Startseite Mass spectrometry based precision diagnostics: on the cusp of selective testing
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Mass spectrometry based precision diagnostics: on the cusp of selective testing

  • Michelle P. van der Helm ORCID logo EMAIL logo , L. Renee Ruhaak ORCID logo und Christa M. Cobbaert ORCID logo EMAIL logo
Veröffentlicht/Copyright: 29. September 2025
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Abstract

New technologies and advances in human biology are paving the way for better patient management and outcomes in laboratory medicine. Precision diagnostics, as an essential component of P5 medicine, implies a shift towards selective testing of defined measurands, enabling a higher understanding of interindividual diversity and (patho-)biology at the molecular level. Precision diagnostics can potentially overcome some of the current inadequacies in diagnostic care pathways, caused by suboptimal tests leading to misclassifications and avoidable patient harm. Additionally, molecular methods have the potential to be standardizable upfront, allowing embedding of the metrological traceability concept. Over the last decade, especially mass spectrometry (MS) is gaining momentum and proving its potential as a selective measurement method for immunoassay replacement, add-on test and/or reference measurement procedure (RMP). In this context, the current place of MS in laboratory medicine is discussed, followed by cases from laboratory developed tests (LDTs), commercially available tests, highlighting also future MS applications. It is time for a wake-up call to promote a selective testing approach that accurately resembles individual biology, principally to be used when molecular definition is clinically relevant for classification ability and patient benefit. We provide a compilation for the laboratory specialist when to opt for molecularly defined tests. Ideally, the evolution to precision diagnostics is part of a changing healthcare landscape, where molecular fingerprints and patient diversity are inclusive. This will enable early detection of preclinical symptoms and start a shift from curative to preventive and personalized care.

Introduction

With improved technologies that enhance selectivity and enable molecular characterization of the measurands intended to be measured, laboratory diagnostics will be transformed in a major way in the coming years. Hence, it is important to understand the clinical need and cost-effectiveness of improved selectivity of medical tests. To that end, we believe it is time to embrace the vision of precision diagnostics (Figure 1 for infographic) for improving patient management and outcomes. Precision diagnostics is a branch of precision medicine, which uses omics technologies (for example mass spectrometry (MS) based proteomics or metabolomics) to identify disease traits for personalized treatment strategies [1], [2], [3], [4]. It has the potential to overcome challenges faced in current diagnostic care pathways, which regularly deal with suboptimal tests not fit for purpose, leading to misclassifications and, with that, preventable patient harm. As part of precision diagnostics, selective measurements focusing on specially defined molecular species rather than biochemical mixtures, can be better correlated to patient outcomes and improve patient classification and subsequent treatment. We are convinced that new developments and discoveries in technology and biology should go hand in hand with the state of metrology and innovation in clinical care pathways in the healthcare sector (Figure 1 for infographic).

Figure 1: 
Infographic of the envisioned holistic approach: Precision diagnostics as part of P5 medicine following the evolution of technology, metrology and biology (state of the science) to improve patient outcomes with reduction in diagnostic uncertainty and reduced misclassifications (curative) and improved individual risk profiling (preventive) promoting targeted therapies. False positives (FP), true positives (TP), true negatives (TN) and false negatives (FN) in comparative diagnostic accuracy studies.
Figure 1:

Infographic of the envisioned holistic approach: Precision diagnostics as part of P5 medicine following the evolution of technology, metrology and biology (state of the science) to improve patient outcomes with reduction in diagnostic uncertainty and reduced misclassifications (curative) and improved individual risk profiling (preventive) promoting targeted therapies. False positives (FP), true positives (TP), true negatives (TN) and false negatives (FN) in comparative diagnostic accuracy studies.

Precision diagnostics as part of P5 medicine

Precision Medicine, originally conceptualized by Leroy Hood et al. [5], [6], [7], has promoted a more sustainable healthcare systems approach, encompassing key features for Predictive, Personalized, Preventive and Participatory healthcare. Later a fifth p for Psychocognitive healthcare was added by Gorini et al. [8], 9]). The approaches focus on digitized medicine with large datasets and molecular networks, with the aim to understand the complexity of disease, and with the intention to view modern medicine from a more proactive point of view rather than reactive [5], [6], [7], [8], [9]. For laboratory medicine this concept focusses on refining laboratory diagnostics (i.e. precision diagnostics) by shifting towards molecular testing of biomarkers. Molecular characterization of the measurands, which entails understanding the exact molecular composition of the measurand (e.g. specific protein variants, metabolites or molecules in bound or complexed form), forms the foundation of the envisioned personalized medicine approach, based on more personalized diagnoses and tailored treatments. Additionally, in the future, a holistic systems approach towards defining health and disease is envisioned by building biomolecular networks for each patient, resulting in data-driven personalized medicine. Laboratory tests that can unravel the interindividual diversity should foster the development of targeted therapies, giving rise to personalized healthcare. As such, precision diagnostics not only hold promise in a curative care setting to reduce diagnostic uncertainty, but also has potential for precision prevention [10], 11] to elucidate risk profiles and prevent disease onset.

MS for precision diagnostics

In the context of precision diagnostics within laboratory medicine, MS has gained considerable momentum over the past two decades, demonstrating its potential as a highly selective analytical measurement method. For instance, the combination of MS with liquid chromatography (LC) has become a powerful molecular separation and quantification technique. Tandem LC- MS/MS, also known as triple quadrupole (quad) MS, is currently the dominant MS analysis technique for clinical applications. Yet, also other MS techniques are used in laboratory medicine, for example matrix-assisted laser desorption ionization (MALDI) and ion trap, see also Tietz Chapter 17 (Section II) [12]. MS is used in a plethora of fields to characterize molecules (i.e. ions) based on different fragmentation patterns and mass-to-charge ratios. Currently, quantitative MS is becoming a key technology for standardization of molecular tests using molecular defined measurands. Also, the In Vitro Diagnostics (IVD)-industry is moving towards clinical mass spectrometry because of its precision diagnostic potential.

Role of SI standardization and defining the measurands

Ideally, medical test results are traceable within allowable measurement uncertainty to higher order reference methods and reference materials (RMs), to ensure accuracy and global comparability of test results and clinical decision limits [13], [14], [15], [16]. The majority of global standardization/harmonization efforts coordinated by the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) Scientific Division (SD) [Scientific Division – IFCC], are accomplished by means of MS-based reference measurement procedures (RMPs).

Challenges in protein-based measurands and why MS is transformative

Because of these global efforts, standardization of small molecules (e.g. steroids, metabolites, peptide hormones, immunosuppressive drugs) with molecular defined MS-based methods is now becoming reality. However, at present, SI standardization of proteins is challenging due to the enormous heterogeneity of proteins, similar in name but not in biological function. This includes genetic variants, isoforms, splice variants and/or post-translational modifications (PTMs) of proteins. Therefore, the clinical significance of molecular variants per protein, named proteoforms, should be thoroughly investigated and addressed if clinically relevant. Defining the measurand(s) of clinical interest is paramount for standardization of tests [17], 18]. Defining measurands, however, has proven to be difficult, not only for proteins with multiple proteoforms, but also for routinely measured, non-protein, clinical chemistry substances, where measurands are not appropriately defined.

Examples include magnesium and vitamin B12 (cobalamine). Magnesium is an analyte harboring physicochemical heterogeneity, as it can be present as protein bound, ionized or complexed. Assay wise, both total and ionized magnesium can be measured, with total magnesium hardly reflecting the biological active compound [19]. Similarly, measurements of vitamin B12 (cobalamine) are also complicated by heterogeneity, with total vitamin B12 assays failing to accurately reflect clinical consequences and harboring a grey area. Accordingly, for these above examples the biological active compounds are not measured, making the scientific validity of the results questionable and the link to possible underlying pathophysiology weak. Another example of a frequently measured non-selective test is serum/plasma creatinine. Here, the measurand is clearly defined (a cyclic derivative of creatine), but the Jaffe test suffers from severe interferences, making the final result unreliable and the scientific validity highly debatable. In this case, choosing for selective tests, especially in adult secondary and tertiary care and in pediatrics, has a huge impact on interpretation of kidney function and patient classification and outcome. Therefore, the main potential of MS lies in the molecular definition of the measurand, enabling the selective measurement of a single molecular entity, making the test also standardizable upfront.

We will first highlight the potential and the place of MS in the medical testing landscape. Subsequently, we will provide examples of MS-based laboratory developed tests (LDTs) (=in-house tests), and commercial tests, emphasizing also future MS applications in laboratory medicine. Finally, we will provide recommendations to laboratory specialists on when to measure selectively (with MS) tailored to specific tests and their specific intended use.

A glossary of terms, abbreviations and acronyms used is provided in Table 1.

Table 1:

Glossary of terms, abbreviations, and acronyms used throughout the publication.

AKI Acute kidney injury
AL Amyloidosis
AML Acute myeloid leukemia
ASMS American Society For Mass Spectrometry
AT AntiThrombin
B2M β2 Microglobulin
Calibration laboratories Laboratories that perform higher order RMPs (sometimes as part of national metrology institutes)
CDG Congenital disorders of glycosylation
CE Conformité Européenne
CE-marked Products with this label purchased in the European Economic area (EEA) have undergone assessment for high safety, health, and Environmental protection
CFDA China Food and Drug Administration
CFTR Cystic fibrosis transmembrane conductance regulator
CKD Chronic kidney disease
CLSI Clinical and Laboratory Standards Institute
CVD Cardiovascular disease
DCM Designated comparison method
EC Executive Committee
EFLM European Federation of Clinical Chemistry and Laboratory Medicine
EQA External Quality Assurance
ESI Electrospray ionization
FDA Food and Drug Administration (in the USA)
FN False negatives
FP False positives
Glyco-proteoform Variant of a genetically encoded protein with different glycosylation
HCG Human chorionic Gonadotropin
IA Immunoassay
IFCC The International Federation of Clinical Chemistry and Laboratory Medicine
IGF-1 Insulin-like growth factor 1
IGF-2 Insulin-like growth factor 2
ISO The International Organization for Standardization
IVD In Vitro Diagnostics
IVDR In Vitro Diagnostics Regulation
JCTLM Joint Committee on Traceability in Laboratory Medicine
LC Liquid chromatography
LC-MS/MS Tandem mass spectrometry
LDT Laboratory developed test (clinically in-house developed laboratory tests)
MACE Major adverse cardiovascular events
MALDI Matrix-assisted laser desorption ionization
Measurand Quantity intended to be measured (ISO 17511:2020)
Metrological traceability Measurement result property referring to the capability to connect the end-result to a (higher-order) reference through an unbroken chain of calibrations (documented in a calibration hierarchy according to ISO 17,511:2020)
MGUS Monoclonal gammopathy of unknown significance
MM Multiple myeloma
MRD Minimal residual disease
MRM Multiple reaction monitoring
MS Mass spectrometry
NGAL Neutrophil gelatinase-associated lipocalin
P5 medicine Holistic systems approach and an expansion of personalized medicine, encompassing elements for predictive, personalized, Preventive, Participatory and psychocognitive healthcare
PCOS PolyCystic ovary syndrome
Precision diagnostics Diagnostics in the context of precision medicine that is personalized, based on “omics” data and focuses on a molecular definition of disease
Proteoform Variant of a genetically encoded protein, e.g. different splice-isoform
PSA Prostate-specific antigen
PTM Post-translational modifications
Q/Quad Quadrupole
QALY Quality-Adjusted Life Years
Random access mode Direct access/24/7 available
RM Reference materials
RMP Reference measurement procedure
RMS Reference measurement system
ROI Return on investment
RPL Recurrent pregnancy loss
SI The International System of Units
SMM Smoldering multiple myeloma
TDM Therapeutic drug monitoring
TGA Therapeutic Goods Administration (in Australia)
TLA Total lab automation
TN True negatives
TOF Time-of-flight
TP True positives
VTE Venous thrombo embolism
VWD Von Willebrand disease

MS in clinical laboratories: where do we stand?

Stakeholders involved in establishing and implementing metrological traceability

Stakeholders involved in establishing and implementing metrological traceability are shown in Figure 2. In Europe, the IVD-industry can only introduce tests to the European market if these tests are compliant with requirements laid down in the In Vitro Diagnostics Regulation (IVDR) 2017/746. In other regions, tests have to be compliant to specific legislations: e.g. the Food and Drug Administration (FDA) in the USA, the China Food and Drug Administration (CFDA) in China, the Therapeutic Goods Administration (TGA) in Australia. In the European context, the IVD-industry develops methods in compliance with the IVDR 2017/746. Also, the IVD-industry acquires CE (Conformité Européenne)-marking by obtaining approval from notified bodies (installed by governments) (left side of Figure 2), for routine assays (mostly immunoassay-based) and potentially MS methods.

Figure 2: 
Stakeholders involved in establishing and implementing metrological traceability (specified for the European union under the IVDR 2017/746). IFCC catalyzes the process of establishing RMPs and RMs for global standardization of prioritized medical tests and in case of clear clinical needs. Calibration laboratories develop RMPs and/or RMs according to relevant metrology focused ISO standards. After approval, RMPs, RMs and services will be listed in the JCTLM database. New RMPs, RMs and RMSs should subsequently be adopted by the IVD-industry for the sake of safe and effective medical tests. EQA-organizers evaluate interlaboratory and intermethod variability whereas accrediting bodies audit the quality management system of medical diagnostic laboratories, currently according to the risk based ISO 15189:2022 guideline in Europe. Reference measurement procedure (RMP), reference materials (RMs), International Federation of Clinical Chemistry and Laboratory Medicine (IFCC), Joint Committee on Traceability in Laboratory Medicine (JCTLM), External Quality Assurance (EQA), Conformité Européenne (CE), I
n Vitro Diagnostics (Regulation) (IVD(R)) and laboratory developed tests (LDT).
Figure 2:

Stakeholders involved in establishing and implementing metrological traceability (specified for the European union under the IVDR 2017/746). IFCC catalyzes the process of establishing RMPs and RMs for global standardization of prioritized medical tests and in case of clear clinical needs. Calibration laboratories develop RMPs and/or RMs according to relevant metrology focused ISO standards. After approval, RMPs, RMs and services will be listed in the JCTLM database. New RMPs, RMs and RMSs should subsequently be adopted by the IVD-industry for the sake of safe and effective medical tests. EQA-organizers evaluate interlaboratory and intermethod variability whereas accrediting bodies audit the quality management system of medical diagnostic laboratories, currently according to the risk based ISO 15189:2022 guideline in Europe. Reference measurement procedure (RMP), reference materials (RMs), International Federation of Clinical Chemistry and Laboratory Medicine (IFCC), Joint Committee on Traceability in Laboratory Medicine (JCTLM), External Quality Assurance (EQA), Conformité Européenne (CE), I n Vitro Diagnostics (Regulation) (IVD(R)) and laboratory developed tests (LDT).

The IFCC SD Executive Committee (EC) prioritizes standardization of medical tests for which currently an RMP and/or RM is lacking. This prioritization is based on unfavorable benefit/harm ratio’s for patients and a clear clinical need (right side of Figure 2). These RMPs are often MS-based. Clinical laboratories can develop their own in-house LDTs, which can be MS-based.

Calibration laboratories, mostly hosted in academia but sometimes also in national metrology institutes, perform higher-order RMPs. Calibration Laboratories develop RMPs and/or RMs according to relevant metrology focused ISO standards (i.e. ISO 15193, ISO 15194, ISO 15195 and ISO 17511). The Joint Committee on Traceability in Laboratory Medicine (JCTLM) lists the endorsed RMPs, RMs and services in the JCTLM database, after a conformity assessment performed by the JCTLM review team(s) [20]. The RMPs can be part of an entire Reference Measurement System (RMS) and used for standardization of commercial kits in laboratory medicine. After establishing the higher order reference method and/or materials, the IVD-industry should adopt and implement new RMPs and RMs in its calibration hierarchies to ensure metrologically traceable test results.

Note that test standardization cannot correct for non-selectivity. The choice for either selective or unselective tests is made by laboratory professionals. They should take care that tests are fit-for-clinical-purpose based on desirable test performance, considering contemporary clinical guideline recommendations and the laboratory context in their care setting (budget, analyzers in place, daily production rate, presence of skilled personnel and degree of total laboratory automation (TLA)). Depending on their context, different test implementation choices can be made for different laboratories. To conclude, External Quality Assurance (EQA)-organizers may identify suboptimal test performance and/or excessive interlaboratory variability depending on the EQA-design, whereas accrediting bodies audit the quality management system of medical diagnostic laboratories, currently according to the risk based ISO 15189:2022 guideline in Europe.

Following the popularity of MS for RMP development by IFCC calibration laboratories and the landmark contribution from Hoofnagle et al. [21], [22], [23], MS has witnessed early adoption in academia, as proven by the current place of MS for in-house testing [18]. Commercial CE-marked MS assays followed later, for example for vitamins, steroids, amino acids, drugs of abuse and TDM. These tests use ready-made kits or closed, fully integrated MS systems. The latter makes the need for special MS operating personnel redundant.

MS based work-flows

Triple quad type MS are popular in laboratory medicine and are used often in special chemistry laboratory settings for selective detection and quantitation of the measurands intended to be measured. To that end, the molecules of interest in the reaction mixture are first separated using the LC method, although other separation methods are also available, such as capillary electrophoresis or direct injection of moderately complex mixtures [18]. The molecules are passed through the column (stationary phase) and elute at different retention times depending on their affinity for the stationary or mobile phase (typically a solvent mixture with a gradient or isocratic flow). Depending on the set-up, their absorbance may first be picked up by the diode array or ultraviolet detector. The separated molecules then enter the mass analyzer.

The mass spectrometer typically consists of three parts: 1) ionization source, 2) mass analyzer, and 3) detector. The ionization source transfers the molecules in gas-phase ions, which are subsequently brought to the mass analyzer. Depending on the type of substance a different ionization source can be used. Popular ionization methods are electrospray ionization (ESI) and MALDI. Also, mass analyzers have different varieties, such as time-of-flight (TOF), ion trap, Orbitrap and quadrupoles (Q). For the most commonly used tandem mass analysis (LC-MS/MS) typically two mass analyzers are used with a collision cell in between. Finally, the ionized molecular fragments arrive at the detector, which is generally an electron multiplier [24], 25].

While for microbiological applications MALDI-TOF has become a standard qualitative analysis technique, in clinical chemistry testing, tandem MS (LC-MS/MS) is preferred for quantitative analysis. In general, in laboratory medicine, MS tests are primarily performed with unit resolution MS instead of high resolution [26]. For accurate quantitative results, typically isotope labeled internal standards are used and the MS operation system is evaluated per run with a system suitability testing procedure. Furthermore, for the absolute quantification of compounds, such as metabolites, proteins, peptides and lipids, a multiple reaction monitoring (MRM) approach can be used, in tandem MS, which has the ability to quantify single compounds in complex mixtures with high specificity and sensitivity and thus selectively target the measurand of interest. Additionally, PTMs, like glycosylation status, can be examined. Moreover, for proteins proteolytic peptides after digestion or entire intact proteins can be studied. Additionally, to target selectively specific low abundant proteoforms MS can be combined with an immunocapture step [27], [28], [29], [30], [31], [32], [33], [34]. In Figure 3 an illustration is provided, showing how different proteoforms are averaged out or missed by routine (activity) assays and in contrast distinguished by molecular methods, such as MS. Noteworthy, genetic analysis can also detect protein mutations, but will not provide quantitative information on the mutated protein vs. the wildtype, which could be relevant for clinical outcome and severity of the pathological condition. Likewise, the evaluation of successful PTM attachment to the target protein cannot be achieved by genetic analysis.

Figure 3: 
Measuring proteins consisting of different proteoforms (created by genetic variation, alternative splicing and PTMs) with routine assays (mostly immune-assay based) vs. molecular methods, such as MS. With the conventional assays a mixture of different proteoforms is measured giving an average activity/mass or concentration of the various proteoforms (only the ones that can be detected by the specific assay), whereas MS-based methods can distinguish different proteoforms and measure selectively individual proteoform activity/concentration. For this infographic we took inspiration from Forgrave et al. [31].
Figure 3:

Measuring proteins consisting of different proteoforms (created by genetic variation, alternative splicing and PTMs) with routine assays (mostly immune-assay based) vs. molecular methods, such as MS. With the conventional assays a mixture of different proteoforms is measured giving an average activity/mass or concentration of the various proteoforms (only the ones that can be detected by the specific assay), whereas MS-based methods can distinguish different proteoforms and measure selectively individual proteoform activity/concentration. For this infographic we took inspiration from Forgrave et al. [31].

Clinical applications of MS

Overall, the benefits of MS over routine assays, mostly immunoassays, are evident. MS has a higher analytical specificity, sensitivity and selectivity, a wider analytical range, several possibilities for multiplexing, multiparametric analysis, patient profiling and above all MS provides structural molecular information about defined measurands that can be directly linked to (patho-)biology. Yet, most tests in laboratory medicine (especially for high-throughput applications) are still immunoassay-based. The choice for immunoassays is made due to their full automation possibilities, adequate reproducibility, low running costs, short turnaround time, and reasonable specificity and sensitivity [35], [36], [37]. Yet, immunoassays come with suboptimalities by design, where analytical error rates due to interferences of endogenous antibodies can be as high as 4 % with clinical consequences [37], 38]. Immunoassays deal with heterogeneous mixtures of unknown composition, hence fail to distinguish a molecular identifiable measurand. This raises the question if these tests are fit-for-purpose [39] in this era of precision medicine. For example, proteins in biology can exist in a variety of proteoforms depending on genetic variations, alternative splicing of their RNA counterpart and PTMs, such as glycosylation, phosphorylation and ubiquitination [31]. Alterations in these biological processes are key to understanding various pathological outcomes, such as phosphorylation of tyrosine kinases in acute myeloid leukemia (AML), glycosylation in the metabolic disease congenital disorders of glycosylation (CDG) and ubiquitination in neurodegenerative disease. From this perspective, it appears odd that examination of proteoforms is often overlooked in hospital laboratory testing. Except for the case of, for example, hemoglobin variants in relation to hemoglobinopathies, transferrin profiling in relation to alcohol consumption and cerebrospinal fluid leakage, this is not the case for a multitude of other proteins measured on a daily basis in routine diagnostics of the clinical laboratory.

We will highlight a collection of relevant LDTs and commercial tests, to show how patient misclassifications (and with that patient harm) can be overcome by measuring selectively with MS, discussing both small molecules and proteins.

Laboratory developed tests

Small molecules

Taking a look at LDTs, MS can be considered as one of the most popular methods. Especially in the field of TDM and toxicology, the potential of MS has already been recognized. As these type of tests mostly deal with exogenous small molecules, setting up the method is less cumbersome than for example for protein assays. Over the last decades, much progress has been made for LDTs and also MS protein tests are becoming reality. For TDM, much effort has been focused on immunosuppressive drugs, such as tacrolimus, sirolimus, everolimus and cyclosporine A. For these drugs, accurate and selective measurements have been established to enable narrow therapeutic target ranges, and to avoid drug under- or overexposure by measuring the single drug target measurand and avoiding cross-reactivity with drug metabolites [40], [41], [42]. These methods could be a direct replacement of the immunoassay and can be used as RMP.

Another elegant example in this context are cystic fibrosis transmembrane conductance regulator (CFTR) modulators for treatment of cystic fibrosis. The Isotope dilution LC-MS/MS assay that has been developed by Habler et al. is robust, highly selective, and has been shown to establish dose-response relationships in clinical trials in order to avoid adverse drug interactions. In addition, these LC-MS/MS methods for TDM have the benefit to also identify and quantify drug metabolites and evaluate the metabolite to parent compound ratio (MPR), which can identify abnormal metabolism. This is a new test, superior to other chromatography methods that measure CFTR modulators. Superior because of the inclusion of isotope dilution standardization and a clinical relevant linear calibration range [43].

For small molecules, much work has also been devoted to the establishment of steroid and other small molecule hormones MS measurements. The benefit of LC-MS/MS in this matter is avoiding cross-reactivity, overcoming interference and matrix effects, decreasing intra- and interlaboratory variation and poor reproducibility and overall expansion of the measurement range and the possibility to set up multiplex hormone assays. As such, these MS tests are used as replacement or add-ons of current immunoassays, but also proposed as RMPs. A small molecule hormone that can be monitored better with MS is for example serum/plasma testosterone. The measurement range is increased to also measure reliably towards the lower limit of detection. Cross-reactivity from other hormone analogues is avoided, which is, for example, important for ageing man with potential hypogonadism [44]. MS methods for testosterone, cortisol and free thyroxine are also less affected by sample matrix, for example to accurately measure hormones in patients with renal failure with altered serum composition [45]. Additionally, thyroid status in pregnant woman has been shown to be more reliably measured with LC-MS/MS [46]. Vitamin D and its metabolites can also be accurately measured with MS. Herrmann et al. have elegantly shown that the vitamin D metabolite ratio can more accurately classify vitamin deficiency than a single 25-hydroxyvitamin D cutoff [47]. Furthermore, MS is key in newborn screening for detecting both hormone disbalances and inborn errors of metabolism. Hormones, such as 21-deoxycortisol for classic congenital adrenal hyperplasia [48], acylcarnitines, and amino acids for inborn errors can be easily picked up [49]. Also for creatinine, an isotope dilution MS method for standardization purposes has been set-up. This method would also have the potential to be used for kidney function evaluation of specific patient groups (as add-on), e.g. for liver failure patients (and patients with high interfering bilirubin concentrations) or patients who receive medications interfering with conventional immunoassays.

Proteins

Shifting from small molecules to protein MS measurement methods in laboratory medicine, Forgrave et al. have recently summarized the latest developments [31]. They highlight that individual proteoforms can be especially important for the following cases: Alpha-1-antitrypsin deficiency, Alzheimer’s disease and amyloid-β peptide variants, Amyloidosis and amyloid typing, hemoglobinopathies and hemoglobin variants, cardiac biomarkers: B-type natriuretic peptides and troponins, D-dimer, immunoglobulins and monoclonal gammopathies, adrenocorticotropic hormone, parathyroid hormone, insulins and erythropoietins. For insulins, MS can distinguish between endogenous and exogenous proteoforms, whereas in immunoassays the use of exogenous substances can lead to interference and unreliable assay results. For erythropoietins, it is also important to distinguish between different glyco-proteoforms for athletes’ doping control.

For establishing metrological traceability of test results, many scientific working groups of the IFCC [50] develop RMPs based on MS for peptides/proteins. The measurands of focus here are apolipoproteins, cardiac troponins I/T, albumin in urine, hemoglobin A2 and fetal hemoglobin, growth hormone, pancreatic enzymes, carbohydrate-deficient transferrin, insulin, procalcitonin, natriuretic peptides and biomarkers for neurodegenerative disease. For the majority of these measurands, the incentive is the establishment of candidate RMPs (compliant to ISO 15193) as an essential part of the calibration hierarchy in accordance to ISO 17511.

Identifying the potential of individual proteoforms in relation to pathophysiology, research is also directed towards tumor markers, as certain proteoforms could be differently expressed in tumors. This has for example been shown for prostate-specific antigen (PSA) glyco-proteoforms [51]. Glycoproteotyping is also important for testing of the major human pregnancy protein hormone: human chorionic gonadotropin (hCG). During pregnancy, the hCG maternal concentration and glycosylation change. Hence, pregnancy outcome is related to the source of production and individual glycoforms of hCG that harbor varying biological roles and activities [52]. Therefore, for hCG, MS methods have been developed to measure different glyco-proteoforms, which have the potential to improve the link to clinical outcome and allow individual profiling, which is for example interesting for the diagnosis of molar pregnancies [53], 54]. Recently, an entire proteomic analysis for the evaluation of predictive biomarkers for malignant transformation in complete hydatidiform moles was published [55]. Current classification of pregnancies of unknown location with serial hCG calculations can lead to misclassifications of ectopic/intrauterine pregnancy [56]. Individual spatial proteoform analysis could be a potential solution and fill the diagnostic gap in the future. Molecular tests for PSA and hCG have the potential to be used as add-on test for specific target populations (e.g. prostate cancer remission and molar pregnancy).

Other biomarker examples that could benefit from a mass spectrometry approach are insulin-like growth factors 1 and 2 (IGF-1/2). An MS test has been developed that can detect proteoforms of the same protein, which is more robust towards interferences and has the potential to provide less (interlaboratory) variation [57]. This test can be used as add-on in diagnostics.

Another protein where selective measurement with mass spectrometry could strongly improve test utilization and interpretation is ferritin. A ferritin protein consists of 24 subunits of different isoforms (H- and L-chains). The H to L subunit ratio of ferritin depends on the origin of the tissue and its development. Serum ferritin, mainly consisting of the L subunit, is thought to be glycosylated and to be quite iron-poor [58]. Serum ferritin is routinely measured with immunoassays. Interlaboratory variation among different IVD-assays is high due to simultaneous use of different RMs [59]. A decade ago an MS test was developed to also evaluate the iron loading of ferritin [60], yet such test has not yet been widely adopted. Considering the simultaneous use of different outdated RMs and non-matching reference intervals by different IVD-manufacturers, misclassification and malpractices occur due to confounded results [61]. The need for a single and unequivocal reference measurement system is obvious [60], 61]. Unequivocal molecular characterization of the measurand and reference material, is key to fix this problem. Beyond serum ferritin, hepcidin is a promising biomarker for the evaluation of body iron status and for the diagnosis and management of disorders in iron metabolism. Hepcidin also consists of different isoforms, which can be measured successfully using mass spectrometry [62], 63]. For molecular defined iron tests the development of RMPs is important, yet future molecular tests could also be used as add-on for more complex iron deficiency target groups.

Other laboratory diagnostic domains where technological innovations are highly needed and the concept of metrological traceability and standardization are barely known, is the field of thrombosis and hemostasis. Clotting factor assays are not standardized in terms of a golden reference method or reference materials, nor are specific proteoforms taken into account, leading to masking of clinical information. Recent laboratory developments show the ability of measuring individual proteoforms, for example for antithrombin (AT) in relation to hereditary thrombophilia and recurrent miscarriages and clotting factors in relation to hemophilia and von Willebrand disease [64], [65], [66], [67], [68]. These next-generation MS methods harbor excellent molecular selectivity and can identify proteins on the molecular level down to the amino acid sequence. These tests have potential as RMPs and can be used as add-ons when activity levels are inconclusive.

Further clinical gaps in care pathways where precision diagnostics with MS could add value is for the timely diagnosis of acute kidney injury. An MS-based urine multiplex protein panel has been developed. It is promising, but it needs further clinical validation [69], [70], [71], [72], [73]. Similarly, for bladder cancer, molecular urine tests could reduce the number of cystoscopies during surveillance and in the long run improve patient quality of life [74]. Perhaps different proteins (including different proteoforms) could also play a role here in distinguishing (different stages of) bladder cancer [75], as for example low-grade bladder cancer has been proven more difficult to monitor by cytology. Furthermore, in addition to proteomic markers, it is expected that genomic markers will also become important in the future for bladder cancer diagnosis and surveillance [76]. Noteworthy, these are new tests that still have to prove their potential in clinical performance studies [77].

Beyond proteomics, clinical lipidomics is receiving a high level of attention. The aim is to convert a single lipid marker to a multiple component lipid panel to enable more comprehensive monitoring of lipid related pathological outcomes and possible treatment benefits [78]. In analogy, for cardiovascular risk prediction and management, a multiplex, molecular defined apolipoprotein panel has been proposed [79] to enable cardiovascular precision diagnostics. The latter test has been developed in the Leiden Apolipoprotein Reference Laboratory in dual [80], 81]: 1) as a semi-automated designated comparison method (DCM) for use in clinical and pharma trials which demand a high (er) throughput; 2) as the highest order RMP for metrology purposes such as test standardization and trueness verification of commercial reagents.

Looking at the future, MS opens up the possibility to measure more selectively, multiplexed, and targeted for specific proteins (eventually encompassing different proteoforms), metabolites with defined measurands and/or personalized lipid profiles. MS offers a unique platform with direct measurement of phenotype (proteins/metabolites) in comparison to the predictive value of gene expression (genomics and transcriptomics). MS may even play a role in measuring molecular interactions, allowing for a more holistic approach and a molecular definition of health and disease. MS may bring us closer to the establishment of a grand overall picture of physiology and pathology as aimed for in current Systems Biology approaches [6], 7], 82].

Commercial CE-marked tests for open- or closed MS analyzers

Industrial applications of MS are available in ready-made kits for a laboratory’s own mass spectrometer, such as vitamin B1/B6 assays. Also fully automated solutions are being developed. A disadvantage of the MS LDTs is the reduced automated handling. Recently, the industry is making progress to solve this issue for small molecule MS methods.

In 2017 SCIEX launched the first fully integrated LC-MS system for clinical diagnostics. The SCIEX Topaz™ LC-MS/MS System offers automation possibilities with both open and locked operation modes. The system has also obtained CE-approval. It offers unique flexibility as it can be used for both in-house tests and ready-made IVD-kits, for example for vitamin D [83]. At the 2025 American Society for Mass Spectrometry (ASMS) conference in Baltimore, it became apparent that MS-companies are heading forward towards clinical use of their latest mass spectrometers, respectively Astral zoom and Stellar MS from Thermo Fisher Scientific, timsMetabol™ MS from Bruker and 6495D QQQ-MS from Agilent.

Advancing further in clinical mass spectrometry, Roche has launched the CobasR Mass Spec with an envisioned broad test menu of CE-marked IonifyR assays for e.g. TDM, endocrinology, drugs-of-abuse and immunosuppressive drugs. Roche did not only focus on full automation with paramagnetic particle-based sample preparation, but also on technology benefits such as improved specificity due to antibody-based sample purification, subsequent LC-separation of potential interferents by physicochemical properties and tandem MS separation of potential interferents by mass over charge ratio of both precursor and fragment ion. Roche has also addressed the issue of poor standardization, by developing independent RMPs. The Ionify testmenu harbors (so far) MS methods for steroids, vitamins, TDM and drugs of abuse/toxicology. Clinical benefits include higher analytical sensitivity and reliability, as well as personalized treatment options with accurate dose-response monitoring. The Roche solution will provide a fully integrated, high-throughput, automated and standardized workflow with CE-marked/IVDR-compliant MS-tests. This will expand the routine availability of MS tests, either as replacement tests for flawed immunoassays or as add-on tests giving more granularity, even in laboratories lacking MS-specialized laboratory technicians [84], [85], [86].

The EXENTR solution from Thermo Fischer Scientific is another recent automated commercial MS instrument that has obtained CE-marking and is available on the European market. This is a fully integrated and automated MALDI-TOF mass spectrometer designed for the detection of M-proteins from monoclonal gammopathies. The EXENT solution addresses the unmet clinical need to detect M-protein concentrations below the limit of detection for conventional techniques (such as protein electrophoresis and immunofixation) and hence enables improved detection of minimal residual disease (MRD) and avoidance of misclassification. Reduced light chains from intact immunoglobulins (produced by the plasma cells) are analyzed by a MALDI-TOF MS. The intended use is to aid in the monitoring of monoclonal gammopathies (monoclonal gammopathy of undetermined significance (MGUS), smoldering multiple myeloma (SMM), multiple myeloma (MM), Waldenström’s macroglobulinemia, amyloidosis (AL) and monitoring of MM and Waldenström’s macroglobulinemia patients) [87], [88], [89]. Noteworthy, also personalized LDTs for M-protein detection have been developed [90], [91], [92], [93]. These tests have the potential as add-ons for detection of MRD [91].

General considerations

The integration of MS analyzers in random access mode (direct access/available 24/7) with a broad test menu, interoperable with TLA concepts in medical laboratories, holds great promise for shaping the future landscape with personalized laboratory diagnostics and precision medicine. The implementation of these automated MS systems needs to be evaluated in the healthcare ecosystem of the medical laboratory, looking at added clinical value, i.e. the balance between clinical and cost-effectiveness, and return on investment (ROI). The first examples of cost-effectiveness analyses of tandem mass spectrometry for neonatal screening, demonstrate promising results based on health outcomes measured in quality-adjusted life years (QALYs) [94], 95]. Compliance with regulatory requirements (i.e. IVDR compliance) and education of all stakeholders involved in the care pathway have to be considered. Interhospital collaborations and/or centralizations of this type of technology are needed to create ROI. It is important to note that the development of LDTs on MS should not be slowed down or hindered by the commercial MS solutions that are entering the diagnostic market. LDTs remain crucial for supporting new developments and breakthrough innovations in the case of orphan diseases, metabolic disorders, and for rapid solutions during pandemic crises. Our vision is that in-house developed tests and commercial MS-based tests are complementary, and together they drive the transition to selective tests or test panels to reach the goal of precision medicine.

Despite all efforts being undertaken, full adoption of MS-based precision diagnostics in laboratory medicine has not yet been reached – it requires staff expertise, with highly-skilled analytical chemists, proper instrumentation, suitable software platforms, quality control and active validation protocols. Adequate implementation will be challenging, due to the variety of MS-based methods from commercial kits to fully automated, closed MS-analyzers and LDTs, and operation by unexperienced operators. The Dutch EQA surveys illustrate huge interlaboratory variations of in-house developed MS-method. It is hypothesized that, beyond standardization efforts, operator training and strict adherence to the CLSI C62-A guideline could lead to reduced variation between laboratories [18], 33], 96]. In addition, to guide the laboratory specialist towards high quality MS operation, Vogeser et al. recommends a minimum set of requirements for the evaluation of the analytical specification of clinical MS procedures. They highlight requirements from professional and ISO-standards (CLSI 62-A and ISO 15189) and also provide practical advice [26]. Medical laboratories will likely strive for automated clinical MS once test menus are sufficiently broad, connectivity to TLA is feasible and daily operations can be performed by regularly trained laboratory technicians.

Conclusions and perspective on testing landscape

A shift from suboptimal tests to selective MS-based tests

It is time for a wake-up call for laboratory professionals. As science, metrology and technology evolve, we have arrived in an era where unprecedented choices are available regarding the degree of granularity of the measurands, and the selectivity and standardizability of tests. For personalized patient care, focus on a more patient-centered individual testing approach, accurately reflecting an individual’s biology, is needed. Early diagnoses of preclinical curable stages of disease are key in order to allow the shift to preventive medicine as well. It is time to re-evaluate the laboratory medicine testing landscape (i.e. modernize the elder biomarkers, where needed) and start with the development, evaluation, validation and implementation of molecular defined methods (for example via MS based proteomics/metabolomics/lipidomics/breathomics) and assess their scientific validity [97], 98].

Prioritization of selective testing with MS

In order to examine the clinical performance of promising “omics” biomarkers, we recommend adhering to the cyclical test evaluation framework developed by the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM) Working Group on Test Evaluation [39]. Adherence to this framework makes sure that only tests that are fit for clinical purpose are selected and prioritized based on patient harm/benefit ratio [77]. As highlighted here for novel MS methods, clinical gaps are the driver for test development. Early international standardization of new tests is of paramount importance. Step-by-step, laboratory specialists in different fields of laboratory medicine (e.g. thrombosis and hemostasis, hematology, endocrinology, immunology) should take a closer look at the current practice and evaluate where more refined selective molecular methods could improve current clinical care pathways. To guide laboratory specialists, we provide a compilation of when selective measurands are considered important to overcome misclassification and mistreatment, leading to patient harm and achieve intended clinical benefit (Table 2). These selective tests are mostly used as immunoassay (or routine test) replacement or add-on, although some test are also developed as RMP. As can be derived from the table, there are many opportunities for precision diagnostics in current clinical care pathways. Selective molecular tests should be chosen for specific intended use and as add-on to the current standard diagnostics by prioritization based on patient benefit/harm ratio. The clinical chemist can guide the clinician on when to opt for a more selective molecular test. We recommend that laboratory specialists should collaborate more and take a more pro-active role in the IVD-test development process and post-market surveillance in order to create awareness about the clinical needs and the necessity to manufacture sufficiently selective tests (Figure 2). Early adopters of clinical MS, such as Roche, Bruker, Agilent, SCIEX and Thermofisher are encouraged to contribute to the transition towards precision diagnostics in laboratory medicine. They should develop a thorough understanding of the drivers behind this transition and understand the concept of metrological traceability of test results, which is relevant for sustainable test standardization. Further research is also needed on the clinical utility and cost-effectiveness [99] of molecular measurement methods, along with the development of clinical studies designed for precision diagnostics [100].

Table 2:

A compilation of tests where molecular measurements lead to better patient management and can resolve clinical gaps in existing clinical care pathways.

Area of expertise Molecular test Measurand (example) (Potential) place in testing landscape Clinical care pathway(s) example Intended use Clinical benefit Ref.


TDM
Immunosuppressive drugs Sirolimus, everolimus, tacrolimus, cyclosporine A RMP and IA replacement Kidney transplantation Monitoring of medication dosage Narrow therapeutic target ranges and avoidance of drug under- or overexposure by measuring a single compound (no cross-reactivity with drug metabolites) [40], [41], [42]
CFTR modulator medication Ivacaftor, lumacaftor, tezacaftor, elexacaftor, and their major metabolites New test Cystic fibrosis Dose response relationships in order to avoid adverse drug interactions. Evaluation of metabolizing enzymes by simultaneous measuring the major drug metabolites. [43]


Clinical chemistry
Apolipoprotein panel Apolipoprotein (a) RMP and add-on test CVD Prediction of MACE and treatment benefit by apolipoprotein profiling Improved CVD prediction and subsequent personalized treatment options [79]
Urinary biomarkers panel Selected proteins for kidney injury (e.g. nephrin, NGAL, B2M) New test AKI and CKD/acute transplant rejection Early detection or prediction of AKI (e.g. in the context of drug nephrotoxicity or transplant rejection) and/or irreversibility of CKD Avoidance of irreversible CKD. In case of medication related AKI, change dosage of medication [69], [70], [71], [72], [73]
Urinary proteome profiling New test Bladder cancer Early detection or recurrence of disease To replace cystoscopies and achieve noninvasive monitoring [74], 75]
Ferritin/hepcidin Ferritin/hepcidin RMP potential and add-on test Iron deficiency anemia Assessment of iron status (including iron loading) and diagnosis of anemia No misclassifications. Oral iron treatment for patients in need. [60], [61], [62], [63]
PSA PSA glyco- proteoforms Add-on test Prostate cancer Diagnosis, screening and monitoring To avoid misclassifications (and over- or underdiagnosis and overtreatment) by measuring relevant individual proteoforms [51], 101]
hCG hCG glyco-proteoforms Add-on test (Molar) pregnancy [52], [53], [54], [55], [56]


Endocrinology
Vitamin D 25-Hydroxyvitamin D [25(OH)D], 24,25-dihydroxyvitamin D [24,25(OH)2D] and the vitamin D metabolite ratio Add-on test Vitamin D deficiency Diagnosis and monitoring Avoidance of interference, matrix effects, cross-reactivities, intra- and interlaboratory variation, poor reproducibility and expansion of measurement range [47], 102]
Thyroid hormones Free thyroxine RMP and IA replacement/add-on test Hypo- and hyperthyroidism [103]
Testosterone Free testosterone RMP and IA replacement/add-on test Hypogonadism and PCOS [45]
IGF-1 and IGF-2 IGF-1 and IGF-2 proteoforms IA replacement or add-on test Growth hormone–related disorders (e.g. acromegaly) [57]


Hematology/Immunology
M-protein and free light chains Ig heavy and/or (reduced) light chains Add-on test Monoclonal gammopathies (such as MM and MGUS) Detection of minimal residual disease

Aid in the diagnosis of monoclonal gammopathies and monitoring of MM and Waldenström’s macroglobulinemia
Avoidance of misclassification [87], [88], [89], [90], [91], [92], [93]


Thrombosis and hemostasis
(Anti) coagulation factors AT glyco-proteoforms RMP and add-on test Hereditary thrombophilia (due to AT deficiency), leading to VTE or RPL Diagnosis and monitoring Reduced measurement uncertainty and accurate diagnosis (no misclassification) [64], 67], 68]
VWF proteoforms RMP and add-on test VWD [65], 66]
  1. TDM, Therapeutic Drug Monitoring; CFTR, Cystic Fibrosis Transmembrane Conductance Regulator; MACE, Major Adverse Cardiovascular Events; CVD, Cardiovascular Disease; B2M, β2 microglobulin; NGAL, Neutrophil Gelatinase-associated Lipocalin; AKI, Acute Kidney Injury; CKD, Chronic Kidney Disease; PSA, Prostate-specific Antigen; hCG, human Chorionic Gonadotropin; PCOS, Polycystic Ovary Syndrome; IGF, Insulin-like growth Factor; MM, Multiple Myeloma; MGUS, Monoclonal Gammopathy of Unknown Significance; AT, Antithrombin; VTE, Venous Thromboembolism; RPL, Recurrent Pregnancy Loss; VWD, von Willebrand disease; RMP, reference measurement procedure; IA, Immunoassay. Glossary of terms, abbreviations, and acronyms.

To conclude, laboratory medicine has arrived in a transformative era due to converging advances in science, metrology and technology. Choices for more granular, selective and standardizable tests can now be made. This requires awareness, education and understanding of the relation of molecular defined measurands with disease or treatment as well as understanding the rationale for selective methods depending on the intended use in specific patient groups. Efforts are ongoing by the IVD-industry and clinical laboratories, to establish and integrate selective tests in the testing repertoire and include MS-testing in their high-throughput, automated routine laboratory test menu. Ultimately, laboratory specialists should discern when selective tests are required and if less selective methods are still fit-for-purpose. The evolution to precision diagnostics, as part of a paradigm shift to P5 medicine [5], is a golden opportunity for leveraging the role of medical laboratories and for making the healthcare system more sustainable.


Corresponding authors: Michelle P. van der Helm, MSc, PhD and Christa M. Cobbaert, Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA, Leiden, The Netherlands, E-mail: (M.P. van der Helm), (C.M. Cobbaert)

Acknowledgement

J.W. Schoones from the Directorate of Research Policy (Leiden University Medical Centre, Leiden, The Netherlands) is acknowledged for his assistance in the final editing and proofing of the language.

  1. Research ethics: Not applicable.

  2. Informed consent: Not applicable.

  3. Author contributions: M.P. v.d. Helm and C.M. Cobbaert: conceptualization. M.P. v.d. Helm: writing the original draft. M.P. v.d. Helm, L.R. Ruhaak and C.M. Cobbaert: review and editing final draft. All authors have accepted responsibility for the entire content of this manuscript and approved its submission.

  4. Use of Large Language Models, AI and Machine Learning Tools: None declared.

  5. Conflict of interest: The authors state no conflict of interest.

  6. Research funding: None declared.

  7. Data availability: Not applicable.

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Received: 2025-04-15
Accepted: 2025-09-16
Published Online: 2025-09-29

© 2025 the author(s), published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

Heruntergeladen am 1.10.2025 von https://www.degruyterbrill.com/document/doi/10.1515/cclm-2025-0461/html
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