LC/MS: Identification of Unknowns by Combining Exact Mass Measurement with the NIST 02 Mass Spectral Database Similarity Search
Electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) tend to produce mass spectra with minimal fragmentation. Positive-ion mass spectra are dominated by protonated molecules and cation attachment, while negative-ion mass spectra usually show molecular anions or ions produced by hydride abstraction. However, by varying the potentials in the atmospheric pressure interface, collision-induced dissociation (CID) can produce mass spectra with extensive fragmentation. This is sometimes referred to as in-source CID. Because the ionization process and ion energies are different for ESI or APCI compared to electron ionization (EI), the fragmentation is often different from the EI mass spectra in common mass spectral databases. Furthermore, the fragmentation pattern can vary depending on in-source CID conditions. This leads one to question whether there is any value to searching an EI mass spectral database for ESI or APCI mass spectra.
The NIST 02 Mass Spectral Search software provides functions for a structure similarity search. This search can be used to search the library for compounds with similar structures based on neutral losses, which is a more suitable method for searching ESI or APCI mass spectra against the library. Compounds that have mass spectra in the library database can often be identified from the search results. The similarity search can provide structural information about compounds that do not have mass spectra in the library by displaying the structures of similar compounds identified by the search.