We’ve all been there. We prepare a batch of samples to analyze, prime our systems, warm up the detector, and within 2-3 injections we receive an error message stating that an integral component has failed for one reason or another. This can be a dreadful experience, especially for a routine production laboratory. 

    While basic troubleshooting can resolve many issues commonly encountered with mass analyzers (specifically, LC-MS/MS systems), more serious problems can require a visit from your local service engineer, ultimately resulting in a period of instrument downtime.   However, as the old adage goes, “an ounce of prevention is worth a pound of cure,” the same can be said for LC-MS/MS operation.

    At first glance, the simplest source of system-fouling contaminants might be the samples themselves. When analyzing biological samples from any matrix, sample preparation is a must!  Some may choose to go the cheapest and dirtiest route with a simple dilute-and-shoot approach. While this is a quick fix, the longevity of your system and overall performance will likely suffer. Analytical column life will decrease, solvent lines may become plugged, and the ion source will become littered with crusty, charred sample remnants.  This is why a good, clean sample preparation is so vital for the modern laboratory. Whether it’s phospholipid depletion (PLD+), supported-liquid extraction (SLE+), or full-on solid phase extraction (SPE), a little clean-up prior to analysis goes a long way.

    The meat and potatoes of any LC-MS/MS system is the “liquid” that drives the chemical interactions with the analytical column to create the desired chromatographic separation. While it may be true to say that water is always water, it is quite UNTRUE to state every source of water is equal. Any liquid or solvent coming into contact with your samples or LC-MS/MS system should be of the highest quality and purity. The purity of a solvent is always listed on the solvent bottle label. If it’s 95% pure, what comprises the other 5%? By-products and impurities from the manufacturing process! Chemicals like this certainly have their place and purpose in the lab, but being used for highly sensitive bio-assays is not one of them. These impurities can cause spectral interferences within your data leading to potential headaches during the review and interpretation process. Furthermore, low purity solvents can wreak havoc on the mechanical components of your system, such as valves, seals, and high-pressure fittings.

    One final pitfall to avoid involves the moment of sample introduction to your LC-MS/MS system. Sample vessels come in all shapes and sizes, plates, vials, large volume, ultra-low volume, conical, round, etc. Similarly, vial caps and plate seals can vary as well. While all autosampler manufacturers make their own suggestions and assurances with regards to sample vessel selection, many end-users find themselves electing to use what they already have lying around their labs. This may be fine, under certain circumstances, but pairing the wrong vial cap or plate seal with your autosampler can be devastating!  Some autosamplers require pre-slit vial caps or seals to be used to prevent damage to the moving parts, while others may be a bit more rugged and adaptable to any number of products. A potential silent killer are self-adhesive plate seals. Some seals may contain sticky adhesives across the entire surface area of the seal. This is not ideal for use by ANY autosampler.  Over time, the repetitive insertion and withdrawal motion of the needle through the sticky adhesive seals can cause the adhesive to buildup on the needle, which can translate to major problems at the injection site and rotor valves of your LC system. When it comes to selecting the proper vial for your autosampler, consult the manufacturer’s suggestions in the User Manual before making a final decision. If a plate seal is to be used for your application, opt for something with minimal or no adhesive (silicone plate seals are a good choice), or a seal that utilizes adhesive only on the outer edges of each well’s window - MicronPlus makes great seals to accommodate various plates and vials.

    In the end, awareness and prevention can save you from encountering lengthy periods of instrument downtime in the lab.  Not sure which sample preparation method is best for your application? Do you need some recommendations on solvent choice or sourcing ultra-pure products? Are you uncertain about sample vessel choice? That’s what we’re here for!  The Applications Chemists here at Biotage are more than happy to offer assistance to keep you running longer between routine service intervals!


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