Direct quantification in bioanalytical LC–MS/MS using internal calibration via analyte/stable isotope ratio

Species-specific oxylipins and the effects of ontogeny and predation on their emission from freshwater snails

Chemical cues play important roles in mediating ecological interactions. Oxylipins, oxygenated metabolites of fatty acids, are one signalling molecule type that influences the physiology and function of species, suggesting their broader significance in chemical communication within aquatic systems. Yet, our current understanding of their function is restricted taxonomically and contextually making it difficult to infer their ecological significance. Snails and leeches are ubiquitous in freshwater ecosystems worldwide, yet little is known about their oxylipin profiles and the factors that cause their profiles to change. As snails and leeches differ taxonomically and represent different trophic groups, we postulated oxylipin profile differences. For snails, we hypothesized that ontogeny (non-reproductive vs reproductive) and predation (non-infested vs leech-infested) would affect oxylipin profiles. Oxylipins were characterized from water conditioned with the snail Planorbella duryi and leech Helobdella lineata, and included three treatment types (snails, leeches, and leech-infested snails) with the snails consisting of three size classes: small (5-6 mm, non-reproductive) and medium and large (13-14 and 19-20 mm, reproductive). The two species differed in the composition of their oxylipin profiles both in diversity and amounts. Further, ontogeny and predation affected the diversity of oxylipins emitted by snails. Our experimental profiles of oxylipins show that chemical cues within freshwater systems vary depending upon the species emitting the signals, the developmental stage of the species, as well as from ecological interactions such as predation. We also identified some candidates, like 9-HETE and PGE2, that could be explored more directly for their physiological and ecological roles in freshwater systems.

Towards clinical adherence monitoring of oral endocrine breast cancer therapies by LC-HRMS-method development, validation, comparison of four sample matrices, and proof of concept

Oral endocrine therapies (OET) for breast cancer treatment need to be taken over a long period of time and are associated with considerable side effects. Therefore, adherence to OET is an important issue and of high clinical significance for breast cancer patients' caregivers. We hypothesized that a new bioanalytical strategy based on liquid chromatography and high-resolution mass spectrometry might be suitable for unbiased adherence monitoring (AM) of OET. Four different biomatrices (plasma, urine, finger prick blood by volumetric absorptive microsampling (VAMS), oral fluid (OF)) were evaluated regarding their suitability for AM of the OET abemaciclib, anastrozole, exemestane, letrozole, palbociclib, ribociclib, tamoxifen, and endoxifen. An analytical method was developed and validated according to international recommendations. The analytical procedures were successfully validated in all sample matrices for most analytes, even meeting requirements for therapeutic drug monitoring. Chromatographic separation of analytes was achieved in less than 10 min and limits of quantification ranged from 1 to 1000 ng/mL. The analysis of 25 matching patient samples showed that AM of OET is possible using all four matrices with the exception of, e.g., letrozole and exemestane in OF. We were able to show that unbiased bioanalytical AM of OET was possible using different biomatrices with distinct restrictions. Sample collection of VAMS was difficult in most cases due to circulatory restraints and peripheral neuropathy in fingers and OF sampling was hampered by dry mouth syndrome in some cases. Although parent compounds could be detected in most of the urine samples, metabolites should be included when analyzing urine or OF. Plasma is currently the most suitable matrix due to available reference concentrations.

Advancing High-Throughput MS-Based Protein Quantification: A Case Study on Quantifying 10 Major Food Allergens by LC-MS/MS Using a One-Sample Multipoint External Calibration Curve

The LC-MS-based method has emerged as the preferred approach for quantifying food allergens. However, the preparation of a traditional calibration curve (MSCC) is labor-intensive and error-prone. Here, a sensitive and robust LC-MS/MS method for quantifying 10 major food allergens was developed and validated, where the one-sample multipoint external calibration curve (OSCC) was employed instead of MSCC. By employing the multiple isotopologue reaction monitoring (MIRM) technique with only one spiked level in the blank, OSCC can be effectively established. Results demonstrate that the proposed method exhibits excellent performance in selectivity, sensitivity, accuracy, and precision, comparable to that of the traditional MSCC. Additionally, this strategy allows for isotope sample dilution by monitoring the less abundant MIRM channel. Moreover, the developed method was successfully applied to investigate the contamination of 10 food allergens in commercial food products. With its high throughput and robustness, the MIRM-OSCC-LC-MS/MS methodology has many potential applications, especially in the MS-based protein quantification analysis.

Integrating a Multiple Isotopologue Reaction-Monitoring Technique and LC-MS/MS for Quantitation of Small Molecules: Ten Mycotoxins in Cereals as an Example

Accurate quantification of mycotoxin in cereals is crucial for ensuring food safety and human health. However, the preparation of traditional multisample external calibration curves (MSCCs) is labor-intensive and error-prone. Here, a multiple isotopologue reaction-monitoring (MIRM)-LC-MS/MS method for accurate quantitation of ten major mycotoxins in cereals was successfully developed and validated, where a novel one-sample multipoint calibration curve (OSCC) strategy is used instead of MSCCs. The OSCC can be established by examining the correlation between the calculated theoretical isotopic abundances and the measured abundance across various MIRM channels. In comparison to the MSCC, the OSCC strategy exhibits outstanding performance including superior selectivity, accuracy (78.4-108.6%), and precision (<12.5%). Furthermore, the proposed OSCC-MIRM-LC-MS/MS method was successfully applied to investigate mycotoxin contamination in cereal samples in China. Considering the advantages of simplified workflows and improved throughput, the OSCC-MIRM-LC-MS/MS methodology holds great promise for accurately quantifying chemical contaminants in foods.

Multitargeted Internal Calibration for the Quantification of Chronic Kidney Disease-Related Endogenous Metabolites Using Liquid Chromatography-Mass Spectrometry

Accurate quantitative analysis in liquid chromatography-mass spectrometry (LC-MS) benefits from calibration curves generated in the same matrix as the study sample. In the case of endogenous compound quantification, as no blank matrix exists, the multitargeted internal calibration (MTIC) is an attractive and straightforward approach to avoid the need for extensive matrix similarity evaluation. Its principle is to take advantage of stable isotope labeled (SIL) standards as internal calibrants to simultaneously quantify authentic analytes using a within sample calibration. An MTIC workflow was developed for the simultaneous quantification of metabolites related to chronic kidney disease (CKD) using a volumetric microsampling device to collect 20 μL of serum or plasma, followed by a single-step extraction with acetonitrile/water and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Since a single concentration of internal calibrant is necessary to calculate the study sample concentration, the instrument response function was investigated to determine the best SIL concentration. After validation, the trueness of 16 endogenous analytes in authentic human serum ranged from 72.2 to 116.0%, the repeatability from 1.9 to 11.3%, and the intermediate precision ranged overall from 2.1 to 15.4%. The proposed approach was applied to plasma samples collected from healthy control participants and two patient groups diagnosed with CKD. Results confirmed substantial concentration differences between groups for several analytes, including indoxyl sulfate and cortisone, as well as metabolite enrichment in the kynurenine and indole pathways. Multitargeted methodologies represent a major step toward rapid and straightforward LC-MS/MS absolute quantification of endogenous biomarkers, which could change the paradigm of MS use in clinical laboratories.

Rapid characterization of isotopic purity of deuterium-labeled organic compounds and monitoring of hydrogen-deuterium exchange reaction using electrospray ionization-high-resolution mass spectrometry

RATIONALE

Deuterium-labeled organic compounds, reagents, and drugs are widely used in many scientific research fields. Isotopic purity as the feature parameter of deuterated compounds is of great importance. In this article, we used electrospray ionization with high-resolution mass spectrometry (ESI-HRMS) to study isotopic purity of deuterium-labeled organic compounds based on assigning and distinguishing the corresponding H/D (hydrogen-deuterium) isotopolog ions of deuterated compounds.

METHODS

We systematically considered the specific requirements of accuracy and resolution of ESI-HRMS when measuring isotopic purity and demonstrated some actual cases using ESI-HRMS and ultraperformance liquid chromatography (UPLC)-HRMS. Meanwhile, ESI-HRMS/MS of deuterated compounds was performed to obtain more information on deuterium-labeled position characterization.

RESULTS

Two isotopic purity calculation methods based on the relative abundance in ESI-HRMS and UPLC-HRMS of H/D isotopolog ions (D0 -Dn ) were compared, which gave consistent isotopic purity values and were in good agreement with the certified isotopic purity values. We further studied and monitored the H/D exchange reaction of ethyl 3-(4-bromophenyl)-3-oxopropanoate (EBPO) by evaluating the dynamic isotopic purity changes in EBPO-D2 in the H/D exchange reaction in situ.

CONCLUSION

The isotopic purity characterization methods using ESI-HRMS discussed in this article have some outstanding advantages: rapid, highly sensitive, very low sample consumption (even below nanogram level), and deuterated solvent-free. Thus, this low-impact analytical method requires less time and is cost effective and might have good application potential for in-situ isotopic purity analysis and for monitoring the H/D exchange reactions.

Straightforward quantification of endogenous steroids with liquid chromatography-tandem mass spectrometry: Comparing calibration approaches

Different calibration strategies are used in liquid chromatography hyphenated to mass spectrometry (LC-MS) bioanalysis. Currently, the surrogate matrix and surrogate analyte represent the most widely used approaches to compensate for the lack of analyte-free matrices in endogenous compounds quantification. In this context, there is a growing interest in rationalizing and simplifying quantitative analysis using a one-point concentration level of stable isotope-labeled (SIL) standards as surrogate calibrants. Accordingly, an internal calibration (IC) can be applied when the instrument response is translated into analyte concentration via the analyte-to-SIL ratio performed directly in the study sample. Since SILs are generally used as internal standards to normalize variability between authentic study sample matrix and surrogate matrix used for the calibration, IC can be calculated even if the calibration protocol was achieved for an external calibration (EC). In this study, a complete dataset of a published and fully validated method to quantify an extended steroid profile in serum was recomputed by adapting the role of SIL internal standards as surrogate calibrants. Using the validation samples, the quantitative performances for IC were comparable with the original method, showing acceptable trueness (79%-115%) and precision (0.8%-11.8%) for the 21 detected steroids. The IC methodology was then applied to human serum samples (n = 51) from healthy women and women diagnosed with mild hyperandrogenism, showing high agreement (R² > 0.98) with the concentrations obtained using the conventional quantification based on EC. For IC, Passing-Bablok regression showed proportional biases between -15.0% and 11.3% for all quantified steroids, with an average difference of -5.8% compared to EC. These results highlight the reliability and the advantages of implementing IC in clinical laboratories routine to simplify quantification in LC-MS bioanalysis, especially when a large panel of analytes is monitored.

From fundamentals in calibration to modern methodologies: A tutorial for small molecules quantification in liquid chromatography-mass spectrometry bioanalysis

Over the last two decades, liquid chromatography coupled to mass-spectrometry (LC‒MS) has become the gold standard to perform qualitative and quantitative analyses of small molecules. When quantitative analysis is developed, an analyst usually refers to international guidelines for analytical method validation. In this context, the design of calibration curves plays a key role in providing accurate results. During recent years and along with instrumental advances, strategies to build calibration curves have dramatically evolved, introducing innovative approaches to improve quantitative precision and throughput. For example, when a labeled standard is available to be spiked directly into the study sample, the concentration of the unlabeled analog can be easily determined using the isotopic pattern deconvolution or the internal calibration approach, eliminating the need for multipoint calibration curves. This tutorial aims to synthetize the advances in LC‒MS quantitative analysis for small molecules in complex matrices, going from fundamental aspects in calibration to modern methodologies and applications. Different work schemes for calibration depending on the sample characteristics (analyte and matrix nature) are distinguished and discussed. Finally, this tutorial outlines the importance of having international guidelines for analytical method validation that agree with the advances in calibration strategies and analytical instrumentation.

Speciation and Semiquantification of Nitrogen-Containing Species in Complex Mixtures: Application to Plastic Pyrolysis Oil

Plastic pyrolysis oil is of particular interest for waste management in the current context of a circular economy. Due to their uncontrolled origin, these oils may contain significant amount of unwanted compounds such as nitrogen-containing species. These compounds are known to be catalyst poisons during refining processes. Therefore, the removal of these species is crucial, and their characterization from structural and quantification points of view is essential for this purpose. This study presents a method to specify and quantify nitrogen-containing classes in a plastic pyrolysis oil by direct infusion mass spectrometry. Two steps were used, namely structural characterization to select suitable standards and semiquantification. The structural speciation of nitrogen-containing compounds was first performed by electrospray ionization Fourier transform mass spectrometry, followed by tandem mass spectrometry using high-resolution mass isolation and infrared multiphoton dissociation fragmentation. A semiquantification is then performed by the standard addition method, which is very appropriate for such complex matrices. Aromatic cores such as quinoline and quinoxaline were evidenced for both N₁ and N₂ classes, allowing 2-methylquinoxaline and 2-butylquinoline to be proposed as standards for the semiquantification of N₂- and N₁-containing compounds, respectively. The amount of nitrogen detected from the sum of the individual species was consistent with the bulk analysis. The reported methodology can be applied to numerous other families of compounds in various other complex matrices.

Uncovering the seasonal brain: Liquid chromatography-tandem mass spectrometry (LC-MS/MS) as a biochemical approach for studying seasonal social behaviors

Many animals show pronounced changes in physiology and behavior across the annual cycle, and these adaptations enable individuals to prioritize investing in the neuroendocrine mechanisms underlying reproduction and/or survival based on the time of year. While prior research has offered valuable insight into how seasonal variation in neuroendocrine processes regulates social behavior, the majority of these studies have investigated how a single hormone influences a single behavioral phenotype. Given that hormones are synthesized and metabolized via complex biochemical pathways and often act in concert to control social behavior, these approaches provide a limited view of how hormones regulate seasonal changes in behavior. In this review, we discuss how seasonal influences on hormones, the brain, and social behavior can be studied using liquid chromatography-tandem mass spectrometry (LC-MS/MS), an analytical chemistry technique that enables researchers to simultaneously quantify the concentrations of multiple hormones and the activities of their synthetic enzymes. First, we examine studies that have investigated seasonal plasticity in brain-behavior interactions, specifically by focusing on how two groups of hormones, sex steroids and nonapeptides, regulate sexual and aggressive behavior. Then, we explain the operations of LC-MS/MS, highlight studies that have used LC-MS/MS to study the neuroendocrine mechanisms underlying social behavior, both within and outside of a seasonal context, and discuss potential applications for LC-MS/MS in the field of behavioral neuroendocrinology. We propose that this cutting-edge technology will provide a more comprehensive understanding of how the multitude of hormones that comprise complex neuroendocrine networks affect seasonal variation in the brain and behavior.

Development and Validation of a Reliable UHPLC-MS/MS Method for Simultaneous Quantification of Macrocyclic Lactones in Bovine Plasma

A fast, accurate and reliable ultra-high performance liquid chromatography–tandem mass spectrometry (UHPLC-MS/MS) method was developed for simultaneous quantification of ivermectin (IVER), doramectin (DORA), and moxidectin (MOXI) in bovine plasma. A priority for sample preparation was the eradication of possible infectious diseases to avoid travel restrictions. The sample preparation was based on protein precipitation using 1% formic acid in acetonitrile, followed by Ostro^® 96-well plate pass-through sample clean-up. The simple and straightforward procedure, along with the short analysis time, makes the current method unique and suitable for a large set of sample analyses per day for PK studies. Chromatographic separation was performed using an Acquity UPLC HSS-T3 column, with 0.01% acetic acid in water and methanol, on an Acquity H-Class ultra-high performance liquid chromatograph (UHPLC) system. The MS/MS instrument was a Xevo TQ-S^® mass spectrometer, operating in the positive electrospray ionization mode and two multiple reaction monitoring (MRM) transitions were monitored per component. The MRM transitions of m/z 897.50 > 753.4 for IVER, m/z 921.70 > 777.40 for DORA and m/z 640.40 > 123.10 for MOXI were used for quantification. The method validation was performed using matrix-matched calibration curves in a concentration range of 1 to 500 ng/mL. Calibration curves fitted a quadratic regression model with 1/x2 weighting (r ≥ 0.998 and GoF ≤ 4.85%). Limits of quantification (LOQ) values of 1 ng/mL were obtained for all the analytes, while the limits of detection (LOD) were 0.02 ng/mL for IVER, 0.03 ng/mL for DORA, and 0.58 ng/mL for MOXI. The results of within-day (RSD < 6.50%) and between-day (RSD < 8.10%) precision and accuracies fell within acceptance ranges. No carry-over and no peak were detected in the UHPLC-MS/MS chromatogram of blank samples showing good specificity of the method. The applicability of the developed method was proved by an analysis of the field PK samples.

Internal calibration as an emerging approach for endogenous analyte quantification: Application to steroids

The use of mass spectrometry methods with triple quadrupole instruments is well established for quantification. However, the preparation of calibration curves can be time-consuming and prone to analytical errors. In this study, an innovative internal calibration (IC) approach using a one-standard calibration with a stable isotope-labeled (SIL) standard version of the endogenous compound was developed. To ensure optimal quantitative performance, the following parameters were evaluated: the stability of the analyte-to-SIL response factor (RF), the chemical and isotopic purities of the SIL, and the instrumental reproducibility. Using six clinically important endogenous steroids and their respective SIL standards, we demonstrated that RFs obtained on different LC-MS platforms were consistent. The quantitative performance of the proposed approach was determined using quality control samples prepared in depleted serum, and showed both satisfactory precision (1.3%-12.4%) and trueness (77.5%-107.0%, with only 3 values outside ±30%). The developed method was then applied to human serum samples, and the results were similar to those obtained with the conventional quantification approach based on external calibration: the Passing-Bablok regression showed a proportional bias of 6.8% and a mean difference of -5.9% between the two methodologies. Finally, we showed that the naturally occurring isotopes of the SIL can be used to provide additional calibration points and increase the accuracy for analytes with low concentrations.

Aptamer-based enrichment of TDP-43 from human cells and tissues with quantification by HPLC-MS/MS

BACKGROUND

There is great interest in detecting, characterizing and quantifying transactive response DNA binding protein of 43 kDa (TDP-43), and its post-translational modifications, due to its association with frontotemporal dementia (FTD) and amyotrophic lateral sclerosis. Unfortunately, detailed analysis of TDP-43 in human biological matrices by immunometric methods has been hindered by the relatively low abundance of TDP-43 and poor antibody reagent specificity.

NEW METHOD

With the goal of developing a selective and multiplex method for characterizing TDP-43, we previously developed a high-performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS) assay for relative quantification of TDP-43 in human brain tissue and cells. To improve analytical sensitivity and to perform absolute quantification, we coupled a novel RNA-based aptamer enrichment workflow (and inclusion of a stable isotope-labeled standard) to HPLC-MS/MS.

RESULTS

The TDP-43 aptamer-enrichment-HPLC-MS/MS assay was linear from 0.37 to 2.55nmol/L, a range suitable for analysis of both human cells and brain tissue homogenates, and had a total CV of 14.8%. Quantitative TDP-43 peptide profiles were developed for cases of FTD with TDP-43 pathology and cases with no neurodegenerative pathology.

COMPARISON WITH EXISTING METHODS

Compared to immunoenrichment, aptamer-enrichment yielded cleaner recoveries of TDP-43. The aptamer-enrichment-HPLC-MS/MS method, compared to our previous method without enrichment, increased analytical sensitivity by 8.7-fold and 11.8-fold for endogenous TDP-43 in human cells and brain tissue, respectively. Critically, inclusion of the aptamer enrichment step improved sequence resolution and enabled identification of TDP-43 C-terminal fragments.

CONCLUSIONS

The aptamer-enrichment-HPLC-MS/MS method enabled highly selective quantification, enhanced sequence coverage and structural characterization of endogenous TDP-43.

Isotopic Distribution Calibration for Mass Spectrometry

Mass spectrometry (MS) is widely used in science and industry. It allows accurate, specific, sensitive, and reproducible detection and quantification of a huge range of analytes. Across MS applications, quantification by MS has grown most dramatically, with >50 million experiments/year in the USA alone. However, quantification performance varies between instruments, compounds, different samples, and within- and across runs, necessitating normalization with analyte-similar internal standards (IS) and use of IS-corrected multipoint external calibration curves for each analyte, a complicated and resource-intensive approach, which is particularly ill-suited for multi-analyte measurements. We have developed an internal calibration method that utilizes the natural isotope distribution of an IS for a given analyte to provide internal multipoint calibration. Multiple isotope distribution calibrators for different targets in the same sample facilitate multiplex quantification, while the emerging random-access automated MS platforms should also greatly benefit from this approach. Finally, isotope distribution calibration allows mathematical correction for suboptimal experimental conditions. This might also enable quantification of hitherto difficult, or impossible to quantify, targets, if the distribution is adjusted in silico to mimic the analyte. The approach works well for high resolution, accurate mass MS for analytes with at least a modest-sized isotopic envelope. As shown herein, the approach can also be applied to lower molecular weight analytes, but the reduction in calibration points does reduce quantification performance.

Development and validation of a UPLC-MS/MS method with a broad linear dynamic range for the quantification of morphine, morphine-3-glucuronide and morphine-6-glucuronide in mouse plasma and tissue homogenates

The aim of this study was to develop and to validate a UPLC-MS/MS method for the quantification of morphine, morphine-3-glucuronide, and morphine-6-glucuronide in mouse plasma and tissue homogenates to support preclinical pharmacokinetic studies. The sample preparation consisted of protein precipitation with cold (2-8 °C) methanol:acetonitrile (1:1, v/v), evaporation of the supernatant to dryness, and reconstitution of the dry-extracts in 4 mM ammonium formate pH 3.5. Separation was achieved on a Waters UPLC HSS T3 column (150 × 2.1 mm, 1.8 µm) maintained at 50 °C and using gradient elution with a total runtime of 6.7 min. Mobile phase A consisted of 4 mM ammonium formate pH 3.5 and mobile phase B of 0.1% formic acid in methanol:acetonitrile (1:1, v/v). Detection was carried out by tandem mass spectrometry with electrospray ionization in the positive ion mode. The method was validated within a linear range of 1-2,000 ng/mL, 10-20,000 ng/mL, and 0.5-200 ng/mL for morphine, morphine-3-glucuronide, and morphine-6-glucuronide, respectively. In human plasma, the intra- and inter-run precision of all analytes, including the lower limit of quantification levels, were ≤ 15.8%, and the accuracies were between 88.1 and 111.9%. It has been shown that calibration standards prepared in control human plasma can be used for the quantification of the analytes in mouse plasma and tissue homogenates. The applicability of the method was successfully demonstrated in a preclinical pharmacokinetic study in mice.

Melatonin-dependent changes in neurosteroids are associated with increased aggression in a seasonally breeding rodent

Aggression is a complex social behaviour that allows individuals to compete for access to limited resources (eg, mates, food and territories). Excessive or inappropriate aggression, however, has become problematic in modern societies, and current treatments are largely ineffective. Although previous work in mammals suggests that aggressive behaviour varies seasonally, seasonality is largely overlooked when developing clinical treatments for inappropriate aggression. Here, we investigated how the hormone melatonin regulates seasonal changes in neurosteroid levels and aggressive behaviour in Siberian hamsters, a rodent model of seasonal aggression. Specifically, we housed males in long-day (LD) or short-day (SD) photoperiods, administered timed s.c. melatonin injections (which mimic a SD-like signal) or control injections, and measured aggression using a resident-intruder paradigm after 9 weeks of treatment. Moreover, we quantified five steroid hormones in circulation and in brain regions associated with aggressive behaviour (lateral septum, anterior hypothalamus, medial amygdala and periaqueductal gray) using liquid chromatography-tandem mass spectrometry. SD hamsters and LD hamsters administered timed melatonin injections (LD-M) displayed increased aggression and exhibited region-specific decreases in neural dehydroepiandrosterone, testosterone and oestradiol, but showed no changes in progesterone or cortisol. Male hamsters also showed distinct associations between neurosteroids and aggressive behaviour, in which neural progesterone and dehydroepiandrosterone were positively correlated with aggression in all treatment groups, whereas neural testosterone, oestradiol and cortisol were negatively correlated with aggression only in LD-M and SD hamsters. Collectively, these results provide insight into a novel neuroendocrine mechanism of mammalian aggression, in which melatonin reduces neurosteroid levels and elevates aggressive behaviour.

STRATEGIES AND CHALLENGES IN METHOD DEVELOPMENT AND VALIDATION FOR THE ABSOLUTE QUANTIFICATION OF ENDOGENOUS BIOMARKER METABOLITES USING LIQUID CHROMATOGRAPHY-TANDEM MASS SPECTROMETRY

Metabolomics is a dynamically evolving field, with a major application in identifying biomarkers for drug development and personalized medicine. Numerous metabolomic studies have identified endogenous metabolites that, in principle, are eligible for translation to clinical practice. However, few metabolomic-derived biomarker candidates have been qualified by regulatory bodies for clinical applications. Such interruption in the biomarker qualification process can be largely attributed to various reasons including inappropriate study design and inadequate data to support the clinical utility of the biomarkers. In addition, the lack of robust assays for the routine quantification of candidate biomarkers has been suggested as a potential bottleneck in the biomarker qualification process. In fact, the nature of the endogenous metabolites precludes the application of the current validation guidelines for bioanalytical methods. As a result, there have been individual efforts in modifying existing guidelines and/or developing alternative approaches to facilitate method validation. In this review, three main challenges for method development and validation for endogenous metabolites are discussed, namely matrix effects evaluation, alternative analyte-free matrices, and the choice of internal standards (ISs). Some studies have modified the equations described by the European Medicines Agency for the evaluation of matrix effects. However, alternative strategies were also described; for instance, calibration curves can be generated in solvents and in biological samples and the slopes can be compared through ratios, relative standard deviation, or a modified Stufour suggested approaches while quantifying mainly endogenous metabolitesdent t-test. ISs, on the contrary, are diverse; in which seven different possible types, used in metabolomics-based studies, were identified in the literature. Each type has its advantages and limitations; however, isotope-labeled ISs and ISs created through isotope derivatization show superior performance. Finally, alternative matrices have been described and tested during method development and validation for the quantification of endogenous entities. These alternatives are discussed in detail, highlighting their advantages and shortcomings. The goal of this review is to compare, apprise, and debate current knowledge and practices in order to aid researchers and clinical scientists in developing robust assays needed during the qualification process of candidate metabolite biomarkers. © 2019 John Wiley & Sons Ltd. Mass Spec Rev.

Calibrating from Within: Multipoint Internal Calibration of a Quantitative Mass Spectrometric Assay of Serum Methotrexate

BACKGROUND

Clinical LC-MS/MS assays traditionally require that samples be run in batches with calibration curves in each batch. This approach is inefficient and presents a barrier to random access analysis. We developed an alternative approach called multipoint internal calibration (MPIC) that eliminated the need for batch-mode analysis.

METHODS

The new approach used 4 variants of 13C-labeled methotrexate (0.026-10.3 µM) as an internal calibration curve within each sample. One site carried out a comprehensive validation, which included an evaluation of interferences and matrix effects, lower limit of quantification (LLOQ), and 20-day precision. Three sites evaluated assay precision and linearity. MPIC was also compared with traditional LC-MS/MS and an immunoassay.

RESULTS

Recovery of spiked analyte was 93%-102%. The LLOQ was validated to be 0.017 µM. Total variability, determined in a 20-day experiment, was 11.5%CV. In a 5-day variability study performed at each site, total imprecision was 3.4 to 16.8%CV. Linearity was validated throughout the calibrator range (r2 > 0.995, slopes = 0.996-1.01). In comparing 40 samples run in each laboratory, the median interlaboratory imprecision was 6.55%CV. MPIC quantification was comparable to both traditional LC-MS/MS and immunoassay (r2 = 0.96-0.98, slopes = 1.04-1.06). Bland-Altman analysis of all comparisons showed biases rarely exceeding 20% when MTX concentrations were >0.4 µM.

CONCLUSION

The MPIC method for serum methotrexate quantification was validated in a multisite proof-of-concept study and represents a big step toward random-access LC-MS/MS analysis, which could change the paradigm of mass spectrometry in the clinical laboratory.

Evaluation of a Stable Isotope-Based Direct Quantification Method for Dicamba Analysis from Air and Water Using Single-Quadrupole LC-MS

Dicamba is a moderately volatile herbicide used for post-emergent control of broadleaf weeds in corn, soybean, and a number of other crops. With increased use of dicamba due to the release of dicamba-resistant cotton and soybean varieties, growing controversy over the effects of spray drift and volatilization on non-target crops has increased the need for quantifying dicamba collected from water and air sampling. Therefore, this study was designed to evaluate stable isotope-based direct quantification of dicamba from air and water samples using single-quadrupole liquid chromatography–mass spectrometry (LC–MS). The sample preparation protocols developed in this study utilize a simple solid-phase extraction (SPE) protocol for water samples and a single-step concentration protocol for air samples. The LC–MS detection method achieves sensitive detection of dicamba based on selected ion monitoring (SIM) of precursor and fragment ions and relies on the use of an isotopically labeled internal standard (IS) (D₃-dicamba), which allows for calculating recoveries and quantification using a relative response factor (RRF). Analyte recoveries of 106–128% from water and 88–124% from air were attained, with limits of detection (LODs) of 0.1 ng mL⁻¹ and 1 ng mL⁻¹, respectively. The LC–MS detection method does not require sample pretreatment such as ion-pairing or derivatization to achieve sensitivity. Moreover, this study reveals matrix effects associated with sorbent resin used in air sample collection and demonstrates how the use of an isotopically labeled IS with RRF-based analysis can account for ion suppression. The LC–MS method is easily transferrable and offers a robust alternative to methods relying on more expensive tandem LC–MS/MS-based options.

Evaluation, identification and impact assessment of abnormal internal standard response variability in regulated LC-MS bioanalysis

Internal standard (IS) plays an important role in LC-MS bioanalysis by compensating for the variability of the analyte of interest in bioanalytical workflow. Due to the complexity of biological sample compositions and bioanalytical processes, a certain level of IS response variability across a run or a study is anticipated. However, an extensive variability may raise doubts to the accuracy of the measured results and also suggest nonoptimal analytical method. In this current paper, recent publications and guidelines regarding IS response in LC-MS bioanalysis were thoroughly reviewed with focus on the evaluation, identification and impact assessment of 'abnormal' IS response variability. A systematic decision tree was proposed to facilitate investigation into abnormal IS response variability after each run.

Development and validation of LC-ESI-MS/MS methods for quantification of 27 free and conjugated estrogen-related metabolites

An imbalance in the estrogen metabolism has been associated with an increased risk of breast cancer development. Evaluation of the estrogen biotransformation capacity requires monitoring of various estrogen metabolites. Up to now, only some estrogen metabolites could be measured in urine. However, in order to offer tailor made nutritional support or therapies, a complete estrogen metabolite profile is required in order to identify specific deficiencies in this pathway for each patient individually. Here, we focused on this need to quantify as many as possible of the estrogen-related metabolites excreted in urine. The method was developed to quantify 27 estrogen-related metabolites in small urine quantities. This entailed sample clean-up with a multi-step solid phase extraction procedure, derivatisation of the metabolites in the less water-soluble fraction through dansylation, and analyses using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The metabolites accurately quantified by the method devised included parent estrogens, hydroxylated and methylated forms, metabolites of the 16α-hydroxyestrogen pathway, sulphate and glucuronide conjugated forms, precursors and a related steroid hormone. This method was validated and enabled quantification in the high picograms and low nanograms per millilitre range. Finally, analyses of urine samples confirmed detection and quantification of each of the metabolites.

Generation of Bioactive Oxylipins from Exogenously Added Arachidonic, Eicosapentaenoic and Docosahexaenoic Acid in Primary Human Brain Microvessel Endothelial Cells

The human blood-brain barrier (BBB) is the restrictive barrier between the brain parenchyma and the circulating blood and is formed in part by microvessel endothelial cells. The brain contains significant amounts of arachidonic acid (ARA), and docosahexaenoic acid (DHA), which potentially give rise to the generation of bioactive oxylipins. Oxylipins are oxygenated fatty acid metabolites that are involved in an assortment of biological functions regulating neurological health and disease. Since it is not known which oxylipins are generated by human brain microvessel endothelial cells (HBMECs), they were incubated for up to 30 min in the absence or presence of 0.1-mM ARA, eicosapentaenoic acid (EPA) or DHA bound to albumin (1:1 molar ratio), and the oxylipins generated were examined using high performance liquid chromatography-tandem mass spectrometry (HPLC/MS/MS). Of 135 oxylipins screened in the media, 63 were present at >0.1 ng/mL at baseline, and 95 were present after incubation with fatty acid. Oxylipins were rapidly generated and reached maximum levels by 2-5 min. While ARA, EPA and DHA each stimulated the production of oxylipins derived from these fatty acids themselves, ARA also stimulated the production of oxylipins from endogenous 18- and 20-carbon fatty acids, including α-linolenic acid. Oxylipins generated by the lipoxygenase pathway predominated both in resting and stimulated states. Oxylipins formed via the cytochrome P450 pathway were formed primarily from DHA and EPA, but not ARA. These data indicate that HBMECs are capable of generating a plethora of bioactive lipids that have the potential to modulate BBB endothelial cell function.

Applying dried blood spot sampling with LCMS quantification in the clinical development phase of tasquinimod

Background: Tasquinimod is an orally active anticancer drug in late clinical development. Here we describe the development and validation of a bioanalytical method based upon dried blood spot analysis in combination with LCMS/MS and stable isotope dilution. Results & discussion: The present method was validated for accuracy, precision, linearity, selectivity, carry-over and ruggedness. Data elucidating stability of tasquinimod in dried blood spots and in blood at ambient temperature was investigated and found adequate. Furthermore, in a clinical study, incurred samples reanalysis was performed, and the correlation of blood concentration versus plasma concentrations of tasquinimod was investigated. Conclusion: The method described here is suitable for bioanalysis of tasquinimod in whole blood from humans in clinical studies.

Reverse-polynomial dilution calibration methodology extends lower limit of quantification and reduces relative residual error in targeted peptide measurements in blood plasma

Matrix effect is the alteration of an analyte's concentration-signal response caused by co-existing ion components. With electrospray ionization (ESI), matrix effects are believed to be a function of the relative concentrations, ionization efficiency, and solvation energies of the analytes within the electrospray ionization droplet. For biological matrices such as plasma, the interactions between droplet components is immensely complex and the effect on analyte signal response not well elucidated. This study comprised of three sequential quantitative analyses: we investigated whether there is a generalizable correlation between the range of unique ions in a sample matrix (complexity); the amount of matrix components (concentration); and matrix effect, by comparing an E. coli digest matrix (∼2600 protein proteome) with phospholipid depleted human blood plasma, and unfractionated, nondepleted human plasma matrices (∼10(7) proteome) for six human plasma peptide multiple reaction monitoring assays. Our data set demonstrated analyte-specific interactions with matrix complexity and concentration properties resulting in significant ion suppression for all peptides (p < 0.01), with nonuniform effects on the ion signals of the analytes and their stable-isotope analogs. These matrix effects were then assessed for translation into relative residual error and precision effects in a low concentration (∼0-250 ng/ml) range across no-matrix, complex matrix, and highly complex matrix, when a standard addition stable isotope dilution calibration method was used. Relative residual error (%) and precision (CV%) by stable isotope dilution were within <20%; however, error in phospholipid-depleted and nondepleted plasma matrices were significantly higher compared with no-matrix (p = 0.006). Finally a novel reverse-polynomial dilution calibration method with and without phospholipid-depletion was compared with stable isotope dilution for relative residual error and precision. Reverse-polynomial dilution techniques extend the Lower Limit of Quantification and reduce error (p = 0.005) in low-concentration plasma peptide assays and is broadly applicable for verification phase Tier 2 multiplexed multiple reaction monitoring assay development within the FDA-National Cancer Institute (NCI) biomarker development pipeline.

Some unnecessary or inadequate common practices in regulated LC–MS bioanalysis

The global bioanalytical community increasingly craves scientifically sound practices and guidance where the rationale is given for each requirement. To this end, it is critical to first evaluate all the existing practices and requirements based on scientific findings and critical thinking. Here we are challenging several important common practices in regulated LC–MS bioanalysis, from the requirement of at least six different calibration concentrations, no extrapolation, use of blank and zero standard in each batch, selection of quality controls, to the way matrix effect and dilution integrity are being validated. Both the reasons why these common practices are unnecessary or inadequate and the potential solutions are presented.

Sample reduction strategies in discovery bioanalysis

It is a constant challenge to provide timely bioanalytical support for the evaluation of drug-like properties and PK/PD profiles for the ever-increasing numbers of new chemical entities in a cost-effective manner. While technological advancement in various aspects of LC–MS/MS analysis has significantly improved bioanalytical efficiency, a number of simple sample reduction strategies can be employed to reduce the number of samples requiring analysis, and as a result increase the bioanalytical productivity without deploying additional instruments. In this review, advantages and precautions of common sample reduction strategies, such as sample pooling and cassette dosing, are discussed. In addition, other approaches such as reducing calibration standards and eliminating over-the-curve sample reanalysis will also be discussed. Taken together, these approaches can significantly increase the capacity and throughput of discovery bioanalysis without adding instruments, and are viable means to enhance the overall productivity of the bioanalytical laboratory.

Systems pharmacology modeling of drug-induced modulation of thyroid hormones in dogs and translation to human

PURPOSE

To develop a systems pharmacology model based on hormone physiology and pharmacokinetic-pharmacodynamic concepts describing the impact of thyroperoxidase (TPO) inhibition on thyroid hormone homeostasis in the dog and to predict drug-induced changes in thyroid hormones in humans.

METHODS

A population model was developed based on a simultaneous analysis of concentration-time data of T₄, T₃ and TSH in dogs following once daily oral dosing for up to 6-months of a myeloperoxidase inhibitor (MPO-IN1) with TPO inhibiting properties. The model consisted of linked turnover compartments for T₄, T₃ and TSH including a negative feedback from T₄ on TSH concentrations.

RESULTS

The model could well describe the concentration-time profiles of thyroid hormones in dog. Successful model validation was performed by predicting the hormone concentrations during 1-month administration of MPO-IN2 based on its in vitro dog TPO inhibition potency. Using human thyroid hormone turnover rates and TPO inhibitory potency, the human T₄ and TSH concentrations upon MPO-IN1 treatment were predicted well.

CONCLUSIONS

The model provides a scientific framework for the prediction of drug induced effects on plasma thyroid hormones concentrations in humans via TPO inhibition based on results obtained in in vitro and animal studies.

Capillary microsampling in the regulatory environment: validation and use of bioanalytical capillary microsampling methods

Capillary microsampling (CMS) has recently been introduced as a response to the demands for more ethical use of laboratory animals according to the 3R principles. In CMS, an exact volume of the blood, plasma or other biofluid is collected in a capillary from which it is washed out, resulting in a diluted sample that can be handled using the existing equipment in the bioanalytical laboratory. CMS differs from traditional large volume sampling as the microsample is diluted before further handling and analysis, and reanalysis is performed using the diluted sample. This has some implications for the validation and this report is an attempt to clarify how to validate and use CMS methods in a regulatory environment. CMS also shows some distinct new opportunities: labile analytes can be immediately stabilized at sample collection and the addition of the internal standard to the whole sample can improve analytical performance. The experiences from 5 years use of CMS of plasma and blood for determination of drug exposure in animal studies are reviewed.

Alternative calibration strategies for the clinical laboratory: application to nortriptyline therapeutic drug monitoring

BACKGROUND

The addition of a calibration curve with every run is both time-consuming and expensive for clinical mass spectrometry assays. We present alternative calibration strategies that eliminate the need for a calibration curve except as required by laboratory regulations.

METHODS

We measured serum nortriptyline concentrations prospectively in 68 patients on 16 days over a 2-month period using a method employing calibration schemes that relied on the measurement of the response ratio (RR) corrected by the response factor (RF), i.e., a measurement of the RR for an equimolar mixture of the analyte and internal standard. Measurements were taken with contemporaneous RF (cRF) measurements as well as sporadic RF (sRF) measurements. The measurements with these alternative calibration schemes were compared against the clinical results obtained by interpolation on a calibration curve, and those differences were evaluated for analytical and clinical significance.

RESULTS

The differences between the values measured by cRF and sRF calibration and interpolation on a calibration curve were not significant (P = 0.088 and P = 0.091, respectively). Both the cRF- and sRF-based calibration results demonstrated a low mean bias against the calibration curve interpolations of 3.69% (95% CI, -15.8% to 23.2%) and 3.11% (95% CI, -16.4% to 22.6%), respectively. When these results were classified as subtherapeutic, therapeutic, or supratherapeutic, there was categorical agreement in 95.6% of the cRF calibration results and 94.1% of the sRF results.

CONCLUSIONS

cRF and sRF calibration in a clinically validated liquid chromatography-tandem mass spectrometry assay yields results that are analytically and clinically commensurate to those produced by interpolation with a calibration curve.

Investigation of absolute and relative response for three different liquid chromatography/tandem mass spectrometry systems; the impact of ionization and detection saturation

RATIONALE

The investigations in this article were triggered by two observations in the laboratory; for some liquid chromatography/tandem mass spectrometry (LC/MS/MS) systems it was possible to obtain linear calibration curves for extreme concentration ranges and for some systems seemingly linear calibration curves gave good accuracy at low concentrations only when using a quadratic regression function.

METHODS

The absolute and relative responses were tested for three different LC/MS/MS systems by injecting solutions of a model compound and a stable isotope labeled internal standard. The analyte concentration range for the solutions was 0.00391 to 500 μM (128,000×), giving overload of the chromatographic column at the highest concentrations. The stable isotope labeled internal standard concentration was 0.667 μM in all samples.

RESULTS

The absolute response per concentration unit decreased rapidly as higher concentrations were injected. The relative response, the ratio for the analyte peak area to the internal standard peak area, per concentration unit was calculated. For system 1, the ionization process was found to limit the response and the relative response per concentration unit was constant. For systems 2 and 3, the ion detection process was the limiting factor resulting in decreasing relative response at increasing concentrations.

CONCLUSIONS

For systems behaving like system 1, simple linear regression can be used for any concentration range while, for systems behaving like systems 2 and 3, non-linear regression is recommended for all concentration ranges. Another consequence is that the ionization capacity limited systems will be insensitive to matrix ion suppression when an ideal internal standard is used while the detection capacity limited systems are at risk of giving erroneous results at high concentrations if the matrix ion suppression varies for different samples in a run.

Determination of dapsone in muscle tissue and milk using high-performance liquid chromatography-tandem mass spectrometry

A precise and selective liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the determination of dapsone in muscle tissue and milk has been developed. The sample preparation was based on extraction with organic solvent and automated solid-phase extraction (SPE) cleanup. At least three product ions were monitored for the analyte. The method was validated according to the European Decision 2002/657/EC. Estimated analytical limits were 0.0018 ng/g for CCα and 0.0031 ng/g for CCβ in meat and milk. An excellent linear concentration range was observed for both matrices with a correlation coefficient better than 0.997. Recoveries were 105-117% in meat and 101-108% in milk, with satisfactory precision and coefficients of variance (CV) less than 8%. Additionally, a simplified quantification approach was successfully evaluated depending only on the response factor (F) without the use of calibration curve. The developed method provides reliable and sensitive identification and quantification of dapsone in meat and milk.

Analyte and internal standard cross signal contributions and their impact on quantitation in LC-MS based bioanalysis

Cross signal contributions between an analyte and its internal standard (IS) are very common due to impurities in reference standards and/or isotopic interferences. Despite the general awareness of this issue, how exactly they affect quantitation in LC-MS based bioanalysis has not been systematically evaluated. In this research, such evaluations were performed first by simulations and then by experiments using a typical bioanalytical method for tiagabine over the concentration range of 1-1000 ng/mL in human EDTA K(3) plasma. The results demonstrate that when an analyte contributes to IS signal, linearity and accuracy can be affected with low IS concentration. Thus, minimum IS concentrations have been obtained for different combinations of concentration range, percentage of cross contribution, and weighting factor. Moreover, while impurity in analyte reference standard is a factor in cross signal contribution, significant systematic errors could exist in the results of unknown samples even though the results of calibration standards and quality controls are acceptable. How these systematic errors would affect stability evaluation, method transfer, and cross validation has also been discussed and measures to reduce their impact are proposed. On the other hand, the signal contribution from an IS to the analyte causes shifting of a calibration curve, i.e. increase of intercept, and theoretically, the accuracy is not affected. The simulation results are well supported by experimental results. For example, good inter-run (between-run) accuracy (bias: -2.70 to 5.35%) and precision (CV: 2.07-10.50%) were obtained when runs were extracted with an IS solution containing 1-fold of the lower limit of quantitation.

Critical topics in ensuring data quality in bioanalytical LC–MS method development

The use of LC–MS for bioanalysis of pharmaceuticals is entering its third decade and may be considered to be a mature technology. In many respects this is true, considering the advances made in such areas as instrument performance, electronics, software and automation of use. However, there remain instrumental and noninstrumental areas that require significant attention to ensure data quality. Increasing regulatory focus on analytical method performance and unaddressed method issues require the bioanalyst to understand those areas that most greatly impact data quality. This review will focus on instrumental and noninstrumental areas that can influence data quality, including reference standard and internal standard quality and physicochemical properties, matrix effects, stability in matrix, sample preparation, LC and MS.