We routinely use both EI and CID (MS/MS) libraries to identify unknowns using the NIST MS Search. The libraries employed include purchased commercial libraries and our in-house created libraries. We do both spectral searches to identify compounds and structure searches to find model compounds. Even if the component of interest is not in the library, spectral search results give valuable insight into substructural groups present in the structure of the unknown!
We can obtain nominal mass CID (collision induced dissociation), accurate mass CID (TOF), in-source CID (quad and TOF), and tandem CID spectra (QTOF, triple quad). Below is an accurate mass QTOF spectrum obtained on our Agilent 6500 QTOF.
The following post on my web page details information on creating and using in-house MS/MS (Tandem) Libraries:
A "Little" Mass Spec and Sailing 
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