Analysis of Data from Different Mass Analyzers

Scott J Cambpell1

1SpectralWorks Ltd, The Heath Business & Technical Park, Runcorn, UK

First Published: PittCon 2004


Mass spectrometer analyzers can be divided into two broad classes, which are scanning and point in time instruments. In scanning instruments, such as a quadrupole or magnetic sector, ions are selected serially and passed to the detector. With point in time instruments, such as time-of-flight and ion traps, packets of ions are sampled at discreet intervals and analyzed. These different approaches of measuring the mass-to-charge ratios have different effects on the reported spectra, especially when the mass spectrometer is connected to a dynamic separation technique such as a gas chromatograph. It is a challenge to data processing software to be able to deal with both types of data.

Figure 1. AnalyzerPro’s method editor

Materials and Methods

Data were acquired in replicate on a three-dimensional ion trap, a quadrupole analyzer and a time-of-flight system, all coupled to gas chromatographs. The temperature program for the chromatograph was optimized for each instrument.

The sample being analysed was 20 g of chrysanthemum tea from China. The sample was extracted overnight in a refrigerator with 200 mL of Hexane. 1 ml of the supernatant was used without further concentration or dilution

 TempRateModeRange (Da)
PolarisQ200 CFull Scan50.0 – 650.0
DSQ200 C1500 Da/sFull Scan35.0 – 550.0
Tempus200 C10 scans/sFull Scan50.0 – 650.0

Figure 2. Example of detected components

Figure 3. Tempus

Results and Discussion

There are differences in the way various types of mass spectrometers work and the spectra they give. These differences can be subtle in some cases and major in others. They occur in various types of mass spectrometer from the same manufacturer and they also occur in the same type of mass spectrometer from different manufacturers.

That is not to say any particular mass spectrometer is right and another is wrong, however this must be kept in mind whilst comparing data from different instruments. Many labs have multiple instruments from multiple vendors, for which they require the data to be compared. Here we are comparing three different types of mass spectrometers from the same vendor. The instruments used where Thermo Electron’s PolarisQ, DSQ and Tempus.

The three files where processed using AnalyzerPro and the processing methods were optimized for the chromatographic conditions. Figure 1 shows the processing method used when analysing the DSQ sample. The number of detected components was comparable between the files. Figure 2 shows an example of the found components detected in the file acquired by the DSQ, 112 components in total were detected. The major components that were found by each instrument were then searched against the NIST02 library and results compared. It was seen that even though there were differences between the spectra it was possible to identify the same components in the extract independent of the instrument that the data was collected on. Figures 3 – 5 displays the sections of the TIC for each file where Benzoic acid- 4-ethoxy-, ethylester was found and the spectra for the component as reported by AnalyzerPro.

Figure 6 shows two of the found components and highlights that the sample extract contained pesticide residue.

Figure 4. PolarisQ

Figure 5. DSQ

Figure 6. Found components with NIST spectra


The results show that all three instrument types generate data that can be analyzed. As long as suitable data processing is undertaken, a similar set of components can be found in each analysis. This is independent of changes in chromatography and signal to noise values for each component between instruments. The use of retention indices enabled the comparison of components run under widely varying chromatographic temperature program, and thus aided analysis of the three data sets. However, it is still a requirement that the chromatographic conditions are suitable for each specific mass analyzer type.