Electron Impact or Chemical Ionization for Mass Spectrometry

The QTOF‐GCMS instrument integrates the excellent mass accuracy of the quadrupole time‐of‐flight (QTOF) mass spectrometer with the proven gas phase chromatography techniques. 1 Da (mass accuracy in the 0.2‐3% range) is the typical mass resolution of a quadrupole mass spectrometer. The QTOF mass spectrometer usually exhibits mass accuracy in the range of 1‐5 ppm.

An electron impact (EI) or a chemical ionization (CI) ion source can be used to operate the mass spectrometer. Electron impact ionization delivers the highest energy to the analytes leading to ‘hard’ ionization and causes a large amount of molecular fragmentation. The fragments observed are usually compared to a mass spectral database for analyte identification. The absence of molecular ion (ion representing the charged analyte) in the EI spectra is quite common, and therefore it would be difficult to identify an analyte for which a database spectrum is unavailable.

Chemical ionization delivers less energy to the analytes and as a result causes less molecular fragmentation. During the analytical run, a reagent gas (usually ammonia, methane, or isobutene) is introduced into the ion source when analyzing an analyte with CI. The electrons which are emitted from the source filament ionize the reagent gas first, and these ions then interact with the analyte molecules to form ions. Compared to EI, this technique provides less energy resulting in “soft” ionization. Mass spectra acquired from a CI source generally contain the molecular ion. This boosts confidence in identification and assignment of the molecular ion, which is crucial in the analysis of unknowns. Individual components in complex matrices can also be identified using chemical ionization. However, in complex samples, all the individual components observed can be difficult to resolve chromatographically. In such situations, co‐eluting peaks can be deconvoluted using CI.

One particular case where analysis by CI can be extremely useful is Extractable and Leachable analyzes. Particularly in the food packaging and medical device industries, it is important to understand the chemicals that can be discharged by a particular component during use. These extracts often contain a wide range of chemical compounds such as polymer degradants, polymeric additives, oligomers and contaminants.

A large number of chemical compounds are often present in the prepared extracts, but many of these may not be present in mass spectral databases. In such cases, structural elucidation of these compounds can be realized through the collection of CI mass spectral data. Moreover, these extracts are often complex and may show co‐eluting compounds. In these cases, CI is very useful in deconvoluting individual compounds.

As an example, shown below is the analysis of mineral oil where the QTOF‐GCMS results are compared using both the CI and EI sources. It also demonstrates the power of the QTOF mass spectrometer when combined with the GCMS.


Figure 1 shows a chromatogram collected from a sample containing a mineral oil using a CI source. The broad peak observed (21 to 30 minutes retention time) represents a wide range of branched and linear alkenes and alkanes. Extracted ion chromatograms of a series of alkenes are included in the lower pane figure. These extracted ion chromatograms demonstrate the ability of QTOF‐GCMS to detect individual components even in the presence of various coeluting compounds.

QTOF‐GCMS chromatograms

Figure 1. QTOF‐GCMS chromatograms collected using CI from analysis of a solution containing a mineral oil.

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Shown in Figure 2 is a similar overlay for the extracted ion and total ion chromatograms from the analyzed solution using both EI and CI EI modes. The most obvious difference was observed in the extracted ion chromatograms. The chromatogram collected in EI mode displays a number of peaks and a broad background signal, whereas the chromatogram collected through CI mode displays a single sharp peak near 22 minutes retention time.

The most powerful signal observed in EI is seen near 23 minutes. Comparison of this retention time against the retention time noted using the CI source, and also the general shape of the chromatogram, indicates that the peaks present in the EI chromatogram represent the fragment ions of later eluting, higher molecular weight compounds. In addition, the hard ionization that occurs in the EI source causes these larger molecules to fragment and form ions which possess a mass similar to the compound of interest.

The more gentle ionization in the CI mode, on the other hand, does not form these fragment ions and provides a cleaner background in the mass range of interest. When the total ion chromatograms were compared, they also showed slightly different shapes. The CI chromatogram specifically tends to have several additional sharp peaks that protrude from the main broad peak. In comparison, the EI chromatograms show a relatively smooth broad peak.

Total Ion and extracted ion chromatograms

Figure 2. Total Ion and extracted ion chromatograms collected using both CI and EI modes from a solution containing a mineral oil.

Table 1. Summary of MFG Results.

RT m/z Best Match Score Diff. (ppm)
22.0 407.4644 C29 H58 77.08 ‐7.6
22.5 421.4789 C30 H60 87.12 ‐5.23
22.9 435.4948 C31 H62 82.77 ‐5.17
23.4 449.5114 C32 H64 74.1 ‐7.37


While CI ionization can be carried out on conventional single‐quadrupole mass spectrometers, these spectrometers do not have the exceptional mass resolution achieved by the QTOF mass spectrometer. In Figure 3, the data collected from the mineral oil sample is used to demonstrate this benefit of the QTOF mass spectrometer. When extracting the molecular ion for the C29H58 compound at a typical resolution for a single‐quadrupole mass spectrometer (±0.5 Da, blue chromatogram), a relatively strong background signal is observed that interferes with the target compound. When the mass window for extraction is decreased to leverage the QTOF mass accuracy (±10 ppm, red chromatogram), this interference is mostly removed and a single sharp peak is noted.

Overlay of Extracted Ion Chromatograms

Figure 3. Overlay of Extracted Ion Chromatograms for the compound identified as C29H58.

Jordi Labs

This information has been sourced, reviewed and adapted from materials provided by Jordi Labs.

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