Tips for Successful GC–MS Tuning and Optimization

Published on: 

LCGC North America

LCGC North America, LCGC North America-10-01-2018, Volume 36, Issue 10
Pages: 782

Proper tuning and calibration of instruments ensure their peak response and an exact mass-to-charge ratio and ion abundance measurement.

In gas chromatography–mass spectrometry (GC–MS), we create radical cations within the ion source, which are then manipulated under the influence of electrostatic fields and introduced into the mass analyzer (typically a quadrupole device, which then uses applied voltages to filter the ions as they pass through the analyzer, according to their mass-to-charge ratio, or m/z). Tuning and calibration ensure optimal instrument response and accurate mass-to-charge ratio and ion abundance measurement across the mass range of the instrument.

Most manufacturers use perfluorotributylamine (PFTBA, also called FC-43 or heptacosafluorotributylamine) for tuning the various elements of the analyzer; the ions typically chosen to tune an instrument have m/z values of 69, 219, and 502, because they cover a reasonable mass range (around half the full mass range for most single-quadrupole instruments) and a wide range of ion and isotopic abundances.

The PFTBA fragment ions used for calibration of the mass axis ensure that ion mass-to-charge ratios are correctly reported, usually to within 0.1 Da (assuming singly charged ions, which is usually the case in GC–MS). It is important to ensure that the mass assignment for the monitored ions matches the manufacturer's specification for mass accuracy.

The same ions are used to optimize the voltages applied to the various elements of the ion source, including the repeller, an element used to accelerate the ions created out of the ion source. Although the autotune routine will set the best average repeller voltage for the three ions, it may be possible for the response of each ion to be "ramped" across the full voltage range to identify the optimum value for the ion closest to the mass of the analytes of interest. There are a range of PFTBA fragment ion masses that can be selected-one does not need to stick to m/z 69, 219, and 502. As the ion source becomes contaminated, the required repeller voltage increases and is a good chronicle of ion source cleanliness; this parameter is a much better indicator of when a source needs to be cleaned than the electron multiplier voltage, which is often used. The other ion source elements (focusing and transport lenses) may also be manually tuned in this fashion to optimize instrument response for masses closest to that of the analyte of interest. It is important to note that after such manual optimization, one needs to check that the absolute and relative ion abundances and isotopic abundances for the standard tune masses still adhere to the manufacturer's specification.

Autotune routines will not only calibrate the mass axis, but also the sensitivity and resolution of the mass analyzer. Although a full treatment of this subject is not possible here (see reference 1 for a more comprehensive explanation), be aware that two voltages are used to control the balance between quadrupole resolution and sensitivity, a common trade-off with quadrupole and other types of mass analyzers. The saddle field within the instrument, which filters on a mass-to-charge basis, is controlled using a DC voltage that controls the offset of each of the quadrupole pairs, while an AC voltage is used to apply a gain function, and in tandem they control the performance of the analyzer and the range of ions that are allowed to pass on a noncollisional trajectory at any moment in time (so-called selected ion monitoring). Further, these voltages can be ramped by the instrument to produce a scan function over a range of mass-to-charge ratios, thus producing a full spectrum in a short space of time.


It is possible to manually alter the offset and gain of the quadrupole to achieve more sensitivity or greater resolution (within the limits of the instrument). Generally, decreasing either the offset or gain will increase the sensitivity of the instrument while reducing the resolution, and vice versa. The gain control has a greater effect on higher masses, whereas the offset affects all masses approximately equally. The manipulation of these parameters is relatively straightforward once you are familiar with the underlying theory, and your instrument manual should explain how to access and use these controls. It is also important to note that when detuning the instrument resolution to gain sensitivity, we lose the ability to detect and filter any interfering masses, which may decrease the accuracy of quantitative analyses.

End users worry about manually tuning mass analyzers, out of concerns about loss of repeatability and standardization compared to the targeted autotune routines. However, if manual tuning brings an improvement in performance, it is possible to save the parameter values to a custom tune file. Using the instrument standard tune as a starting point for any manual tuning is always a good idea.

The recommended frequency of tuning and calibration is debatable, usually relating to the need for regular calibration given the inherent stability of modern instruments. The alternative argument is to tune and calibrate daily (or on the days the instrument is used). It typically takes less than 5 min to complete the tune algorithm and print the report.


1. T. Taylor, "Drive It Like You Stole It-Getting the Most from Your GC Quadrupole MS," The LCGC Blog, February 6, 2017.