Hi Peter,
The shape of your spectrum looks different from the one in the library because your spectrum is not corrected for the response of your instrument or the absorption of the atmosphere. You can see an example of this for the Star Analyser in the VSpec tutorial lesson 5 here
http://www.astrosurf.com/vdesnoux/tutorial5.html
You can also see the same process in my BAA Workshop presentations
http://www.threehillsobservatory.co.uk/astro/spectroscopy_10.htm
Cheers
Robin