Varian 4000 MS, User Manual

 11 

Scanning Ions to Collect Mass Spectra 

The scanning process for chemical ionization is similar to that for electron 
ionization. After ionization, trapping, and ion preparation steps, ions are scanned 
out to the conversion dynode and electron multiplier. Mass scanning is 
implemented by increasing the RF voltage on the ring electrode; the mass 
spectrum is collected in order from low to high mass over the user-designated 
scan range. In positive modes, electrons are ejected from the conversion 
dynode, held at -10,000 V, and repelled to the electron multiplier. In negative 
mode, positive ions are ejected from the conversion dynode, held at +10,000 V, 
and repelled toward the electron multiplier. The signal is amplified by ~10

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 by the 

electron multiplier and sent through an integrator to collect an intensity for each 
m/z. MS data are stored as sets of ion-intensity pairs for each m/z over the 
acquired mass range. A complete mass spectrum is stored for each analytical 
scan. There is no prescan in internal PCI; the ionization time is calculated based 
on the base peak intensity of the previous scan. Ions are formed for this 
ionization time and the analytical scan is carried out. 

Library Searching 

The 4000 MS has small CI libraries generated using internal configuration ion 
trap GC/MS systems. The libraries are organized by the CI reagent, which 
include methane, methanol, and isobutane. 

Selectivity Considerations 

Type of Matrix 

An advantage of chemical ionization is selectivity. In PCI, hydrocarbons have a 
poor response in methane CI. It is easier to locate target compounds in a sample 
contaminated with hydrocarbons using methane PCI than using EI. Because of 
these selectivity considerations, the time spent to develop a method using the 
different ionization and ion preparation options is well spent.   

Using EI and PCI to Get More Information 

Generating EI and CI data on a single sample gives both the ion-intensity 
fingerprint information allowing library searching as well as the molecular weight 
information to confirm species identification. Fatty acid methyl ester (FAME) 
analysis is an example. Under EI conditions, the FAME fragmentation is 
extensive and molecular ion intensity is weak. Using CI, the molecular weight is 
obvious and the most intense ion is M+1. 

Because the 4000 MS is able to switch between EI and CI in a single run, the 
best analytical conditions can be used for a given compound. 

NOTE: Wait several seconds to switch between EI and CI. The CI segment 
should not be less than 60 seconds wide and the CI peak should be at least 20 
seconds into the segment to allow CI reagent stabilization.