Advances in mass spectrometry: Perspectives from UC San Diego Health

• Clinical mass spectrometry provides unmatched accuracy and specificity, but its widespread adoption has been hindered by the extensive labor, manual review of results, and validation demands of laboratory-developed tests (LDTs)
• An FDA cleared automated mass spectrometry platform eliminates the time-consuming process of designing, developing, implementing, and maintaining mass spectrometry-based LDTs
• Automated mass spectrometry assays, anchored to reference measurement procedures, ensure harmonized results, and free up vital lab resources to pursue future innovations like protein mass spectrometry

Mass spectrometry has long been considered the gold standard for accuracy and specificity in the clinical laboratory, particularly for small molecules (e.g., steroid hormones, urine drug testing, therapeutic drug monitoring, and metabolic biomarkers) that antibody-based immunoassays struggle to measure reliably.^1-3 Yet despite its analytical power, clinical mass spectrometry has remained at the periphery of laboratory medicine. Virtually all mass spectrometry based clinical lab tests today are laboratory-developed tests (LDTs). LDTs are labor-intensive, require extensive in-house validation, a highly specialized workforce, and expert manual review of every result.^4,5 That complexity has confined the technology to a relatively small number of specialized laboratories and has limited how quickly results can reach patients.

Fully automated mass spectrometry is a new approach that combines automated sample preparation, liquid chromatography, mass spectrometry, and results interpretation into a single, random-access “sample-in, result-out” workflow. It operates much like the automated immunoassay platforms already common in clinical chemistry laboratories. 

To understand what advances in mass spectrometry could mean for laboratories and the patients they serve, we spoke with Raymond Suhandynata, Associate Director for Clinical Chemistry and Co-Director of Toxicology at UC San Diego Health, and Robert Fitzgerald, Director of the Clinical Toxicology Laboratory at UC San Diego Health.

LL: Why is mass spectrometry an important technology for you, and what is the benefit of using LC-MS versus other techniques?

Suhandynata: Mass spectrometry offers our patients an unparalleled level of accuracy, especially in the context of unusual interferences that are common when you test large and diverse patient populations. We perform in-house testing by mass spectrometry based on need and demand; however, we cannot support every test internally. As a result, we end up sending out low-volume LC-MS/MS testing to large reference labs. Send-out testing is something many clinical laboratories struggle with. There’s a lot of demand from our providers for in-house testing because of the accuracy mass spec provides, but we also have to consider the overall cost to patient care. It’s somewhat a financial decision: We look at how much we’d actually test in-house versus what it costs to send out. But it’s also in the interest of patient care: We’re trying to lower patient costs while still offering the best quality testing. Automated mass spectrometry reduces overhead by bringing in low-volume clinical mass spec testing, enabling an implementation of mass spec that would otherwise be difficult to support and justify operationally.

Fitzgerald: When you think about laboratory-developed tests—which is what most mass spectrometry is today—the regulatory burden is such that we have to validate about thirty different chemicals for an LDT, whereas with automated mass spec that all comes prepackaged, which is a huge time savings. By using liquid chromatography coupled to mass spectrometry, we combine both sensitivity and specificity.

LL: How long have you been using mass spectrometry, and what types of instruments do you use?

Suhandynata: My experience with mass spectrometry dates to about 2006 to 2008, when I started my career in high-resolution protein mass spectrometry. My interests have since condensed towards the utilization of targeted mass spectrometry approaches, which aligns well with my career path in laboratory medicine where we utilize well-validated assays for patient care. My experience has been with Orbitraps, TOFs, and triple quadrupole mass spectrometers. In our clinical toxicology and mass spectrometry laboratory, we routinely use triple quadrupole mass spectrometers and while we have a high-resolution QTOF for interesting or unusual patient workups, the workhorse in the lab remains the triple quadrupole, which is similar to most routine labs performing clinical mass spectrometry testing.

Fitzgerald: I started my graduate work in toxicology. I was an analytical chemist interested in applications with real impact, and as a forensic toxicologist I was helping to investigate cause and manner of death. I started doing mass spectrometry during my PhD, looking at metabolism, and realized the power and specificity of mass spectrometry compared with immunoassays. Mass spectrometry gives you a molecular fingerprint that is very specific for individual compounds, whereas immunoassays are antibody-based and more class-specific. The power of mass spectrometry is that you use an isotopically labeled internal standard—the exact same compound, shifted in mass so the mass spectrometer can easily distinguish it from the compound of interest, say estradiol in a patient sample. Using stably labeled isotopes lets us account for matrix effects and pipetting inaccuracies; once the internal standard is added, it’s a fixed ratio, and that ratio is what we measure. We’ve used mass spectrometry here at the Center for Advanced Laboratory Medicine since we built this facility, because there are certain analytes that can only be done by mass spectrometry—immunoassays just don’t have the specificity to measure them.

LL: What do you currently use mass spectrometry for?

Suhandynata: We perform serum testosterone for women and children; therapeutic drug monitoring, including for antifungals, which our providers rely on for correct dosing; a large menu of drugs-of-abuse confirmatory testing, phosphatidylethanol, a longer-term alcohol-use biomarker used in the transplant setting; and methylmalonic acid, which is used to monitor vitamin B12 insufficiency.

Fitzgerald: Essentially, we target small molecules that aren’t done well by immunoassays.

LL: Are there particular clinical scenarios or patient cohorts that specifically benefit from mass spectrometry-based tests?

Suhandynata: We view mass spec as a way to get ground-truth, reference-method accuracy, specifically in patient populations with low concentrations of the analyte. Serum testosterone is a good example: Immunoassays don’t perform well in the low concentration range, and there have been publications questioning whether the immunoassay is even better than a guess. That matters to us because we want the results we report to be actionable by our providers. The other setting where mass spectrometry is invaluable is when there is no suitable immunoassay available, or when existing immunoassays are analytically limited. In these cases, mass spectrometry is the only way, and it’s typically a send-out test due to operational limitations. Steroid hormones are a good example. Tests such as 17-hydroxyprogesterone are often relatively low volume and may not be cost-effective to bring in-house using traditional batch-based mass spectrometry workflows. 

LL: How important is the standardization of testing results, and why hasn’t this been achieved in the past for mass spec-based testing?

Fitzgerald: Harmonizing laboratory results is a critical component of laboratory medicine. Our biggest success has been hemoglobin A1c—if you’re diabetic and go to one hospital, you get pretty much the same result as at another provider. That’s not true for most other immunoassay-based testing. To standardize the practice of medicine, we need harmonized results: The same answer regardless of how we do the measurement. Mass spectrometry hasn’t always delivered that, because we didn’t have a reference method. With reference methods, we can all anchor to a known value, calibrate our systems, and harmonize. Just because something is done by mass spectrometry doesn’t mean it’s right; a harmonized assay helps ensure we actually get the right answer.

LL: How do you envision the future of your lab, and what role does innovation play in achieving your aspirations?

Suhandynata: What we’re really interested in is protein mass spectrometry, there’s clinical impact there, but we still have to maintain and manage the assays we routinely perform; an automated mass spectrometry platform takes that load off. So I’m looking forward to what’s next, and to freeing up our triple quadrupole mass spectrometers to take on the next challenge. A lot of my colleagues would say that if you’re not moving forward, you’re moving backwards. Innovation is something we embrace in laboratory medicine because it allows us to provide the best care for our patients through quality testing.

Fitzgerald: I think we need to embrace innovation. We can’t always see what the future impact will be, but if you look at the history of laboratory medicine, when we embrace innovation we make positive changes for patient care.