Best Practice for Identifying Leaks in GC and GC/MS Systems (Part 2)


 Checking GC Connections

Checking all fittings for leaks immediately after installation, maintenance, and periodically while in use is an excellent practice. A handheld electronic detector capable of detecting a helium leak of 0.0005 mL/min in air is available commercially. Handheld leak detectors are particularly useful for finding leaks quickly either inside or outside the GC oven. It is good practice to always use a leak detector to check for leaks each time a column, fitting, or cylinder is changed. An excellent starting point for system troubleshooting is to first check for

potential leaks. Avoid using water soap solutions, as these can be drawn back into the GC flow path, severely impacting chromatographic results even to the point of causing permanent column damage.

Checking a GC/MS for Leaks

A vacuum or ion gauge, if ordered with your instrument, is useful for monitoring vacuum pressures under typical operating conditions in GC/MS. A vacuum gauge is very useful for isolating potential leaks to either the vacuum (MS) or pressurized (GC) side of the instrument. Vacuum readings in the 10–5 or 10–6 Torr range are typical for a system holding vacuum with a flow rate of 1.0 mL/min on a 30 m × 0.25 mm, 0.25 μm GC column. When the MSD is capped and pumped down, vacuum readings typically drop to the 10–6 or 10–7 Torr range in the absence of a leak. If the vacuum pump does not reach these levels relatively quickly, a leak somewhere in the MS is indicated. Make sure the purge vent is closed, the transfer line fitting is installed correctly, and that the large O-ring on the vacuum side plate is positioned correctly.

A software-based performance check of air and water is available in most GC/MS. This check looks at GC/MS ion traces of molecules typically found in air relative to ion 69 found in the calibrant. Ions 18 (water), 28 (N2), 32 (O2), 44 (CO2), and 69 (typical base peak from PFTBA used during auto-tune) are all monitored. Nitrogen (28) levels above 10% relative to the 69 peak indicate that the system has not had sufficient time to pump down or that there is an air leak. An air leak will typically show nitrogen:oxygen in a 4:1 ratio. Water (18) is also typically present, particularly after a system had been vented and exposed to ambient air. An equilibrated leak-free system should show nitrogen (28) well below 10% with oxygen 32 at approximately ¼ of the signal seen for nitrogen, and ideally water (18) lower than the N2 (28) peak.

Troubleshooting leaks in GC/MS is a process of elimination, looking at each site where a leak can occur. A fluorocarbon (for example, 1,1,1,2-tetrafluoroethane, ions 69 and 83) or argon (ion 40) spray can with a plastic tube to direct the flow is very useful in isolating a leak. A short spray at a suspect point and monitoring the appropriate ions in manual tune is a powerful tool for isolation. Key points to check are the transfer line connection in the oven, septum nut, column nut, and the large O-ring on the vacuum plate of the MS. Once a leak has been isolated the leak can be remedied by replacing a septum, resetting a column connection, or cleaning the O-ring on the vacuum plate, and reinstalling it back into the groove on the plate.

Innovations to Minimize Leaks

Figure 2 shows a total-ion chromatogram for an air and water check on a system that is operating normally. In this case, self-tightening column nuts were installed at the transfer line and inlet fittings. These column nuts provide a leak-free seal using a short polyimide/graphite ferrule at both column connections, without the need to retighten the fitting after more than 300 heat cycles. Use of these column nuts eliminates the need to retighten the inlet or mass spec transfer-line connections after oven heat cycling. Furthermore, because very low torque is needed to make a leak-free seal when using the self-tightening column nuts, these nuts are installed using only fingers, not wrenches, which eliminates the risk of over tightening and damage to the fittings (see Figure 3)

                                                                                                                                                                                               Figure 3. Agilent self-tightening column

     Figure 2. Example air and water check                                             nuts installed at the transfer line and inlet fittings.


By using tools, supplies and best practices that provide a leak-free GC or GC/MS, analysts can improve performance and productivity of their system. Agilent UltiMetal Plus Flexible Metal ferrules provide robust leak-free column connections, along with an inert surface for fittings in the sample flow path. The Agilent innovative self-tightening column nuts using standard short polyimide/graphite ferrules eliminate the need to retighten GC column fittings, including the mass spec transfer line, after repeated heat cycling. These new fittings also have the advantage of using only short polyimide/graphite ferrules for inlet, detector, and

mass-transfer-line connections. Following the best practices described in this technical overview and accessing the references below will help GC and GC/MS users identify potential air leaks, where to find them, and how to fix and prevent them quickly. One rule of thumb is to adjust fittings, septa, and O-ring seals to be JTE

for the best results



Best Practice for Identifying Leaks in GC and GCMS:  Technical Note, Agilent Technologies


Written by Muyiwa Adebola

[email protected],

07084594001, 07084594004