When I first launched the Concentrating on Chromatography interview series, I knew I would be talking to some of the brightest minds in separation science. What I didn’t fully realize was that, regardless of whether my guest was searching for life on Mars, tracking "forever chemicals" in drinking water, or repurposing cancer drugs to fight malaria, the conversation would almost always circle back to the same high-stakes bottleneck: sample preparation.
As I reflect on our first 50 episodes, a clear "Sample Prep Mantra" has emerged. As Wade Hasenour from Genevac put it, many errors in the lab come down to "PSIC error"—the "person sitting in a chair". But beyond human error, the technical hurdles of getting a complex biological or environmental matrix ready for a mass spectrometer are immense. If you don't do the preparation right, you pay for it during the analysis.
One of the most eye-opening themes has been the sheer ubiquity of contamination. This is especially true in the world of PFAS analysis. Holly Lee from SCIEX and Edward Faden from MAC-MOD both emphasized that when you are looking for analytes at the parts-per-trillion level, the lab environment itself becomes a minefield.
Edward’s team discovered that even something as mundane as the gas line tubing supplying a nitrogen generator could be a source of PFAS contamination. This resonates with Megan Farrah of Tuft University's work on Martian biosignatures; she has moved to an entirely glass-and-metal benchtop because plastic pipet tips can leach siloxanes and other plasticizers that ruin the baseline of a GC-MS.
Monique Mello, an expert in metrology, gave us a sobering statistic: she attributes 99% of analytical failures to sample preparation. Whether it’s dirty tubes, lab air, or reagent carryover, if the sample isn't handled with extreme care from the moment of collection, the final number produced by the software—no matter how fancy the instrument—is essentially meaningless.
Another recurring challenge is the physical compatibility between the sample and the instrumentation. Schyler Odum, PhD, a medicinal chemist, shared a frustrating but common story about using UPLC. Because their system is set up for reverse phase (acetonitrile and water), injecting samples from a normal phase system (like DCM or ethyl acetate) often causes the sample to "crash out" in the tiny pores of the UPLC lines. This leads to over-pressure issues and pump failures.
The solution, though "super annoying and time-consuming," is the mandatory dry-down. Researchers must blow down every organic sample to total dryness and then resuspend it in a compatible mobile phase. This is a critical step for ensuring that "you don’t breathe on the sample" and break a million-dollar instrument.
Working with non-volatile or highly polar compounds adds another layer of complexity. Jessica Whitehouse, an undergraduate researcher, walked us through the necessity of derivatization for haloacetic acids (HAAs) in pool water. Because HAAs aren't naturally volatile, they won't move through a GC column unless they are chemically altered to lower their boiling point.
Similarly, Ryland Giebelhaus discussed the challenges of analyzing fecal microbiome transplants (FMT). To see polar metabolites using GCxGC-TOFMS, his team had to extract the metabolites and dry them down completely before adding TMS groups through derivatization—all while meticulously keeping water out of the system to prevent the reagents from failing.
For those working with biological samples, the challenge isn't just chemical; it’s temporal. Subhoja Chakraborty, researching malarial drug targets, pointed out that whole cell lysates are "pretty rough to begin with". They are packed with DNases, RNases, and proteases that start degrading your protein of interest the moment the cells are broken apart.
Her advice? Keep everything as cold as possible and cut the preparation time to the absolute minimum. Andrea, who studies how PFAS affects hormones, found a creative way around the "derivatization tax." By using radio chromatography, she could detect androgens with minimal sample manipulation because the radioactive label is already there, whereas traditional MS would require a day-long derivatization process because androgens don't ionize well.
We also learned that skipping the "boring" steps like filtration is a recipe for disaster. Jim Averso from IW Tremont reminded us that syringe filters are the primary line of defense for expensive HPLC columns. A buildup of microscopic particles doesn't just skew your peaks; it creates back-pressure that can ultimately kill the flow rate and the instrument's ability to produce reproducible data. He even shared a great "pro-tip": you can stack syringe filters (male-to-female) to perform a coarse pre-filtration and an absolute filtration in a single shot.
Finally, Isaiah Speight and Daniel Reddy challenged us to think about the environmental cost of our prep. Chromatography is notoriously solvent-heavy. Isaiah’s group focuses on "solvent-minimal" mechanochemistry to reduce the waste footprint. Dan’s work with dried matrix spots (DMS) offers a glimpse into a greener future where we might eliminate the need for dry ice shipping and massive organic solvent extractions by sampling directly from a piece of laser-patterned paper.
If there is one thing I’ve learned from these incredible scientists, it’s that the "magic black box" of the mass spectrometer is only as good as the vial you put into it. Sample preparation is the foundation of reliable outcomes. It is the most challenging, most underestimated, and yet most rewarding part of the analytical journey.
At Organomation, we have spent over 65 years listening to these exact challenges. Our founder, a PhD chemist, built the first multiple-sample nitrogen evaporator because he saw the need to automate the tedious dry-down steps that Schyler described.
Whether you are performing trace PFAS analysis according to EPA Method 537.1, concentrating food matrices in 2 mL vials ahead of TQMS, or managing large-batch extractions with our ROT-X-TRACT systems, Organomation’s tools are designed to be intuitive and long-lasting. Our N-EVAP line remains the most cited nitrogen blowdown evaporator in U.S. EPA methods because it offers the independent gas flow control and precise temperature regulation needed to protect your most sensitive analytes.
Sample preparation shouldn't be the reason your research stalls. Let us help you accelerate your breakthroughs with equipment that is as resilient and dedicated as the scientists who use it. Visit Organomation.com to find the right solution for your lab’s unique workflow.