Avoiding downtime in the lab: top tips for GC/MS success

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GCMS success

Efficient laboratories manage their workloads by avoiding downtime, navigating bottlenecks, and creating solutions to the challenges that regularly drain time. A GC/MS lab is no different, and many have repeatable and avoidable challenges that could be prevented by following best practice.


Practical, hands-on troubleshooting tips for GC/MS help reduce unplanned downtime and improve confidence in your results. Some key steps to follow for GC/MS success include looking for leaks, routine tuning, and improving detection limits.


Looking for leaks

Leaks should be located ahead of time. Although it may be tedious, it is worthwhile because lingering leaks can allow nitrogen and oxygen to permeate the GC/MS system. The most efficient way is to use a highly sensitive leak detector to quickly identify leaks. In a pinch, an electronics duster can be also used.


Fortunately, there are many ways to pro-actively prevent leaks. Here are some of our top tips:


The analyzer side plate
Tip 1: Stop engaging side plate thumbscrews. They are there to prevent damage during shipment. Over-tightening these thumbscrews can damage the side-plate – preventing the formation of a good seal – or even generate metal shavings that damage the vacuum system.

Tip 2: The O-ring can be inadvertently dislodged upon opening. Any kinks or bumps in the O-ring can disrupt seal integrity. It’s a good idea to develop a habit of visually or physically inspecting seal integrity before closing the analyzer door.

Tip 3: Lint and dust can be problematic if the mass spectrometer is in a confined space or not properly ventilated. Dust can accumulate beneath the covers or adhere to surfaces on the mass spectrometer, such as on the O-ring or fans – and impact performance as a result. It’s important to assess the location of the MS to ensure appropriate ventilation and cleanliness.


The vent valve
Tip 4: It is possible either forget to tighten the vent valve or to overtighten it. If this happens, the vent valve O-ring can be compressed which prevents a leak-free seal formation. Immediately after venting, make sure to gently retighten the vent valve before carrying out maintenance.

The transfer line interface
Tip 5: Consistently over-tightening the mass spectrometry column nut will eventually damage the transfer line threads and prevent formation of a leak-free seal. If the transfer line threads become stripped, the interface will need to be replaced by a service engineer, resulting in costly downtime. To prevent, avoid over-tightening and consider self tightening column nuts

Tip 6: The ferrules should be correctly oriented and of appropriate material and size. Incorrect material or size, improper orientation, or re-use of ferrules can all cause leaks. Vespel/graphite ferrules are recommended for use with a mass spectrometer. Graphite-only ferrules are too malleable, and their tendency to crumble renders them inappropriate for use with GC/MS.


Routine tuning

Routine tuning and careful evaluation of tune reports for indicators of future maintenance can contribute to the success of the GC/MS lab. The routine tune report you’re already running provides a wealth of diagnostic information that can be used to monitor your mass spectrometer’s health. Accurate interpretation enables the lab to identify the need for maintenance pro-actively and to consequently avoid unplanned downtime.

Tips for maximizing your tuning reports include:

a) Tune routinely – ideally at least once a week to allow for detailed comparisons to be made over time.
b) Always tune before or after changes to the GC/MS to provide a reference point if anything goes wrong.
c) Create a maintenance method and pair it with a tune file that automatically programs cooler temperature zones, and load it before venting the MS. Alternatively, schedule it at the end of a sequence for convenient cool-down.
d) Monitor tune reports over time for signs of a dirty source. Jagged ion peaks, consistently low tune ion abundances, improper isotopic ratios, and sudden spikes in electron multiplier voltage are all indicators that the ion source will soon require cleaning.


Improving detection limits

Another major impact on time in the lab is dealing with poor sensitivity.  Achieving trace detection limits and proper identification of unknowns depends on generating high-quality spectra.  Identify sources of noise and implement techniques for increasing signal to improve mass spectral quality.


Our tips include:

1. Stop the bleeding: reduce column bleed by choosing the right columns and consumables (inert columns and liners). Ensure that your column is not exposed to oxygen: it irreversibly damages the column’s stationary phase. Maintain the carrier gas flow and cap the column when it’s not in use.

2. Take care of your consumables: the use of poor quality consumables or misuse of consumables can be detrimental to sensitivity. It is important to not overtighten the septum nut and to choose high-quality vials and caps.

3. Eliminate oxygen in the carrier gas: its presence is harmful to the GC/MS, resulting in damage to the column, impaired electron multiplier function, and several other symptoms, which lead to excessive maintenance. The use of UHP carrier gases combined with high-quality gas filters is recommended.

The Agilent checklist for GC/MS success includes:

1. Prevent and quickly identify leaks and minimize their recurrence.
2. Read a tune report like a pro to help prevent unplanned downtime.
3. Identify sources of mass spectral background and noise.
4. Optimize GC/MS conditions for superior spectral quality.


Click here for more insight into solving your GC/MS challenges, or watch our helpful on-demand webinar.


Keywords: GCMS success; tips for GCMS; time-saving tips for GCMS; Optimizing GCMS; lab best practice

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