Ask any analytical chemist which hyphenated technique has become indispensable over the past decade, and the answer will almost certainly be the same: tandem chromatography–mass spectrometry. Whether it is LC–MS/MS quantifying a novel biologic’s metabolic fate, or GC–MS/MS chasing per- and polyfluoroalkyl substances (PFAS) down to sub-part-per-trillion levels in municipal water, the combination of chromatographic separation with the specificity of tandem mass detection has become the analytical workhorse of choice across virtually every regulated sector.
Below we examine the key forces propelling this expansion, from biopharma pipeline dynamics and PFAS regulatory mandates to AI-driven automation and reshoring of pharmaceutical manufacturing—and explore what each trend means for laboratories managing sample preparation and analytical workflows.
Biopharma: The Engine Room of LC–MS/MS Demand
GLP-1 Agonists and the Metabolomics Gold Rush
The explosive commercial and scientific interest in GLP-1 receptor agonists—semaglutide and related peptide therapeutics for diabetes and obesity—has dramatically expanded the analytical demands placed on tandem MS platforms. Discovery programs require precise quantification of peptide drug candidates and endogenous biomarkers across complex biological matrices. These workflows rely on high-sensitivity LC–MS/MS for pharmacokinetic profiling, receptor occupancy studies, and metabolomics characterization. Metabolomics is, in fact, projected to be the fastest-growing application segment in mass spectrometry, driven in part by its growing role in cancer screening, biomarker discovery, and metabolic disease research.
I have been spending more time learning about GLP-1s because this is the hot topic that people want to discuss on the Concentrating on Chromatography podcast. With that said, I was astounded looking at CNBC.com during breakfast this morning to see that one in eight Americans are currently taking one of these drugs such as Ozempic.
Antibody–Drug Conjugates and Gene Therapy: Complexity at Every Step
The ascent of antibody–drug conjugates (ADCs) and gene therapies has introduced a new level of analytical complexity. ADCs blend the target specificity of monoclonal antibodies with the cytotoxic potency of small-molecule payloads—and characterizing the linker chemistry, drug-to-antibody ratio (DAR), and conjugate stability demands high-resolution LC–MS/MS at every stage from discovery through QC release testing. Gene therapy vectors require equally rigorous characterization of impurities, aggregates, and empty/full capsid ratios.
This translates into a direct need for low-evaporation, high-recovery concentration methods that preserve labile protein structures and maintain sample integrity prior to LC–MS/MS injection. Nitrogen evaporation workflows that minimize oxidative stress and maintain sample temperature are increasingly critical in these pipelines.
Precision Medicine and Multi-Omics Integration
The shift toward precision medicine has accelerated adoption of high-throughput, multi-analyte MS platforms. Proteomics, metabolomics, and lipidomics workflows are converging on a single analytical platform—tandem MS—and generating datasets of a scale and complexity that were unimaginable ten years ago.
Make no mistake: the triple quadrupole serves an irreplaceable role in quantitative targeted analysis. At the same time, Orbitrap and Q–TOF hybrid platforms are growing rapidly as researchers demand full-scan accurate mass for untargeted discovery.
Environmental Mandates: PFAS Testing Drives Adoption
Environmental testing is something that every person, chemist or not, can understand the importance of. Mounting mandates from the U.S. Environmental Protection Agency and European regulators regarding PFAS—the “forever chemicals” whose extraordinary environmental persistence is matched only by the analytical challenge of detecting them at trace levels—have created immediate, compliance-driven investment in LC–MS/MS infrastructure.
The Regulatory Framework Chemists Need to Know
The EPA has codified a suite of LC–MS/MS-based methods as the analytical standard for PFAS in water and solid matrices:
- EPA Method 533: Weak anion exchange SPE combined with LC–MS/MS; covers 25 PFAS including short-chain compounds in drinking water.
- EPA Method 537.1: Reversed-phase SPE followed by LC–MS/MS; covers 18 PFAS including the GenX compound, with method detection limits in the low ng/L range.
- EPA Method 8327: LC–MS/MS for selected PFAS in prepared extracts of aqueous and solid matrices.
- EPA Draft Method 1633: The emerging benchmark for PFAS in non-aqueous matrices—aqueous, solid, biosolids, and tissue—quantifying up to 40 PFAS.
- ADC and gene therapy characterization workflows require gentle, low-temperature evaporation that preserves protein structure and prevents aggregation prior to LC–MS/MS. Nitrogen evaporation under controlled conditions is the preferred approach.
- PFAS trace analysis demands evaporation systems constructed from PFAS-inert materials, with rigorous attention to avoiding fluoropolymer surfaces throughout the sample path.
- High-throughput pharmaceutical QC driven by reshoring demands parallel processing capability—multi-position evaporators that maintain consistent flow and temperature across all positions simultaneously.
- Multi-omics and metabolomics workflows generate large sample batches that benefit from automated, walk-away evaporation with programmable endpoints to ensure reproducible final volumes across a cohort.
All of these methods designate LC–MS/MS, specifically LC coupled to triple quadrupole or tandem-in-time platforms operating in negative electrospray ionization mode with multiple reaction monitoring (MRM), as the required or recommended analytical technique. PFAS analysis is, at its core, an LC–MS/MS problem.
The Sample Preparation Bottleneck
Chemists who have worked with PFAS methods understand the particular demands they place on sample preparation. The ubiquity of PFAS in laboratory materials—PTFE tubing, some SPE sorbents, standard bench supplies—means that blank contamination control is as analytically demanding as the detection itself. EPA 537.1 requires that sample volumes of approximately 250 mL be extracted and reconstituted in as little as 1 mL, creating a 250:1 concentration factor that can expose even trace contamination in the sample processing chain. The installation of a delay column between the LC pump and autosampler to prevent instrument background interference is now standard practice.
This is precisely where robust, inert nitrogen evaporation systems earn their keep. PFAS workflows that use nitrogen-assisted evaporation to concentrate extracts prior to reconstitution benefit from materials that avoid PTFE and other fluoropolymers that can leach PFAS background—a consideration Organomation addresses in its concentration system designs.
The analytical community is also moving beyond targeted PFAS analysis. High-resolution accurate mass (HRAM) spectrometry via Orbitrap technology, paired with non-targeted screening workflows, is gaining traction for the identification of the more than 5,000 currently catalogued PFAS compounds and the novel structures that continue to emerge. LC–MS/MS remains the quantitative gold standard; HRAM provides the discovery layer.
Technological Trends Reshaping the LC–MS/MS Workflow
Artificial Intelligence and Automated Data Interpretation
The datasets generated by modern tandem MS platforms—particularly in omics applications—are too large and too complex for conventional manual review. AI-driven spectral deconvolution, automated peak integration, and AI-assisted hypothesis generation are now embedded in the software suites accompanying leading instruments. Agilent’s acquisition of Virtual Control’s ACIES software specifically to automate LC–MS and GC–MS data analysis is emblematic of this direction.
For laboratory managers, AI integration means smaller specialized teams can operate high-throughput multi-analyte workflows—but it also means that the front-end sample preparation must be even more reproducible, since algorithmic interpretation amplifies inconsistencies introduced upstream.
Online SPE Coupling and “Chromatography Without Walls”
A significant trend is the integration of solid-phase extraction directly into the HPLC flow path—so-called online SPE–HPLC coupling. Systems that combine extraction and chromatographic separation in a single analytical instrument reduce manual transfer steps, minimize the risk of sample loss or contamination, and dramatically increase throughput. For analytes at very low concentrations, online SPE provides the on-column concentration capability that traditional offline preparation achieves with manual evaporation steps.
That said, offline sample preparation—including nitrogen-assisted evaporation under controlled conditions, liquid–liquid extraction, and protein precipitation—retains significant advantages in flexibility, matrix handling, and the ability to process sample volumes that exceed online system capacity. The two approaches are increasingly complementary rather than competitive in well-designed analytical laboratories.
High-Purity Solvents and Reference Materials
As detection limits push further into the femtogram range and regulatory methods demand demonstrable blank performance, the quality of analytical consumables—mobile phase solvents, derivatization reagents, reference standards—has moved from background consideration to front-of-mind. Method validation in regulated environments now routinely requires vendor certification of solvent purity at a level that directly interfaces with instrument performance.
The Ever-Present Need for Sample Evaporation
As LC–MS/MS methods push detection limits lower, the analytical burden shifts increasingly upstream. The quality of the concentration, cleanup, and reconstitution steps preceding injection determines whether the instrument’s theoretical sensitivity is achievable in practice.
Several specific developments are particularly relevant:
- ADC and gene therapy characterization workflows require gentle, low-temperature evaporation that preserves protein structure and prevents aggregation prior to LC–MS/MS. Nitrogen evaporation under controlled conditions is the preferred approach.
- PFAS trace analysis demands evaporation systems constructed from PFAS-inert materials, with rigorous attention to avoiding fluoropolymer surfaces throughout the sample path.
- High-throughput pharmaceutical QC driven by reshoring demands parallel processing capability—multi-position evaporators that maintain consistent flow and temperature across all positions simultaneously.
- Multi-omics and metabolomics workflows generate large sample batches that benefit from automated, walk-away evaporation with programmable endpoints to ensure reproducible final volumes across a cohort.
Tandem chromatography–mass spectrometry is not merely growing; it is becoming structurally embedded in the analytical workflows of every major regulated industry. The convergence of biopharma complexity, PFAS regulatory mandates, AI-enabled data analysis, and pharmaceutical reshoring is creating a multi-year demand cycle that will require laboratories to invest not only in instruments, but in the entire sample preparation ecosystem that makes those instruments perform.
For analytical chemists, the practical takeaway is this: as mass spectrometry sensitivity continues to advance, the sample preparation step becomes the binding constraint on method performance. Whether you are developing a new PFAS method to meet EPA 1633, characterizing an ADC’s drug-to-antibody ratio, or running a 500-sample metabolomics cohort overnight, the reliability and cleanliness of your concentration and cleanup workflow determines the quality of every data point that follows.