Recently, LCGC held a roundtable discussion to learn about some of the key challenges facing environmental laboratories. The discussion included some of the leading minds in the industry offering their view points including William A. Lipps, chief science officer at Eurofins Eaton Analytical (Monrovia, California), Kevin Schug, PhD, the Shimadzu Distinguished Professor of Analytical Chemistry at the University of Texas at Arlington, Jennifer Field, PhD, a professor in the Department of Environmental and Molecular Toxicology at Oregon State University, and Sascha Usenko, PhD, an associate professor in the Department of Environmental Science at Baylor University.

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Technological challenges

Many environmental chemists also say they feel current analytical technologies don’t adequately meet their current needs—although they cite a wide variety of reasons for that view. Many environmental chemists share the perception that innovation in environmental analytical instrumentation and methods has lagged behind the more lucrative pharmaceutical and life science markets. Other scientists, typically those working in unregulated academic laboratories, seek instrumentation for highly specific, complex measurements that aren’t possible with standard commercial systems. And for many laboratories across the spectrum of environmental analysis, advanced instrumentation and the skilled personnel required to operate it to its full potential are economically out of reach.

Lipps, who formerly worked in marketing and product management for several instrument manufacturers, describes something of an innovation stalemate in the environmental sector. Instrument manufacturers are hesitant to spend money to develop a new technology for environmental applications because the EPA continues to base its methods on older technologies, and laboratories are reluctant to buy new instrumentation unless it is specifically blessed by EPA-approved methods. Usenko says if laboratories can’t afford to acquire the technologies they need, they have to “ask different questions based on the technology they have in hand.” He says he personally devotes significant time and money to modify instruments to achieve desired measurements. “For my proton-transfer reaction (PTR) MS system, I actually built a cold trap system so I could reduce the amount of moisture” when measuring compounds like formaldehyde in atmospheric samples. “All of a sudden I’ve got to put a $50 000 modification onto that instrument—and that’s just me building stuff.”

Laboratories that do manage to acquire advanced instrumentation such as high-resolution mass spectrometers for chromatographic analysis can feel hindered by the incompatibility of the various manufacturers’ proprietary data platforms. Field says in the case of her laboratory’s recent purchase of a quadrupole time-of-flight (Q-TOF) MS system intended to be used in collaboration with another laboratory, the decision was based more on the need to share data than on the capabilities of the data collection hardware. “There are people trying to fix that with independent programs and ways to translate files so they are comparable, but it’s not routine and not commercially available yet, to my knowledge,” she says.

Environmental monitoring and sample preparation

Role of untargeted analysis

Advances in full-scan mass spectrometry in recent years have enabled analytical chemists to determine large numbers of substances in a variety of sample types without knowing in advance what they were looking for. Untargeted analysis also enables users to search stored data from previous samples for the presence of compounds of emerging interest. The environmental analysis community seems to be gradually moving in the direction of untargeted analysis, although the change isn’t happening overnight.

“There’s absolutely a wave in that direction,” Field says. “The amazing power—and the challenge, resource-wise—is in the reduction and analysis of the data. The files are huge. They collect everything all the time.” Advanced tools like Q-TOF, she says, can determine targeted analytes, suspected compounds of interest, and complete unknowns. “The instrument has all these capabilities,” she says, “but the magic and the mystery and the challenge is dealing with the data. There’s tremendous strength and power, but it’s going to require a very talented workforce. It’s going to take very expensive instrumentation. It takes faster computers just to deal with it. And of course data storage is a monster. The regulatory world isn’t even close to dealing with things for which there are no standards—which is where this instrument shines.”

Lipps agrees. “In my opinion, there’s a very big demand to do untargeted testing, but it takes somebody that really, really knows what they’re doing to ensure the resulting data that is actually useful,” he says.

Sample preparation issues

Problems with sample collection, preparation, and introduction are perpetual challenges in environmental analysis, and account for the vast majority of errors. Sample preparation is a complicated and often tedious step in the experimental process that many experienced chemists take pains to avoid. And like method development, the time and expertise required for efficient sample prep is rarely appreciated by colleagues from other disciplines.

Despite these challenges, not everyone dislikes this part of the analytical process. “I enjoy sample prep” says Usenko. “There’s a lot of opportunity within sample preparation to improve your overall analytical throughput, where you have less instrument downtime because the bulk of the heavy lifting is done with sample prep.”

Field has taken the opposite approach in her lab. “I have dumped as much sample prep as I humanly can,” she says. “Our lab hasn’t run SPE for anything through an LC–MS in probably 12 years.”

Nevertheless, laboratories using EPA methods are routinely required to perform SPE before analysis, adding to the sample handling complexity of analyzing samples like those containing PFAS-containing substances. PFAS samples typically contain high concentrations of suspended particulate matter and organics that can clog SPE columns and cause matrix effects. Removal of suspended solids before extraction using conventional filtration can absorb analytes of interest, contaminate the sample, and results in the determination of only the dissolved fraction of the sample.

EPA methods mandate other sample-handling procedures that cause headaches for contract laboratories. For example, according to EPA methods, PFAS samples cannot be held for more than two weeks before analysis. “The PFAS has been out in the environment for 20 years and hasn’t changed,” Field says. “But contract laboratories are stuck with a lot of things that are mandated for which there just simply isn’t any scientific basis. As an academic, I would love to create methods for that community, yet these laboratories are constrained.”

Filtration solutions for environmental analysis labs

Potential solutions

Acknowledging his bias as an editor of ASTM standards, Lipps says closer collaboration between the EPA and ASTM would help method development proceed more quickly. He gets the impression that the EPA is reluctant to share information with volunteer consensus bodies because of legal or other concerns. He says EPA worked much more closely with organizations like ASTM in the 1980s and 1990s, but those close collaborations aren’t as common anymore.

“It would really help if (academics) were able to get their methods out there a little bit quicker and EPA could just adopt them or post them in the Federal Register and say, ‘These things are allowed,’” As it is, he says, contract laboratories are unable to use methods unless they first appear in the Federal Register. “People at universities develop methods and we just can’t use them. Even though we know we’re going to get the right number with it [a new method], it doesn’t matter. We know that we might be reporting the wrong number [by using an outdated but approved method], but that doesn’t matter. The wrong number is EPA-approved, so that’s what we report.”

From the academic perspective, Usenko believes policy-makers, regulators, and research funders must return to the idea that investing in new technologies and method development work is worth taxpayer dollars. “There are always going to be new threats or new issues, but if we want to do the best for environmental and human health, it’s a worthwhile investment.”

Another step forward—although “a bit of a pipe dream”—says Field, would be for the United States to follow the European Union’s lead in requiring manufacturers to disclose more data (and analytical methods) about their new compounds before they are permitted to market them. “One of my beefs,” she says, “is that I get federal dollars to reverse-engineer proprietary formulations that were released on a large scale to the environment. Taxpayers are getting hit over and over again in this country to pay for solving problems they didn’t create. This is how you basically let industry slide on their responsibilities toward environmental stewardship and public health.”

Future outlook

Environmental chemists may face some significant challenges, but the next generation of environmental chemists is a source of optimism that things will get better. “There’s a lot of talent out there,” Field says. “There are a lot of young people who want to make a difference. It’s a wonderful field to be in and I’ve really enjoyed watching it unlock the ingenuity and creativity in students. Method development is challenging. It’s fun. And, it’s our way of saving the world.”

Click here to go back to part I of this article.


The article was created by LCGC for Cytiva. The views expressed here are the views of the individuals quoted, and do not necessarily reflect the views of any other organization.


  1. EPA’s Per- and Polyfluoroalkyl Substances (PFAS) Action Plan, EPA 823R18004, February 2019,
  2. J. Shoemaker, P. Grimmet, and B. Boutin, Method 537, Determination of Selected Perfluorinated Alkyl Acids in Drinking Water by Solid Phase Extraction and Liquid Chromatography/Tandem Mass Spectrometry (LC/MS/MS), U.S. Environmental Protection Agency, Washington, DC, 2008.
  3. J. Shoemaker and Dan Tettenhorst, Method 537.1, Determination of Selected Per- and Polyfluorinated Alkyl Substances in Drinking Water by Solid Phase Extraction and Liquid Chromatography/Tandem Mass Spectrometry (LC/MS/MS). U.S. Environmental Protection Agency, Washington, DC, 2018.