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Gas Chromatography/
​Mass Spectrometry Fundamentals

Frequently asked questions

What’s the difference between electron ionization and chemical ionization?

Electron ionization (EI) operates in a high vacuum with a relatively high (70 eV) ionization energy. It is often referred to as a “hard” ionization technique, because spectra are characterized by extensive fragmentation and low levels of molecular ion abundance. The advantages of EI include repeatable spectral data and the availability of extensive spectral libraries. For example, the NIST EI library contains over 300,000 unique compounds, making EI an excellent choice for compound identification.

Chemical ionization (CI) adds a reagent gas, like methane or ammonia, to the GC/MS source. Reagent gas molecules are ionized in the CI source and form ions that react with the analyte molecules in the source. Traditionally CI has been called a “soft” ionization technique, because its lower ionization energy results in less ion fragmentation than with EI. It also generally (but not always) retains the molecular mass as M+1 for positive CI and M-1 for negative CI. Also, CI sometime generates aducts, such as M+C2H5 (C2H5=29) and M+C3H5 (C3H5=41). An alternative to CI is low energy EI, available on the Agilent 7250 GC/Q-TOF. This software-controlled capability makes it easier to preserve molecular ions for identification.

More than 90% of GC systems run EI for more than 90% of their operating life. Although CI is less commonly used, some CI techniques do give improved results over EI.

What other ion sources are available for gas chromatography/mass spectrometry instruments?

Agilent offers several source types and lens diameters to maximize performance for different applications.

  • Our HydroInert source improves chromatographic efficiencies and spectral fidelity with hydrogen carrier gas.
  • The patented Agilent JetClean self-cleaning ion source greatly reduces—or eliminates—the need for source cleaning on Agilent single and triple quadrupole GC/MS systems. See it in action.

What’s the difference between GC/MS and GC/MS/MS?

GC/MS/MS refers to highly selective operational modes where more than one fragmentation and filtering step is performed, as with multiple reaction monitoring (MRM) on a GC/TQ. A mass filter is applied to the first quadrupole, further fragmentation occurs in the collision cell, and another mass filter is applied to the second quadrupole.

How does a library identify spectral data collected from a GC/MS?

After background subtraction, the newly obtained mass spectrum of an unknown compound is compared against a library of spectra from known compounds in a database. An algorithm is employed to match the mass-to-charge ratios and their relative abundances between the new and database spectra, creating a match score. Common spectral libraries include NIST, Wiley, and Maurer/Pfleger/Weber, which contain spectra for hundreds of thousands of different chemicals. You can also explore the Agilent collection of spectral libraries.

This figure shows an overlay of the analytical spectrum (upper) over the inverted library spectrum (lower). Depending on how the search is performed (Search Index – SI vs Reverse Search Index – RSI) the matching score and ion ratios can be different. RSI is typically recommended.

How do I quantitate a particular analyte in the sample?

First, calibrate the mass spectrometer by introducing the analyte in question at several known concentrations. Your data system will create a calibration curve by plotting these nominal concentrations against the abundance of the response at each concentration. You can then compare the abundance of the analyte in your newly acquired data against this calibration curve.

Do GC/MS responses scale linearly with concentration?

Most molecules measured by single or triple quadrupole GC/MS have linear regions in their response curve. As you get closer to the detection limit, the response becomes less linear, and drops further as you approach detector saturation. Generally, there can be three to four orders of linear range between extremes, but higher results are possible.

How do elements with multiple isotopes affect a GC/MS detector?

A molecule generates a spectrum. As mass numbers change between isotopic ions (such as C12 and C13), the corresponding molecular mass will change, and the MS analyzer will detect that change. The corresponding mass spectrum or spectra will reflect this difference in mass intensity, based on abundance.

A GC/MS instrument is sensitive enough to notice the difference between ions made from different isotopes of the same element. The presence of isotopes can often be used as a tool to selectively identify different compounds, especially for data collected on a GC/Q-TOF.

The GC/Q-TOF exhibits high mass accuracy and reliable data. In this example the red outer line represents the theoretical Isotopic response/ratio for the compound, and the inner black line represents the calculated ion and isotopic ratio. As you can see, the intensity of the calculated ions are within 90% of the theoretical ions.

How can I verify that my GC/MS is working properly?

First, perform an instrument autotune to adjust the electronic setpoints of the ion source and quadrupole in your GC/MS system for optimal performance. Then, run some known samples and compare their spectra to the spectra of known standards. Check tunes can be performed periodically to check the tune against expected performance.

How do I maintain good performance on my GC/MS?

You can prevent a significant amount of unplanned instrument downtime by following GC/MS best practices. Get tips on sample preparation and screening—and learn about features like the Agilent JetClean self-cleaning ion source and backflush—that keep your GC/MS in peak operating condition.

Does mass spectrometry destroy the sample?

Yes, because it exposes the sample to ionization. The good news is that only a small volume of material is needed—typically as little as 1 µL. Modern GC/MS instruments are routinely used to detect concentrations down to the parts-per-billion (ppb) level. Additionally, you can use a Capillary Flow Device to split the sample for simultaneous analysis by other GC detectors, if desired.

What is high-resolution GC/MS?

A high-resolution GC/MS is a GC system coupled to a mass spectrometer with high-resolution capability. An example is a GC/Q-TOF with a quadrupole time-of-flight detector that delivers full-spectrum, high-resolution, accurate mass data (HRAM) with a wide dynamic range.

High-resolution GC/Q-TOF enables accurate mass screening by GC/MS and enhanced compound identification through MS/MS, low-energy electron ionization, and complimentary chemical ionization techniques.

This data shows the mirror image of the analytical spectrum to the library spectrum. The analytical spectrum is high resolution with 4 decimal points obtained from the GC/Q-TOF. The library spectrum is a unit mass spectrum from NIST. As you can see, the spectrum generated by the GC/Q-TOF matches the spectrum from the NIST library with a high confidence score. Although we recommend a high resolution accurate mass library be used for high resolution data, the NIST library data base—which is very extensive—can also be used with high confidence.