The Thermo GC Orbitrap is a very powerful tool for the identification of unknowns easily switching from EI to CI modes. However, one must be aware of the differences in the EI spectra obtained with the Orbitrap compared to standard quadrupole and magnetic spectra found in commercial and user libraries.
The following links shed some insight into those differences from a mechanistic point of view.
Study Comparing 480 Spectra by Eastman for EI
Literature Reference for EI
Two Other Literature References
Literature Reference for Tandem
Thermo and Personal User’s Libraries:
Thermo has and on-going effort to create a database of EI GC-Orbitrap spectra. Release Version 1.0 contains 766 spectra. They are spectra of contaminants related to PCB’s, environmental contaminants, and pesticides.
A user should also consider adding spectra to their personal NIST library noting the origin of the spectrum. I believe that in 70-80% of the cases the hit will be lower (700-800 fit). If no other spectrum from a standard quadrupole is present, the user will still find the EI orbitrap spectrum at the top of the list. Smaller MW compounds and TMS derivatives might be more confusing yielding much lower hits.
I try to keep the most current manuals for AMDIS and NIST MS Search as they are updated. Sometimes they could appear here before actually updated on NIST site. Makes it convenient for keeping my links in presentations current. See the links below:
A "Little" Mass Spec and Sailing 