Decisions across a drug program, from selecting a lead candidate to setting a clinical dose, rely on measuring the drug and its effects in biological samples. As a molecule moves through development, the method behind those measurements has to change with it. A research method that supports lead optimization is not the fully developed method a regulated clinical study needs, and changes and re-validations should be expected until Phase 3.
So the useful question is not which bioanalytical method is best, but which one fits the stage the program has reached. Below, we look at how that choice works for small molecules, large molecules, immunogenicity and biomarkers, based on how Ardena’s bioanalytical services team approaches it.
Not every stage needs the same level of regulation
Bioanalysis supports every phase of development: discovery, preclinical work and clinical Phases I to IV, including clinical trial services. The regulatory requirements differ across those phases. In Ardena’s bioanalysis work, about half of the studies run under GLP or GCP, 10% are multi-site GLP, and 40% are non-regulated. Roughly 60% of the work is clinical and 40% preclinical.
For regulated pharmacokinetic studies, methods are validated according to the ICH M10 guideline, which harmonized previous FDA and EMA bioanalytical method validation guidance. Methods are developed in house.
Small molecules: start from the structure
For a new drug entity, the method development strategy is based on the molecular structure, and development is aimed at the development phase the molecule is in. Several generic compounds already have in-house validated methods.
LC-MS/MS remains the reference technique for small molecules, peptides and protein biomarkers, using triple-quadrupole and high-resolution accurate mass instruments. Ardena’s bioanalytical laboratory runs 16 LC-MS/MS systems, with automated sample preparation for liquid-liquid and solid-phase extraction. Specific assays include ultrasensitive determination of cannabinoids and targeted lipid analysis, such as hexosylceramides and sphingosines in various matrices. Oligonucleotides are measured in plasma, CSF and tissues.
Large molecules: reagents and range decide the platform
For large molecule PK, three questions shape the method: which reagents are available (for example, anti-idiotypic antibodies or the target), what range of detection the study requires, and which platform fits. MSD, for example, can support a broader range than ELISA. Other ligand binding platforms include Gyrolab, AlphaLISA and Ella, and hybrid LBA-MS is used for complex biologics and ADCs.
Assay development is phase appropriate. Research methods support lead optimization, while fully developed methods, ready for validation, are prepared for preclinical toxicology studies and clinical applications.
For antibody-drug conjugates, Ardena runs assays for several analytes: total antibody, total ADC, conjugated and free payload, and ADA.
Immunogenicity: from minimal qualification to a full tiered approach
ADA assays show clearly how requirements grow with the program. The preferred format is the bridging assay, and the MSD platform is used for most ADA work.
For preclinical studies, a minimal assay validation or qualification is applied, following European Bioanalysis Forum recommendations. Clinical studies call for a tiered ADA approach of screening, confirmatory and titer assays, together with domain-specific characterization and neutralizing antibody assays. Clinical validation follows FDA and EMA guidelines.
Biomarkers: context of use sets the level of validation
Biomarker work starts with practical questions. Is a commercial kit available? Does the assay need commercial or newly generated reagents, and which platform suits it?
For clinical studies, validation or qualification is fit for purpose. What matters is the context of use: whether the biomarker is exploratory or supports a primary or secondary endpoint. The extent of qualification or validation also depends on how the data will be interpreted (trends within one individual, or also between individuals), on interim analysis (whether data from different runs will be used together), and on the anticipated effects.
Platform choice matters for multiplexed panels too. Ella runs a multiplexed assay in 1.5 hours, compared with 8 hours on MSD. Sponsors looking for a specific marker can search Ardena’s online biomarker catalogue, which lists 228 biomarkers across 12 disease areas on immunoassay, LC-MS/MS and flow cytometry platforms.
Timelines that keep pace with the program
A method only helps a program if the data arrive in time for the next decision. Typical lead times at Ardena are:
- Method development: 4 to 6 weeks for LC-MS/MS and 4 to 8 weeks for ligand binding assays
- Validation: 2 weeks to QA-checked data
- Sample receipt to analysis: within 3 days
- QC-checked results: within 5 working days after the experimental phase ends
- Draft report: within 15 working days after the QC-checked results
- Final report: within 5 working days after the sponsor’s comments
The sponsor works with a project team of a project manager, lab scientists and technicians, and receives regular progress reports covering technical, regulatory and scientific considerations.
Ardena’s bioanalytical laboratories
Ardena’s main bioanalytical site in Assen, the Netherlands, was founded in 1969 and covers 3,500 m². It has been GLP certified since 1992, has been audited by the FDA and for GCP, and hosts more than 15 sponsor audits per year. Data are managed in a LabWare LIMS that is 21 CFR Part 11 compliant. Ardena’s bioanalysis team runs more than 600 studies per year.
Bioanalysis is also offered at Ardena Oss in the Netherlands and Ardena Somerset in New Jersey, where a new bioanalytical laboratory opened in April 2026. Ardena has more than 800 validated methods and experience with FDA and EMA submissions.
As your program approaches its next stage, our scientists can help you select the right bioanalytical method for where it is today and adapt it, through further development and re-validation, as it advances.