Liquid chromatography–tandem mass spectrometry (LC-MS/MS) has never been more powerful or more in demand. Clinical labs now rely on it to quantify hormones, vitamins, and other critical biomarkers at picogram levels. But as instrument sensitivity increases, sample prep has become the critical step to ensure interference-free analysis. Even low-level contamination or matrix effects can compromise results.
Rajashree Chakravarti, Global Product Manager at Phenomenex, has spent years helping labs modernize their sample preparation. She’s now focused on supported liquid extraction (SLE)—a technique that uses partitioning, not chemical binding, to isolate analytes. In this Q&A, she explains how SLE fits the needs of today’s LC-MS/MS labs, especially when targets remain neutral in solution.
What are the main barriers to effective sample prep in clinical LC-MS/MS?
One of the biggest is labor. Preparing biological fluids for LC-MS/MS isn’t a routine task—it takes trained technicians who understand how to handle complex matrices without introducing error. But many clinical labs are short-staffed. That’s where automation becomes important. If a method needs more people to run, it only makes the shortage worse.
The other is contamination. With today’s highly sensitive instruments, even small amounts of background can interfere with detection. As the list of analytes grows, and the detection limits drop, labs need sample prep that removes matrix cleanly and consistently. Traditional methods don’t always meet that need.
How does supported liquid extraction differ from solid-phase extraction?
Solid-phase extraction depends on binding. You have to select the right chemistry, then fine-tune the loading, wash, and elution conditions to keep your analyte intact. That process can take time to develop and often needs re-optimization when a subtle change occurs in any component.
Phenomenex’s Strata synthetic extraction (SE) SLE uses a different approach. It works by partitioning the analyte into an organic phase, without relying on surface interactions. To make that happen, you only need to understand three parameters:
- log P: the analyte’s partition coefficient
- log D: its distribution coefficient at a specific pH
- pKa: the pH at which the analyte remains neutral
If the analyte stays neutral, it will move cleanly into the organic solvent. There’s no need for multiple wash or elution steps. That simplifies the method and reduces variability, especially in routine or automated workflows.
What does the SLE workflow look like in practice?
It’s a simple set of steps. Once the sample is pre-treated to make sure the analyte is in its neutral form, it’s loaded onto the plate. A light vacuum helps distribute it evenly through the sorbent bed. Then there’s a short wait, about five minutes, for the aqueous portion to infiltrate fully.
Next comes the elution. Instead of using polar chlorinated solvents like dichloromethane, this step relies on greener organics such as ethyl acetate or a hexane-ethyl acetate mix. After another brief wait, vacuum is reapplied to collect the eluate. A second elution can be performed if needed. In most cases, the result is a clean extract with very little matrix left behind.
What kind of performance have you seen with this approach?
We tested a panel of eleven steroids, including testosterone, estrogens, and progesterone derivatives. The goal was to hit single-digit picogram-per-milliliter detection limits. Using LC-MS/MS, we saw near quantitative, with low matrix effects and high process efficiency.
One result that really stood out was estrone and estradiol. We were able to reach below 10 pg/mL without any derivatization. That’s usually a challenging step in estrogen workflows, so being able to skip it saves time and reduces complexity for a significant number of samples.
What’s pushing labs to rethink prep strategies for LC-MS/MS?
Several pressures are converging. Regulatory agencies, especially in the U.S. and Europe are moving away from dichloromethane solvents. At the same time, automation is becoming essential. Labs are expected to handle more samples without increasing staff, so prep methods need to fit into existing robotic platforms.
The Strata SE SLE plate was designed for that shift. It uses alternative solvents like ethyl acetate and fits directly into standard 96-well liquid handlers. Batch-to-batch reproducibility typically stays well below ±20% CV, the spec followed by clinical labs, which helps with method validation and scaling.
What kinds of labs are best suited to adopt SLE platforms?
Any lab working with LC-MS/MS and looking to reduce hands-on time. It fits well in clinical and bioanalytical workflows, especially where automation is already in place. As long as the extraction can be done under neutral pH, the method applies.
To learn more about Strata SE SLE and see how it supports cleaner extractions for LC-MS/MS workflows, visit phenomex.com/SLE.
Meet the Expert
 | Rajashree Chakravarti, PhD Rajashree Chakravarti, PhD, is the Global Product Manager at Phenomenex, where she focuses on driving innovation in products for chromatographic solutions. She has a decade of experience in clinical diagnostics and research with a variety of roles in R&D, Operations, and Product Management. |
