American Association for Clinical Chemistry
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September 2010 Clinical Laboratory News: Mass Spec in Clinical Labs

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September 2010: Volume 36, Number 9

Mass Spec in Clinical Labs
What Does It Take to Bring This Technology Online?
By Genna Rollins

Once the domain of organic chemistry labs and a variety of other analytical applications, mass spectrometry coupled with liquid chromatography (LC-MS) or gas chromatography (GC-MS) is gaining more acceptance in clinical labs. While the technique clearly is no longer merely a research method, it still hasn’t been widely adopted in clinical chemistry due to issues such as cost, manpower, and ease of implementation. However, that may be changing in the near future. Proponents of mass spectrometric analysis say that several factors are converging to bring the application into the mainstream of clinical laboratory testing.

“Right now penetration is episodic and variable, but it’s a matter of breaking down the barriers surrounding something we’re not as familiar with. Within five years or less—probably less—people will look at it just like an autoanalyzer,” predicted David Herold, MD, PhD, chief of clinical chemistry at VA San Diego Healthcare System and professor of pathology at University of California San Diego. “The technology’s getting better, the manufacturers are starting to emphasize the clinical aspects, and staff training opportunities are available.” He also is president and chairman of the Association for Mass Spectrometry Applications to the Clinical Lab (MSACL).

As optimistic as Herold’s vision appears, many labs remain reluctant to get into mass spectrometry. However, early adopters say any implementation challenges are well worth the effort. “It’s quite doable. You just need to be patient,” explained Elizabeth Pattison, BS, CASCP, technical specialist at the ARUP Institute for Clinical and Experimental Pathology Technology in Salt Lake City. “It’s a good technology because we can measure things we can’t by any other method and that really improves patient care.” Pattison was a bench tech on ARUP Laboratories’ first mass spectrometry assay team, and now works on method development and improvement.

Addressing the Fear Factor

Labs stepping into the world of mass spectrometry will need to consider their options carefully, make detailed plans, and be prepared to adapt as issues arise. An important concern for many is whether they have the appropriate personnel to even consider the technology. “There’s a fear factor of ‘how am I going to work with this non-FDA-approved technology? How do I work with a lab-developed test?’ That’s intimidating for many non-academic labs,” said Judith Stone, PhD, research and development scientist at The Permanente Medical Group (Kaiser Permanente) Regional Laboratory—Northern California in Richmond.

A lingering misperception is that labs need doctoral level clinical chemists to operate the instrument on a day-to-day basis, according to Michael Vogeser, MD, professor of laboratory medicine at the Hospital of the University of Munich, Germany. “You need an expert who is familiar with the technology and has a special relation to analytics, but a PhD or MD is not necessary for running the analyzer. However, such a person is needed for implementing tests and to be in the background in case of problems,” he explained. Vogeser oversees four mass spectrometers, along with 10 technologists who run the assays. “I don’t have to look into everyday operations, but the technologists wouldn’t be able to implement a new method or do deeper trouble-shooting. There’s a cut between what the technologists can do in terms of trouble-shooting and what I can do, and a cut between what I can do and what the service department can do,” he explained.

Finding Talent

Pattison pointed out that even PhD chemists may not have hands-on experience with mass spectrometry. “You’re not going to find anyone with experience in this area unless they come from other industries like pharma, or happened to have worked with it in another lab,” she said. However, Herold believes the pool of trained mass spectrometry specialists is deepening. “There’s a lot of interface between clinical and classical mass spec these days and a lot of people from pharma and other industries looking for jobs could jump right into clinical positions. They could make a real contribution because they’ve been working in situations where mass spec was used in almost an industrial fashion,” he said.

Stone also believes that clinical chemists have an innate talent that’s beneficial to the development and maintenance of mass spectrometry methods. “One of the things that work in our favor is that we document quite a bit. To make mass spec work well, you have to track a lot of things, like pressures and reagents. When something changes with the assay, you can go back and look at what you did,” she explained. “When you apply our compulsive tracking to tandem mass spec, it’s that much more likely to be successful.”

Pattison also emphasized that the lion’s share of technical problems usually involve the chromatograph—either LC or GC—not the spectrometer. “There’s very little the end user has to do with the mass spec. What you can do is very easy, and what you can’t do, you have to call for service anyway,” she explained. “The liquid chromatography is usually where the problems come from, and we’ve been running those for decades.”

Brushing Up On Skills

Staff training initiatives need to include brushing up on chemistry skills that probably haven’t been used for a while, according to Stone. “Over the last 20 years there are fewer people who actually do hands-on type chemistry—pipetting, extraction, following a procedure with multiple steps—but this all fits into the skill set of clinical laboratory scientists. There’s no reason any CLS in the mid to upper range of performance can’t do these things,” she said. In recognition of the need to bring laboratorians up-to-speed on mass spectrometry, both AACC and MSACL have established certification or training programs (See Box, below).

Training Laboratorians to Run Mass Spec

Both AACC and the Association for Mass Spectrometry Applications to the Clinical Lab (MSACL) recognize that staff education is a major implementation issue for mass spectrometry, and both organizations have developed certification or training programs to support wider dissemination of the technology in clinical labs.

AACC’s new nine-course certificate program, “Using Tandem Mass Spectrometry in the Clinical Laboratory,” is open for enrollment now, with course work starting on November 1, 2010. The online curriculum, which offers category 1 ACCENT® credit for each course, was developed to provide laboratorians with an understanding of key areas in the field, including basics of mass spectrometry theory, maintenance and troubleshooting, method validation, and tips for achieving and maintaining consistent high quality production.

“The skill set for successfully operating mass spec is analogous to sitting in the kitchen cooking with your grandmother. It’s not so much what’s in the written procedure or what you can get by reading a book, but what you can learn from being around a person who has done it a long time,” explained course coordinator Judith Stone, PhD, research and development scientist at The Permanente Medical Group (Kaiser Permanente) Regional Laboratory—Northern California in Richmond. “We hope that we can substitute that experience with an online program for people who might not be able to attend meetings where they talk about those kinds of things.”

Although the course will mix theory and practice, the emphasis will be on practical problem-solving and understanding tandem mass spectrometry systems, according to Stone. “A lot of working with mass spec is counter-intuitive, and in fact, a lot of times, the thing you think you should do is actually the wrong thing to do,” she said. As an example, it might seem logical to clean the system with water or organic solvent, but if not done properly, “it could kill the column and pump,” Stone indicated. “It’s true that putting organic solvent in the system could be a good thing, but you have to make sure it’s compatible with whatever else you have in there.”

Stone has asked four vendors to provide trouble-shooting information that is specific to their systems. This is in addition to the module that deals with generic maintenance and troubleshooting.

The goal of the course is to give laboratorians the skills and confidence necessary to implement mass spectrometry successfully.

Meanwhile, MSACL offers 1- and 2-day short courses during its annual meeting, to be held next in February 2011. The 1-day courses cover topics such as an introduction to mass spectrometry and metabolomics, while the 2-day courses focus on methods development and validation, among other topics. ACCENT® credit is available for these courses as well. More information is available online.

Douglas F. Stickle, PhD, DABCC, FACB, advised that labs train a core staff to work on mass spectrometry and not rotate technologists through that station as is typical with other analyzers. “In modern lab management it’s considered good to have people be interchangeable. That’s sounds nice, but it doesn’t work well for this technology,” he said. “It’s better to have a dedicated staff so they’ll have a better ability to pick up on problems before they develop into major issues.” Stickle is professor of pathology and director of clinical chemistry at Jefferson University Hospital in Philadelphia.

If mass spectrometry doesn’t require extraordinary skills or expertise to operate, it would be a mistake to give short shrift to manpower concerns, according to Herold. “Historically, the training and commitment of personnel has made the difference in successful versus unsuccessful installations. People not only need to be trained, but trained at a level to understand the problems that are out there,” he said. Vogeser agreed. Despite the success of mass spectrometry in his lab, he worries that if he were to leave, the hospital would revert to immunoassays because there would not be anyone with a guiding hand overseeing and promoting the technology.

Sticker Shock

A major sticking point for many labs is the relatively hefty price tag for mass spectrometry—about $300,000 for one instrument. However, while that clearly exceeds the cost of a run-of-the-mill analyzer, the technology can save money in the long run, according to experts. For instance, Emory University invested in LC-MS about 8 years ago to improve performance and reduce costs related to therapeutic drug monitoring (TDM) of immunosuppressants.

“At that time there was no other way to measure rapamycin that was technically feasible in our hands. We were paying a very high cost for immunochemistry reagents, so we did the math and found we could do cost avoidance, pay for an expensive piece of equipment, and gain added benefits by being able to do other measurements,” recalled James Ritchie, PhD, professor of pathology and laboratory medicine. Each TDM test by immunoassay was costing his lab about $15, but Ritchie calculated that the operating cost of LC-MS would be about $3.40 per sample, and that the lab would recoup its nearly $300,000 investment in about 2 years. That estimate held up and Ritchie’s lab has since purchased a second unit and is implementing vitamin D and urine steroid assays.

Emory’s experience is by no means isolated, according to Stickle. “Immunoassays are specialized technology and a tremendous cost of production goes into them. So in converting to mass spec, you’re going from something that’s dependent on a manufacturer to something that’s not dependent on anything other than the availability of organic solvents,” he explained. “It’s a reagent-less system.”

Given the cost associated with mass spectrometry, experts recommended preparing a very thorough request for proposal with any wish list items specified upfront. “You need to be prepared to buy everything you can think of beforehand. For example, if you need a column switcher, it’s better to include it in the initial purchase because it will be a lot easier to get when you put in the initial capital request than later on,” advised Pattison.

Which Assay to Implement First?

Although the cost-savings can be dramatic, that’s not the main motivation for most labs to get into mass spectrometry. “One of the needs that people are trying to fulfill is they can’t get an accurate result any other way but through mass spec,” Pattison explained. For instance, fractionated vitamin D results are not available through immunoassay, and the accuracy of testosterone measurements for women and children by immunoassay have been called into question, but are considered more reliable by mass spectrometry.

The superior performance of mass spectrometry for certain tests is just one factor in deciding which assay to implement first. The most common LC-MS applications in clinical labs appear to be TDM for immunosuppressants and analysis of classes of small molecules such as steroid hormones, vitamins, amino acids, and thyroid hormones (See Box, above). Researchers are pushing the envelope to quantify proteins in cancer diagnostics, but these techniques are much further from everyday use. “What’s being done routinely in clinical labs is relatively simple types of analyses,” said Stickle. “There’s an extensive frontier in microbiology and protein analysis, but right now, we’re in a period where there’s still a huge opportunity for labs to become state-of-the-art by just using mass spec for things like vitamin D testing or therapeutic drug monitoring.”

While Emory chose to take on TDM for immunosuppressants as its initial mass spectrometry assay, other labs have shied away from that application. “Of the things you can do by mass spec, that’s the one with the highest requirement for uptime. You just can’t afford to say, ‘sorry, we aren’t able to meet our turnaround times because of instrument problems’,” explained Stone. “We had specific discussions about implementing that assay and our concern was that it was too critical of an issue and we might not be able to support the turnaround times needed.” Her lab chose instead a urine benzodiazepine confirmation assay as its first foray into the field.

Top Mass Spec Assays

Many assays have been developed for mass spectrometry. Here’s a list of the most popular tests.

Therapeutic Drugs

  • Immunosuppressant drugs
  • Antiepileptic and anticonvulsant drugs
  • Busulfan 
  • Clozapine and norclozapine
  • Digoxin


  • Testosterone
  • Aldosterone
  • 4-Androstene-3,17-dione
  • Corticosterone
  • Cortisol
  • 11-Deoxycortisol
  • Dehydroepiandrosterone
  • Dehydroepiandrosterone sulfate
  • Progesterone
  • 17a-Hydroxyprogesterone
  • 25 OH Vitamin D3
  • 1, 25 dihydroxy Vitamin D3
  • Urinary  metanephrines

Drugs-of-abuse and Pain Management

  • Benzodiazepines
  • Opiates
  • Synthetic opioids
  • Tetrahydorcannabinol and carboxytetrahydorcannabinol
  • Buprenorphine and norbuprenorphine
  • Fentanyl and nonfentanyl
  • Ethyl glucuronide and ethyl sulfate

Newborn screening

Source: Jeff Zonderman and Subodh Nimkar, Thermo Fisher Scientific

Vendor Vetting

Regardless of the assays chosen, labs will do well to do their homework before purchasing a mass spectrometer. It’s widely acknowledged that vendor support generally was lacking in the past, but has improved markedly as more clinical labs have implemented the technology. “The manufacturers for many years were used to selling the instrument, saying ‘here are the capabilities’ and walking away,” Ritchie explained. “But clinical labs don’t operate that way. We tend to want things cradle-to-grave and having someone check out things for us quickly. The companies are slowly but surely responding to this need, because they see the clinical market as a growth area.”

Even though vendors have made considerable strides in service, contingency plans for downtime are crucial. Some organizations start with one mass spectrometer, but most people recommend having a back-up in place from the beginning. “One instrument is no instrument,” said Vogeser. “If a vacuum pump fails, by the time an engineer comes out, orders parts, and comes back, altogether it can take 10 days. You have to have a plan for ongoing operations.”

Focus on Automation and Software

Even as vendors beef up their support for clinical applications of mass spectrometry, some areas are not ideal and require special attention by labs. “Reaching the tipping point where mass spec will be common in most every hospital lab will depend on more automation of the front end and computerization of the back end,” observed Ritchie. Vogeser, who has written extensively about mass spectrometry applications in clinical labs, also believes automation will be crucial to wide dissemination of the technology. “A major step forward would be a plug-and-play instrument which is applicable for ordinary technicians,” he said.

Mass spectrometry software is sophisticated, which makes it challenging for staff to learn and stay proficient with, according to Stone. However, she contended that a greater hurdle by far is that, for the most part, there is no interface between this software and the laboratory information system (LIS). This results in an unavoidable manual process of exporting data from the mass spectrometer system and importing it into the LIS. Stone views this lack of interoperability as a “huge gap. If it’s not dealt with soon, the vendors will loose their momentum,” she said.

Stone also has been pressing vendors to do more in terms of method validation. “We need a supply of robust, fully-validated methods. That’s absolutely necessary for labs that don’t have access to research and development personnel. We need a standardized protocol for validation for clinical LC-MS assays,” she asserted. So far, Waters has the only FDA-cleared mass spectrometry-based clinical diagnostic kit, for the quantification of the immunosuppressant tacrolimus. The company is continuing to develop fully validated solutions inclusive of the system platform, reagent kits and LIS integration, complemented with service, training, and on-site support, according to Patrick Martell, director of clinical marketing.

Planning the Implementation

Given all the considerations involved, Pattison indicated that it takes about 1 year to bring the first mass spectrometry assay on line. “By the time you bring in the instrument, train the staff, do research and development, and tweak the assay it will take that long. If you beat that year, that’s fantastic, but you need to give yourself that time,” she explained. Pattison also cautioned that assays require continual updating. “The assay you bring online usually doesn’t stay in its current state. It will need some method improvement because new technology—like liquid chromatography columns—is coming out constantly.”

As part of an implementation plan, Herold recommends visiting other labs that are already using the technology. “You’d be wise to watch every step they’re doing. Sometimes people with years of experience think ‘I don’t need to write that down; everybody knows how to do it,’ but in fact, everybody doesn’t know that particular nuance,” he said. Stone went a step further and observed vendors before selecting a product. “We actually extracted our own samples here and hand-carried them to the vendors. We watched them run the assays. It gave me a better handle on the sensitivity of one instrument compared to another,” she recalled.

Even though implementing mass spectrometry in clinical labs has its share of challenges, early adopters emphasize that the rewards far outweigh any complications. “It’s very satisfying and fun, but more importantly, it’s about being able to provide better service,” said Stickle. “That’s the bottom line.”

Dr. Herold has served in a consultant or advisory capacity for Thermo Fischer Corporation and Pathway Genomics Corporation.

Learn from Other Laboratorians

On November 15, 2010, AACC will host a one-day conference “Practical Applications of Mass Spectrometry in the Clinical Laboratory” on the Johns Hopkins Medical Institutions campus in Baltimore, Md.

Program organizers William Clarke, PhD (Johns Hopkins), and Steven Soldin, PhD (Georgetown University), invite interested lab professionals to hear leading experts discuss the advantages and challenges of mass spectrometry vs. immunoassay and the basics of mass spectrometry method validation. In addition, conference faculty will examine some of the applications already in use in the clinical lab, including therapeutic drug management, pain management/toxicology, vitamin D, and thyroid testing.

For more information or to register, visit events on the AACC web site.

Further references about mass spectrometry in the clinical lab:

  • Garg, U, Hammett-Stabler, CA, eds., Clinical Applications of Mass Spectrometry: Methods and Protocols, Humana Press, 2010
  • Mass Spectrometry in the Clinical Laboratory: General Principles and Guidance; Approved Guideline, CLSI 2007; 27
  • Vogeser, M, Kirchhoff, F. Progress in automation of LC-MS in laboratory medicine. Clin Biochem 2010. Doi:10.1016/j.clinbiochem.2010.06.005
  • Vogeser, M, Seger, C. A decade of HPLC-MS/MS in the routine clinical laboratory— Goals for further developments. Clin Biochem 2008;41:649-662.
  • Ibid. Pitfalls associated with the use of LC-MS/MS in the clinical laboratory. Clin Chem. Doi/10.1373/chlinchem.2009.138602