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Agilent GC-MS Maintenance: Restek’s Quick Reference Guide

  • Replacement parts for Agilent ion sources now available.
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  • Restock your ion source cleaning supplies to keep your instrument up and running.

You have your GC-MS method, your samples, and a deadline. You need your instrument to operate properly so you can collect the data you need to get your job done. However, we all know that into every lab a little instrument maintenance must fall. Be prepared so that you can get your mass spectrometer back in the game quickly by having all the necessary GC-MS supplies on hand for when the time comes to service your instrument.

Whether you’re performing routine maintenance on your ion source, replacing a used-up filament or aging electron multiplier, or keeping your rough pump humming away, Restek has you covered. Let us help you maintain—and even enhance—the performance of your instrument with our line of routine GC-MS maintenance and replacement parts for Agilent mass spectrometers.

Preventing Detector-Related Problems

The GC-MS Interface

Even though the parts associated with the interface between the gas chromatograph and the mass spectrometer are simple in nature, they can be the source of the trouble when poor GC-MS performance is observed.

Making sure the GC column is correctly installed in the mass spectrometer is a critical first step in preventing analytical problems. A leak or improper installation distance can decrease sensitivity, introduce peak tailing, or even prevent your instrument from operating at all, so take care to tighten connections carefully and be sure to set the correct installation distance.

MSD Source Nut & Ferrules

Tightening the brass MSD source nut seems simple enough, but care must be taken to ensure it is not damaged as a result of overtightening or cross threading, both of which can cause leaks at this connection. In cases of severe damage, brass filings can even be introduced into the mass spectrometer’s vacuum chamber.

What makes this point of connection so susceptible to damage is the force necessary to create a seal between the column and the graphite/Vespel ferrules that are used at the interface. Using graphite/Vespel blended ferrules solves the problem of pure graphite’s semipermeability to air and avoids the risk of soft graphite fragments getting into the MS source. However, because they are not as soft as graphite alone, they require more force to create the seal, which leads to a greater risk of overtightening.

The graphite/Vespel ferrule will also shrink a little after the initial heating and cooling cycles, so be sure to snug the fitting back up to prevent a leak from developing. Once you retighten the nut, the connection shouldn’t require further adjustment.

In cases where the transfer line threads have been damaged, proper GC-MS maintenance requires an additional step: first use Restek’s rethreading tool to help repair the damage before installing another source nut.

Column Installation Gauge

For certain Agilent mass spectrometers, an installation gauge may be a useful tool for installing the column at the correct installation distance. However, take care to make sure you have properly seated the relatively hard graphite/Vespel ferrule on the column so it doesn’t slip while you’re installing the column into the MS.

The column installation gauge is not compatible with all Agilent MS source types, so be certain to check instrument compatibility information before purchasing. The gauge can be used with a 5973 MS, a 5975 MS with a chemical ionization (CI) source, and a 5977 MS with the extractor or high-efficiency sources. Do not use the installation gauge on a 5975/5977 MS with an electron ionization (EI) source (inert or SS) because it will result in the column extending too far into the ion source.

The Vacuum

When you marry a technique such as gas chromatography, which operates under pressure, with mass spectrometry, which operates under vacuum, you’d better have some hardworking pumps to evacuate the GC gas out of your mass spectrometer!

Typically, mass spectrometers have two types of pumps: a rough pump to start the evacuation process and a high-vacuum pump to further lower the pressure inside the mass spectrometer to the point where an ion can fly from the ion source through the mass analyzer (e.g., quadrupole) to the detector (electron multiplier) without encountering any molecules floating around inside the mass spectrometer.

There is very little service that an end user will normally perform with either pump type, but replacing the pump oil is one activity that everyone with a mechanical rough pump that requires oil (e.g., rotary vane pumps) should have on a preventative maintenance schedule. Ensuring that the proper amount of clean oil is in your pump will help make sure your mass spectrometer can reach and maintain the appropriate vacuum.

It is generally recommended that rough pump oil be replaced once every six to 12 months. Restek offers two replacement pump oil types and, while both will work, we recommend using Inland 45: it produces less vapor pressure and achieves a better vacuum with less risk of oil backstreaming into the mass spectrometer.

The Ion Source

The power of mass spectrometry relies on the creation of ions. Turning a neutral species into a charged one places it at the mercy of electric and magnetic fields that can push and pull the ion along predetermined flight paths and ultimately separate ions from each other based on their masses and charges. As compounds elute from the gas chromatography column, their first stop is the ion source, where some of those molecules will become ions. That process is inherently inefficient, so make sure your source is clean and optimized to make the most of the ionization process and to give your analysis the best sensitivity possible.

Ion Source Cleaning

With use, any ion source will gradually become dirty and require cleaning. Dirty sources could result in lower ionization efficiencies, which could manifest as a decrease in sensitivity or an increase in the voltage applied to the electron multiplier (fewer ions arriving at the electron multiplier means it has to work harder to boost the signal).

However, by following the manufacturer’s instructions for your particular model of mass spectrometer, most ion source parts can be removed and cleaned. This is typically accomplished through the use of some abrasive material, typically a slurry of aluminum oxide and reagent-grade methanol. To avoid creating a long-lasting source of contamination after you’ve taken the care to clean the ion source parts, be sure to handle all MS parts with clean, lint-free gloves. Finger oils can become persistent sources of background contamination if you touch the parts with bare hands.

To simplify maintenance, Restek offers a complete line of GC-MS supplies, from a start-up mass spec kit with everything you need to individual replacement consumables for when you start to run low. It’s important to note that the Dremel tool provided in one of Restek’s kits is a small battery-powered tool, not a full-power Dremel tool. Using a particularly powerful Dremel could rapidly wear and ruin the stainless steel parts.

Ion Source Consumables


The most commonly replaced ion source parts are the filaments, which will wear out over time, deforming to the point that ionization efficiency drops and the instrument has difficulty tuning. Restek offers replacement filaments that are compatible with most models of Agilent mass spectrometers.

Electron Multipliers

Well beyond the ion source, at the other end of the mass analyzer, is the electron multiplier (EM). Often boosting the small signal that makes it through the ionization and analysis stages in mass spectrometry by 100,000 times or more, the EM plays a critical role in the successful operation of your instrument. Even though their lifetime is comparatively long for a consumable part, eventually you will need to replace the electron multiplier.

The lifetime of the EM is typically monitored by the voltage that is applied to it, with higher and higher voltages being an indication that the EM is having to work harder and harder to provide the necessary sensitivity. It is possible that elevated EM voltages could be due to poor ionization, but if you’ve ruled that out, it might just be time for GC-MS maintenance to install a new EM.

The surfaces of the EM that produce the ever-increasing cascade of electrons are called dynodes, and electron multipliers commonly fall into one of two categories: continuous dynode or discrete dynode. Simply speaking, a continuous dynode EM is one where there is only one dynode which has a surface, commonly shaped like a curved horn that is coated with a material that will generate a cascade of secondary electron emissions after the initial charged particle strikes the surface. In contrast, discrete dynode designs often have as many as 24 distinct surfaces, focusing secondary electrons generated at one dynode to the next. These designs offer increased ion detection efficiency as well as longer lifetimes.

Restek offers a number of discrete dynode electron multipliers that work for a variety of models of Agilent mass spectrometers.

One-Stop Shopping for Your Agilent GC-MS Maintenance Needs

Whether you need GC-MS supplies for your gas chromatograph or for your mass spectrometer, Restek has you covered with an extensive offering of products for both.