Targeted quantitative bioanalysis in plasma using liquid chromatography/high-resolution accurate mass spectrometry: an evaluation of global selectivity as a function of mass resolving power and extraction window, with comparison of centroid and profile modes

Resolving Challenges in Detection and Quantification of D-2-hydroxyglutarate and L-2-hydroxyglutarate via LC/MS

D-2-Hydroxyglutarate and L-2-Hydroxyglutarate (D-2HG/L-2HG) are typically metabolites of non-specific enzymatic reactions that are kept in check by the housekeeping enzymes, D-2HG /L-2HG dehydrogenase (D-2HGDH/L-2HGDH). In certain disease states, such as D-2HG or L-2HG aciduria and cancers, accumulation of these biomarkers interferes with oxoglutarate-dependent enzymes that regulate bioenergetic metabolism, histone methylation, post-translational modification, protein expression and others. D-2HG has a complex role in tumorigenesis that drives metabolomics investigations. Meanwhile, L-2HG is produced by non-specific action of malate dehydrogenase and lactate dehydrogenase under acidic or hypoxic environments. Characterization of divergent effects of D-2HG/L-2HG on the activity of specific enzymes in diseased metabolism depends on their accurate quantification via mass spectrometry. Despite advancements in high-resolution quadrupole time-of-flight mass spectrometry (HR-QTOF-MS), challenges are typically encountered when attempting to resolve of isobaric and isomeric metabolites such as D-2HG/L-2HG for quantitative analysis. Herein, available D-2HG/L-2HG derivatization and liquid chromatography (LC) MS quantification methods were examined. The outcome led to the development of a robust, high-throughput HR-QTOF-LC/MS approach that permits concomitant quantification of the D-2HG and L-2HG enantiomers with the benefit to quantify the dysregulation of other intermediates within interconnecting pathways. Calibration curve was obtained over the linear range of 0.8-104 nmol/mL with r 2 ≥ 0.995 for each enantiomer. The LC/MS-based assay had an overall precision with intra-day CV % ≤ 8.0 and inter-day CV % ≤ 6.3 across the quality control level for commercial standard and pooled biological samples; relative error % ≤ 2.7 for accuracy; and resolution, R s = 1.6 between 2HG enantiomers (m/z 147.030), D-2HG and L-2HG (at retention time of 5.82 min and 4.75 min, respectively) following chiral derivatization with diacetyl-L-tartaric anhydride (DATAN). Our methodology was applied to disease relevant samples to illustrate the implications of proper enantioselective quantification of both D-2HG and L-2HG. The stability of the method allows scaling to large cohorts of clinical samples in the future.

Determination of alkaloid-inspired molecule vindeburnol in rabbit plasma by UPLC-HRMS and its application to pharmacokinetic studies and preliminary metabolite identification

The eburnamine-vincamine alkaloids exhibit a range of pharmacological activities. There is a limited understanding of the pharmacokinetics and pharmacodynamics of vindeburnol, a synthetic derivative of this chemical class of alkaloids. A fast and reliable UPLC-HRMS method was developed and validated to quantify vindeburnol in Soviet Chinchilla rabbit plasma from pharmacokinetics studies. An ultra-performance liquid chromatography system equipped with a Waters Acquity UPLC HSS T3 column was used for chromatographic separation by gradient elution with 0.1% (v/v) formic acid in water and acetonitrile. An Impact II QqTOF high-resolution mass spectrometer equipped with an Apollo II electrospray ionization source was used for analysis in positive mode; the ions [M+H]+m/z 269.1648 ± 0.003 and m/z 351.2067 ± 0.003 were monitored for vindeburnol and internal standard (vinpocetine), respectively. Preliminary metabolite profiling was also performed, and the pharmacokinetics of the identified metabolites were evaluated. The mean retention times for vindeburnol and vinpocetine were 2.0 and 3.5 min. The UPLC-HRMS method was validated with accuracy and precision within the 15% acceptance limit (8.2% and 11.0%, respectively). The mean extraction recovery value of vindeburnol from rabbit plasma was 77%. Pharmacokinetic evaluation of vindeburnol revealed that the compound is distributed rapidly with a short elimination half-life. Vindeburnol undergoes extensive first-pass metabolism and is metabolized into hydroxyvindeburnol and vindeburnol glucuronide.

Is Nontarget Analysis Ready for Regulatory Application? Influence of Peak-Picking Algorithms on Data Analysis

The use of peak-picking algorithms is an essential step in all nontarget analysis (NTA) workflows. However, algorithm choice may influence reliability and reproducibility of results. Using a real-world data set, the aim of this study was to investigate how different peak-picking algorithms influence NTA results when exploring temporal and/or spatial trends. For this, drinking water catchment monitoring data, using passive samplers collected twice per year across Southeast Queensland, Australia (n = 18 sites) between 2014 and 2019, was investigated. Data were acquired using liquid chromatography coupled to high-resolution mass spectrometry. Peak picking was performed using five different programs/algorithms (SCIEX OS, MSDial, self-adjusting-feature-detection, two algorithms within MarkerView), keeping parameters identical whenever possible. The resulting feature lists revealed low overlap: 7.2% of features were picked by >3 algorithms, while 74% of features were only picked by a single algorithm. Trend evaluation of the data, using principal component analysis, showed significant variability between the approaches, with only one temporal and no spatial trend being identified by all algorithms. Manual evaluation of features of interest (p-value <0.01, log fold change >2) for one sampling site revealed high rates of incorrectly picked peaks (>70%) for three algorithms. Lower rates (<30%) were observed for the other algorithms, but with the caveat of not successfully picking all internal standards used as quality control. The choice is therefore currently between comprehensive and strict peak picking, either resulting in increased noise or missed peaks, respectively. Reproducibility of NTA results remains challenging when applied for regulatory frameworks.

Stochastic Dynamic Mass Spectrometric Quantitative and Structural Analyses of Pharmaceutics and Biocides in Biota and Sewage Sludge

Mass spectrometric innovations in analytical instrumentation tend to be accompanied by the development of a data-processing methodology, expecting to gain molecular-level insights into real-life objects. Qualitative and semi-quantitative methods have been replaced routinely by precise, accurate, selective, and sensitive quantitative ones. Currently, mass spectrometric 3D molecular structural methods are attractive. As an attempt to establish a reliable link between quantitative and 3D structural analyses, there has been developed an innovative formula [DSD″,tot=∑inDSD″,i=∑in2.6388.10−17×Ii2¯−Ii¯2] capable of the exact determination of the analyte amount and its 3D structure. It processed, herein, ultra-high resolution mass spectrometric variables of paracetamol, atenolol, propranolol, and benzalkonium chlorides in biota, using mussel tissue and sewage sludge. Quantum chemistry and chemometrics were also used. Results: Data on mixtures of antibiotics and surfactants in biota and the linear dynamic range of concentrations 2–80 ng.(mL)−1 and collision energy CE = 5–60 V are provided. Quantitative analysis of surfactants in biota via calibration equation ln[D″SD] = f(conc.) yields the exact parameter |r| = 0.99991, examining the peaks of BAC-C12 at m/z 212.209 ± 0.1 and 211.75 ± 0.15 for tautomers of fragmentation ions. Exact parameter |r| = 1 has been obtained, correlating the theory and experiments in determining the 3D molecular structures of ions of paracetamol at m/z 152, 158, 174, 301, and 325 in biota.

2020 White Paper on Recent Issues in Bioanalysis: BMV of Hybrid Assays, Acoustic MS, HRMS, Data Integrity, Endogenous Compounds, Microsampling and Microbiome (Part 1 - Recommendations on Industry/Regulators Consensus on BMV of Biotherapeutics by LCMS, Advanced Application in Hybrid Assays, Regulatory Challenges in Mass Spec, Innovation in Small Molecules, Peptides and Oligos)

The 14^th edition of the Workshop on Recent Issues in Bioanalysis (14^th WRIB) was held virtually on June 15-29, 2020 with an attendance of over 1000 representatives from pharmaceutical/biopharmaceutical companies, biotechnology companies, contract research organizations, and regulatory agencies worldwide. The 14^th WRIB included three Main Workshops, seven Specialized Workshops that together spanned 11 days in order to allow exhaustive and thorough coverage of all major issues in bioanalysis, biomarkers, immunogenicity, gene therapy, cell therapy and vaccine. Moreover, a comprehensive vaccine assays track; an enhanced cytometry track and updated Industry/Regulators consensus on BMV of biotherapeutics by Mass Spectrometry (hybrid assays, LCMS and HRMS) were special features in 2020. As in previous years, this year's WRIB continued to gather a wide diversity of international industry opinion leaders and regulatory authority experts working on both small and large molecules to facilitate sharing and discussions focused on improving quality, increasing regulatory compliance and achieving scientific excellence on bioanalytical issues. This 2020 White Paper encompasses recommendations emerging from the extensive discussions held during the workshop and is aimed to provide the Global Bioanalytical Community with key information and practical solutions on topics and issues addressed, in an effort to enable advances in scientific excellence, improved quality and better regulatory compliance. Due to its length, the 2020 edition of this comprehensive White Paper has been divided into three parts for editorial reasons. This publication covers the recommendations on (Part 1) Hybrid Assays, Innovation in Small Molecules, & Regulated Bioanalysis. Part 2A (BAV, PK LBA, Flow Cytometry Validation and Cytometry Innovation), Part 2B (Regulatory Input) and Part 3 (Vaccine, Gene/Cell Therapy, NAb Harmonization and Immunogenicity) are published in volume 13 of Bioanalysis, issues 5, and 6 (2021), respectively.

High-Resolution Mass Spectrometry Quantification: Impact of Differences in Data Processing of Centroid and Continuum Data

High-resolution mass spectrometry (HRMS) in full scan mode acquires all ions present in the sample of interest offering a lot of qualitative information. This, in combination with the improved performance of the new generation HRMS systems, triggers more (bio) analysts to switch from triple quad MS systems to HRMS for quantitative analysis. Quantitative processing of HRMS data is performed based on narrow mass extraction windows rather than on nominal mass product ion chromatograms (SRM or MRM). Optimal processing of HRMS data requires different considerations and software tools and can have an impact on data processing and final results. The selection of centroid versus continuum/profile data for processing, selection of the optimal narrow mass extraction window, using theoretical versus measured accurate mass for the extraction of the ion chromatograms as well as differences in calculations and data handling residing in the different vendor software packages are tackled in the presented manuscript. These differences are illustrated on HRMS data acquired for the same plasma samples on three different platforms, i.e., a Sciex QToF, a Waters QToF, and a Thermo Orbitrap system, and processed in four different software packages, i.e., Sciex Analyst® TF, Waters Masslynx, Waters Unifi, and Thermo Xcalibur. The impact of these differences on quantitative HRMS performance was evaluated on calibration curves of eight small molecule compounds in plasma using four different ways of processing. Simple guidelines are provided for the selection of an optimal mass extraction window for continuum and centroided data. Graphical Abstract.

Direct injection high performance liquid chromatography coupled to data independent acquisition mass spectrometry for the screening of antibiotics in honey

The targeted analysis of veterinary drug residues in honey traditionally involves a series of extraction and purification steps prior to quantification with high performance liquid chromatography coupled to high resolution or tandem mass spectrometry. These steps, designed to separate the target analytes from interferences, are generally time-consuming and costly. In addition, traditional cleanup steps are likely to eliminate other compounds whose analysis could prove decisive in current or future assessment of the honey sample. Alternatively, direct injection without complex sample preparation steps has been introduced for the fast analysis of trace compounds in environmental and food matrices. The aim of this study was to develop a rapid method for the targeted analysis of 7 key veterinary drug residues in honey based on direct injection high performance liquid chromatography coupled to quadrupole time-of-flight, while simultaneously recording data-independent MS/MS (e.g. All Ions MS/MS data) for future re-examination of the data for other purposes. The new method allowed for the detection of the target residues at levels approximately 20-100 times lower than current regulatory limits, for a total analysis time of about 45 min. The recoveries (103-119%), the linearity (R ≥ 0.996) and the repeatability (RSD ≤ 7%) were satisfactory. The method was then applied to 35 honey samples from the Canadian market. Residues of tylosin A, tylosin B, sulfamethazine and sulfadimethoxine were detected in 6, 9, 6 and 23% of the samples respectively, at levels below the regulatory limits in Canada. The possibility of adding a hydrolysis step to study sulfonamides in honey was tested, which provided good results for this family of compounds but lead to degradation of some of the other analytes. Finally, the non-targeted identification of several compounds was demonstrated as a proof of concept of future re-examination of All Ions MS/MS data. This paper illustrates the capacity of this novel method to combine targeted and non-targeted screening of chemical residues in honey.

A highly selective and sensitive LC–MS/HRMS assay for quantifying coproporphyrins as organic anion-transporting peptide biomarkers

Aim: Coproporphyrin-I (CP-I) and coproporphyrin-III (CP-III) in plasma and urine have been proposed as biomarkers for assessing drug–drug interactions involving hepatic drug transporters such as organic anion-transporting peptides (OATP), 1B1 and 1B3. Materials & methods: Plasma and urine extracts were analyzed for CP-I/CP-III using a TripleTOF API6600 mass spectrometer. Results: Previously unreported, CP-I/CP-III doubly charged ions (m/z 328.14) were used as precursor ions to improve the assay sensitivity and selectivity over the singly charged precursor ions (m/z 655.28). Levels of CP-I and CP-III measured ranged 0.45–1.1 and 0.050–0.50 ng/ml in plasma and 5–35 and 1–35 ng/ml in urine, respectively. Conclusion: The described highly selective and sensitive CP-I/CP-III LC–HRMS assay offers options for earlier characterization and clinical safety projections for OATP1B1/3-mediated drug–drug interactions along with pharmacokinetic analyses of a new chemical entity as part of first-in-human clinical studies.

Unconjugated payload quantification and DAR characterization of antibody–drug conjugates using high-resolution MS

Aim: The application of high-resolution MS to antibody–drug conjugate (ADC) drug development may provide insight into their safety and efficacy. Quantification of unconjugated cytotoxic drug (payload) and characterization of drug-to-antibody ratio distribution were determined in plasma using orthogonal acceleration quadrupole-time-of-flight MS. Results: Unconjugated payload quantification determined by quadrupole-time-of-flight-based MRMhighresolution and triple quadrupole-based multiple reaction monitoring were comparable and achieved detection limits of 0.030 and 0.015 ng/ml, respectively. As determined by immunocapture and TOF-MS, drug-to-antibody ratio remained unchanged up to 3-weeks postdose for an ADC containing engineered glutamine linkers, but declined from four to three over 2 weeks in an ADC containing engineered cysteine linkers. Conclusion: The use of high-resolution MS in ADC drug discovery confirms its utility within the bioanalytical discipline.

Characterization and quantification of oxyntomodulin in human and rat plasma using high-resolution accurate mass LC–MS

Background: A thorough understanding of the biological role of oxyntomodulin (OXM) has been limited by the availability of sensitive and specific analytical tools for reliable in vivo characterization. Here, we utilized immunoaffinity capture coupled with high-resolution accurate mass LC–MS detection to quantify OXM and its primary catabolites. Results: Quantification of intact OXM 1–37 in human and rat plasma occurred in pre- and post-prandial samples. Profiles for the major catabolites were observed allowing kinetic differences to be assessed between species. Conclusion: A validated assay in human and rat plasma was obtained for OXM 1–37 and its catabolites, 3–37 and 4–37. The value of full scan high-resolution accurate mass detection without selected reaction monitoring for low-abundance peptide quantification was also demonstrated.

Characterization of matrix effects in developing rugged high-throughput LC-MS/MS methods for bioanalysis

AIM

There is an ever-increasing demand for high-throughput LC-MS/MS bioanalytical assays to support drug discovery and development.

RESULTS

Matrix effects of sofosbuvir (protonated) and paclitaxel (sodiated) were thoroughly evaluated using high-throughput chromatography (defined as having a run time ≤1 min) under 14 elution conditions with extracts from protein precipitation, liquid-liquid extraction and solid-phase extraction. A slight separation, in terms of retention time, between underlying matrix components and sofosbuvir/paclitaxel can greatly alleviate matrix effects.

CONCLUSION

High-throughput chromatography, with proper optimization, can provide rapid and effective chromatographic separation under 1 min to alleviate matrix effects and enhance assay ruggedness for regulated bioanalysis.

LC–MS-based quantification of intact proteins: perspective for clinical and bioanalytical applications

Bioanalytical LC–MS for protein quantification is traditionally based on enzymatic digestion of the target protein followed by absolute quantification of a specific signature peptide relative to a stable-isotope labeled analog. The enzymatic digestion, nonetheless, limits rapid method development, sample throughput and turnaround time, and, moreover, makes that essential information regarding the biological function of the intact protein is lost. The recent advancements in high-resolution MS instrumentation and improved sample preparation techniques dedicated to protein clean-up raise the question to what extent LC–MS can be applied for quantitative bioanalysis of intact proteins. This review provides an overview of current and potential applications of LC–MS for intact protein quantification as well as the main limitations and challenges for broad application.

Effect of sample dilution on matrix effects in pesticide analysis of several matrices by liquid chromatography-high-resolution mass spectrometry

This study used two LC columns of different adsorbents and liquid chromatography-electrospray ionization-high-resolution mass spectrometry to study the relationship between matrix effects (ME), the LC separations, and elution patterns of pesticides and those of matrix components. Using calibration standards of 381 pesticides at three dilution levels of 1×, 1/10×, and 1/100×, 108 samples were prepared in solvent and five different sample matrices for the study. Results obtained from principal component analysis and slope ratios of calibration curves provided measurements of the ME and showed the 1/100× sample dilution could minimize suppression ME for most pesticides analyzed. Should a pesticide coeluting with matrix components have a peak intensity of 25 times or higher, the suppression for that pesticide would persist even at 1/100× dilution. The number of pesticides had enhancement ME increased with increasing dilution from 1× to 1/100×, with those early eluting, hydrophilic pesticides affected the most.

Integration of microfluidic LC with HRMS for the analysis of analytes in biofluids: past, present and future

Capillary LC (cLC) coupled to MS has the potential to improve detection limits, address limited sample volumes and allow multiple analyses from one sample. This is particularly attractive in areas where ultrahigh assay sensitivity, low limits of detection and small sample volumes are becoming commonplace. However, implementation of cLC–MS in the bioanalytical–drug metabolism area had been hampered by the lack of commercial instrumentation and the need for experts to operate the system. Recent advances in microfabricated devices such as chip-cube and ion-key technologies offer the potential for true implementation of cLC in the modern laboratory including the benefits of the combination of this type of separation with high-resolution MS.

Introduction of a routine quan/qual approach into research DMPK: experiences and evolving strategies

After graduating with an Oceanography degree from Swansea University, Lloyd has spent over 20 years in the field of bioanalysis and metabolite profiling. He started his career in large pharma at Wyeth UK, where he was involved in setting up the first GC and LC–MS/MS systems for both QC and early DMPK assays, employing EI/CI, thermospray, and the then new electrospray ionization techniques. Lloyd then joined Celltech, now UCB, where he is primarily tasked with metabolite profiling by LC–MS and NMR to support both early research projects and late-stage clinical studies.

The application of liquid chromatography high-resolution mass spectrometry for simultaneous quantitative and qualitative (quan/qual) analysis has gained momentum across a range of different scientific arenas in recent years. The ability to acquire high quality quantitative data, whilst also capturing qualitative data for either parallel or retrospective analysis, is a powerful resource, especially in view of ever-reducing cycle times, laboratory space and budgets. The quan/qual approach employing a Q-Exactive™ Orbitrap high-resolution mass spectrometer has been successfully introduced into UCB's research DMPK department. This article describes our experiences in introducing quan/qual, issues that we discovered in establishing this new working paradigm, the evolution of the strategy and its future potential.

Current position of high-resolution MS for drug quantification in clinical & forensic toxicology

This paper reviews high-resolution MS approaches published from January 2011 until March 2014 for the quantification of drugs (of abuse) and/or their metabolites in biosamples using LC-MS with time-of-flight or Orbitrap™ mass analyzers. Corresponding approaches are discussed including sample preparation and mass spectral settings. The advantages and limitations of high-resolution MS for drug quantification, as well as the demand for a certain resolution or a specific mass accuracy are also explored.

Evaluation and optimization of high-performance liquid chromatography coupled with high-resolution mass spectrometry for phospholipid quantitation

RATIONALE

High-performance liquid chromatography coupled with high-resolution mass spectrometry (HPLC/HRMS) provides an attractive alternative to the traditional triple quadrupole mass spectrometry selected reaction monitoring (SRM) methodology in the field of quantitation.

METHODS

An LTQ Orbitrap Velos mass spectrometer coupled with a Shimadzu UHPLC system was used. A mass extraction window (MEW) was defined to mathematically correlate with mass resolving power (MRP). Five MRP measurement conditions at 7500, 15,000, 30,000, 60,000, and 100,000, and five MEW widths at 10%, 20%, 50%, and 100% of ±1000000/MRP, and were utilized as the experimental conditions. Comparison of profile and centroid algorithms was evaluated as well.

RESULTS

Selection of pH 8.5 buffer, C4 column, 20% IPA, and 10 ppm H3 PO4 , minimized hydrophobic and silanol interactions to enhance separation. Narrowing the MEW minimized background noise, while over-narrowing the MEW gave signal loss due to mass accuracy deviation. The mass accuracy deviation was larger for lower MRP measurements especially with centriod data, and hence a profile algorithm was recommended. The post-ionization signal suppression was observed with low MRP and was further confirmed with the analysis of multi-level linearity.

CONCLUSIONS

It was found that the HPLC/HRMS method with conditions of 20% ±1000000/MRP as MEW, 30,000 or 60,000 MRP, and profile algorithm, provide optimum results for quantitation of seven model phospholipids.

Performance assessment of microflow LC combined with high-resolution MS in bioanalysis

BACKGROUND

There continues to be consistent pressure for bioanalytical scientists to achieve lower limits of quantitation. The reasons range from smaller sample volumes available for analysis, to more potent analytes and the growth of biologics in drug development. This has led scientists to investigate alternative LC techniques, including microflow and nanoflow. These techniques have been shown to increase sensitivity of electrospray methods and reduce ionization matrix effects. Because high-resolution MS has significant benefits for the analysis of biologics, this type of mass spectrometer is becoming increasingly important in bioanalysis.

RESULTS

For microflow analysis, a new ion source and significant extra sample preparation or chromatographic separation are not required. However, increased sensitivity and reduced matrix effects were consistently demonstrated when compared with UHPLC flow rates. The extent of matrix effects observed were compound dependent.

DISCUSSION

This paper presents the utility of combining high-resolution/accurate mass with microflow LC from a quantitative standpoint. This includes evaluating the typical quantitative parameters of sensitivity, linearity/dynamic range, precision and accuracy. It also includes the evaluation of changes in signal suppression using microflow LC and microspray ionization. The benefits and disadvantages of using the combination of these two technologies for quantitative bioanalysis are also discussed.

High-throughput bioanalysis of bile acids and their conjugates using UHPLC coupled to HRMS

Background: Quantitative assessment of bile acids in biological matrixes is of growing interest, primarily due to hepatic toxicity resulting from drug interactions with the bile salt export pump. Nevertheless, many bile acids demonstrate poor fragmentation in MS, making conventional MS/MS not a good match for their selective quantitation in biological matrices. Results: The current study was designed to evaluate the feasibility of simultaneous quantitation of 19 bile acids using HRMS coupled to UHPLC separation with minimal instrument optimization. An effective chromatography was developed using an Agilent Zorbax® Eclipse XDB-C18 column (1.8 µm, 50 x 2.1 mm internal diameter), achieving separation of 19 compounds in 10 min. Excellent assay reproducibility was demonstrated, with two sets of standard curves, run 42 days apart. Conclusions: The results show that LC–HRMS is a viable platform for high throughput bioanalysis of bile acids especially in a drug-discovery setting.

Comparison of high-resolution and tandem mass spectrometry for the analysis of nerve agent metabolites in urine

RATIONALE

Although use is prohibited, concerns remain for human exposure to nerve agents during decommissioning, research, and warfare. High-resolution mass spectrometry (HRMS) was compared to tandem mass spectrometry (MS/MS) analysis for the quantitation of five urinary metabolites specific to VX, Russian VX, soman, sarin and cyclosarin nerve agents. The HRMS method was further evaluated for qualitative screening of metabolites not included in the test panel.

METHODS

Nerve agent metabolites were extracted from urine using solid-phase extraction, separated using hydrophilic interaction chromatography and analyzed using both tandem and high-resolution mass spectrometry. MS/MS results were obtained using selected reaction monitoring with unit resolution; HRMS results were obtained using a mass extraction window of 10 ppm at a mass resolution of 50 000. The benchtop Orbitrap HRMS instrument was operated in full scan mode, to measure the presence of unexpected nerve agent metabolites.

RESULTS

The assessment of two quality control samples demonstrated high accuracy (99.5-104%) and high precision (2-9%) for both HRMS and MS/MS. Sensitivity, as described by the limit of detection, was overlapping for both detectors (0.2-0.7 ng/mL). Additionally, the HRMS method positively confirmed the presence of a nerve agent metabolite, not included in the test panel, using the accurate mass and relative retention time.

CONCLUSIONS

The precision, accuracy, and sensitivity were comparable between the current MS/MS method and this newly developed HRMS analysis for five nerve agent metabolites. HRMS showed additional capabilities beyond the current method by confirming the presence of a metabolite not included in the test panel.

Comparison of the quantitative performance of a Q-Exactive high-resolution mass spectrometer with that of a triple quadrupole tandem mass spectrometer for the analysis of illicit drugs in wastewater

RATIONALE

Analysis of drugs in wastewater is gaining more interest, as new approaches to estimate drug consumption from the amount of drug residues in wastewater have been proposed. The aim of this study was to compare the quantitative performance of high-resolution mass spectrometry with that of triple quadrupole mass spectrometry.

METHODS

A Q-Exactive mass spectrometer was operated in full scan (HRFS) (70 000 FWHM) and product scan (HRPS) (17 500 FWHM) modes. The first and third quadrupoles of the QqQ MS/MS instrument were operated at 0.7 FWHM. A mass-extracted window of 5 ppm around the theoretical m/z of each analyte was used to construct chromatograms. An HESI-II ion source was used for the ionization of target compounds. In-line-SPE-LC configuration was used for the extraction and separation of target analytes.

RESULTS

All three methods showed good linearity and repeatability. High-resolution detection of product ions exhibited better sensitivity and selectivity for some compounds. For most of the tested compounds, LOQs ranged from 0.46 to 20 ng L(-1) . Good agreement between measured and nominal concentrations was observed for most of the compounds at different levels of fortification. Both MS/MS methods showed good selectivity, while HRFS gave some false positive results.

CONCLUSIONS

The Q-Exactive mass spectrometer proved to be suitable for trace detection and quantification of most of the tested drugs in wastewater, with performance comparable to that of the commonly used MS/MS triple quadrupole, but with better selectivity.

A tool to evaluate correspondence between extraction ion chromatographic peaks and peptide-spectrum matches in shotgun proteomics experiments

Chromatographed peptide signals form the basis of further data processing that eventually results in functional information derived from data-dependent bottom-up proteomics assays. We seek to rank LC/MS parent ions by the quality of their extracted ion chromatograms. Ranked extracted ion chromatograms act as an intuitive physical/chemical preselection filter to improve the quality of MS/MS fragment scans submitted for database search. We identify more than 4900 proteins when considering detector shifts of less than 7 ppm. High quality parent ions for which the database search yields no hits become candidates for subsequent unrestricted analysis for PTMs. Following this rational approach, we prioritize identification of more than 5000 spectrum matches from modified peptides and confirmed the presence of acetylaldehyde-modified His/Lys. We present a logical workflow that scores data-dependent selected ion chromatograms and leverage information about semianalytical LC/LC dimension prior to MS. Our method can be successfully used to identify unexpected modifications in peptides with excellent chromatography characteristics, independent of fragmentation pattern and activation methods. We illustrate analysis of ion chromatograms detected in two different modes by RF linear ion trap and electrostatic field orbitrap.

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.

Applications of high-resolution MS in bioanalysis

High-resolution MS (HRMS) in conjunction with LC (LC–HRMS) has become available to many laboratories in the pharmaceutical industry. Due to its enhanced, though sometime perceived, specificity using the high-resolution power and its capability of simultaneous quantitation and structural elucidation using the post-acquisition data mining feature, utilization of LC–HRMS for bioanalysis could lead to potential rapid and reliable method development as well as sample analysis, thus generating both cost and resource savings. Here, we would like to share our perspectives about several current and future applications of LC–HRMS in bioanalysis. We will also discuss the factors influencing the quality of method establishment and potential pitfalls that need to be considered for the utilization of LC–HRMS in the field of regulated bioanalysis. We believe when utilized appropriately, LC–HRMS will play a significant role in the future landscape of quantitative bioanalysis.

High-resolution MS in regulated bioanalysis: where are we now and where do we go from here?

While triple quadrupole MS remains the workhorse of bionanalytical laboratories, LC coupled with high-resolution MS (LC–HRMS) is making headway in drug discovery. LC–HRMS is well suited for quantitative bioanalysis with the inherent advantage of post-acquisition data mining, which is not possible with triple quadrupole systems operated in SRM mode. LC–HRMS can, thus, accomplish the core task of a bioanalytical laboratory – accurate determination of a targeted analyte – with the added bonus of being able to monitor other compounds of interest either at the time of sample analysis, or as an afterthought, after sample analysis, with no additional effort in sample preparation, chromatographic optimization or sample reinjection. Despite these advantages, LC–HRMS has not been broadly adopted in regulated bioanalytical laboratories. The slow progress in embracing the technology may be due, in part, to difficulties in replacing an entire fleet of triple quadrupole MS. Additional reasons are that data mining is of less benefit in development, especially late-stage, than in discovery and that the technical and regulatory challenges associated with the change of platform are perceived to be significant. In addition, the current platform of LC–HRMS introduced by instrument companies has not been tailored to the core responsibility of the bioanalytical community. In marketing current LC–HRMS systems, there is a tendency to combine the needs of the bioanalytical community with those of the drug metabolism community, despite their inherent differences. As a result, the current HRMS systems available lack some basic features desired for bioanalysis, but include features that are not important for bioanalysis making the systems unnecessarily complex and expensive. A simple, cost effective, ideal HRMS system for a bioanalytical laboratory would provide HRMS with high resolving power (the higher the better), no MS/MS capability, and with software suitable for quantitative analysis and appropriate for use in regulated laboratories. Under this scenario, one can foresee a future where part of the regulated bioanalytical work will be accomplished using LC–HRMS, reserving triple quadrupole-based LC–MS/MS for assays that require exquisite sensitivity.

High-throughput liquid chromatography/mass spectrometry method for the quantitation of small molecules using accurate mass technologies in supporting discovery drug screening

RATIONALE

Drug discovery samples are routinely analyzed using liquid chromatography/tandem mass spectrometry (LC/MS/MS) methods on triple quadrupole mass spectrometers employing multiple reaction monitoring (MRM). In order to improve analysis throughput, quantitation of small molecules on a quadrupole time-of-flight (QqTOF) instrument using TOF scan and high-resolution MRM (MRM-HR) modes was evaluated in this study.

METHODS

Cassette dosed plasma and brain samples from nine compounds were extracted using a protein precipitation method. Separation was achieved by reversed-phase liquid chromatography. Mass spectrometric analysis was performed using TOF scan and high-resolution MRM approaches on a QqTOF mass spectrometer with turbo-ionspray ionization. Results were compared to those obtained on a triple quadrupole mass spectrometer.

RESULTS

The dynamic range varied depending on compounds and instruments and was similar between the MRM on QqQ and full TOF scan mode on QqTOF. Linear or quadratic regression and 1/x(2) weighting were used. Resolution on the QqTOF instrument was around 32000 and mass accuracy was within 4.4 ppm. The MRM-HR method showed better sensitivity compared to the TOF scan method, and was comparable to the MRM on a QqQ mass spectrometer. Assay accuracy was within ±25%.

CONCLUSIONS

A TOF scan method allowed the use of the generic method without compound-specific optimization and was an alternative choice for routine high-throughput quantitation of small molecules. The MRM-HR method on the QqTOF showed good sensitivity which was comparable to that obtained by the MRM method on the triple quadrupole mass spectrometer.

Evaluation of the interrelationship between mass resolving power and mass error tolerances for targeted bioanalysis using liquid chromatography coupled to high-resolution mass spectrometry

The determination of acceptable mass error tolerances for high-resolution mass spectrometry based signals has been evaluated in a comprehensive way. This was achieved by using a technical approach which is based on the post-column infusion of an analyte containing solution. This well-known experimental setup was not used to spot signal suppression regions of a particular analyte, but to spot regions of the chromatogram where a systematic mass drift of the analyte ion can be observed (isobaric interference plot). Not the changing signal intensity but the stability of the measured analyte mass was observed. A wide range of different analytes in combinations with potentially interfering matrices has been evaluated. Furthermore, different mass resolving power settings were evaluated. Isobaric interferences between matrix compounds and analytes were common at mass resolving powers <50,000 full width at half maximum. The proposed post-column infusion technique is a useful tool for the determination of the assay and matrix-specific mass error tolerances. It aims to ensure the highest possible selectivity, at the same time preventing the encounter of detrimental mass error related peak deformations as well as false negative findings. Unlike conventional matrix spiking approaches, isobaric interference plots provide information of potential interferences across the whole chromatographic time range. This becomes relevant when there is a relative retention time shift between the analyte and potential interfering matrix compounds. Furthermore, the described setup can be used to study how the mass accuracy of any mass spectrometer is affected by a widely varying total ion current.

Utility of high-resolution accurate MS to eliminate interferences in the bioanalysis of ribavirin and its phosphate metabolites

BACKGROUND

The polar nucleoside drug ribavirin (RBV) combined with IFN-α is a front-line treatment for chronic hepatitis C virus infection. RBV acts as a prodrug and exerts its broad antiviral activity primarily through its active phosphorylated metabolite ribavirin 5´-triphosphate (RTP), and also possibly through ribavirin 5´-monophosphate (RMP). To study RBV transport, diffusion, metabolic clearance and its impact on drug-metabolizing enzymes, a LC-MS method is needed to simultaneously quantify RBV and its phosphorylated metabolites (RTP, ribavirin 5´-diphosphate and RMP). In a recombinant human UGT1A1 assay, the assay buffer components uridine and its phosphorylated derivatives are isobaric with RBV and its phosphorylated metabolites, leading to significant interference when analyzed by LC-MS with the nominal mass resolution mode.

RESULTS

Presented here is a LC-MS method employing LC coupled with full-scan high-resolution accurate MS analysis for the simultaneous quantitative determination of RBV, RMP, ribavirin 5´-diphosphate and RTP by differentiating RBV and its phosphorylated metabolites from uridine and its phosphorylated derivatives by accurate mass, thus avoiding interference.

CONCLUSION

The developed LC-high-resolution accurate MS method allows for quantitation of RBV and its phosphorylated metabolites, eliminating the interferences from uridine and its phosphorylated derivatives in recombinant human UGT1A1 assays.

The future key role of LC–high-resolution-MS analyses in clinical laboratories: a focus on quantification

For the last decade, high-resolution (HR)-MS has been associated with qualitative analyses while triple quadrupole MS has been associated with routine quantitative analyses. However, a shift of this paradigm is taking place: quantitative and qualitative analyses will be increasingly performed by HR-MS, and it will become the common ‘language’ for most mass spectrometrists. Most analyses will be performed by full-scan acquisitions recording ‘all’ ions entering the HR-MS with subsequent construction of narrow-width extracted-ion chromatograms. Ions will be available for absolute quantification, profiling and data mining. In parallel to quantification, metabotyping will be the next step in clinical LC–MS analyses because it should help in personalized medicine. This article is aimed to help analytical chemists who perform targeted quantitative acquisitions with triple quadrupole MS make the transition to quantitative and qualitative analyses using HR-MS. Guidelines for the acceptance criteria of mass accuracy and for the determination of mass extraction windows in quantitative analyses are proposed.

LC–MS systems for quantitative bioanalysis

LC–MS has become the method-of-choice in small-molecule drug bioanalysis (molecular mass <800 Da) and is also increasingly being applied as an alternative to ligand-binding assays for the bioanalytical determination of biopharmaceuticals. Triple quadrupole MS is the established bioanalytical technique due to its unpreceded selectivity and sensitivity, but high-resolution accurate-mass MS is recently gaining ground due to its ability to provide simultaneous quantitative and qualitative analysis of drugs and their metabolites. This article discusses current trends in the field of bioanalytical LC–MS (until September 2012), and provides an overview of currently available commercial triple quadrupole MS and high-resolution LC–MS instruments as applied for the bioanalysis of small-molecule and biopharmaceutical drugs.

Challenges in the development of bioanalytical liquid chromatography-mass spectrometry method with emphasis on fast analysis

The development of bioanalytical methods has become more and more challenging over the past years due to very demanding requirements in terms of method reliability, sensitivity, speed of analysis and sample throughput. LC-MS/MS has established itself as a method of choice for routine analysis of biological materials. A development of such method consists of several steps including sample preparation and clean-up step, efficient chromatographic separation, sensitive and selective detection of analytes in complex matrices, a choice of convenient data processing and calibration approach and finally method validation. Each of these steps has its own constraints and challenges, which are discussed in detail in this review. Novel and modern approaches in sample preparation, chromatography and detection are especially emphasized. Attention is paid to proper calibration approach and matrix effects that can seriously affect method accuracy and precision.

Importance of MS selectivity and chromatographic separation in LC-MS/MS-based methods when investigating pharmaceutical metabolites in water. Dipyrone as a case of study

Pharmaceuticals are emerging contaminants of increasing concern because of their presence in the aquatic environment and potential to reach drinking-water sources. After human and/or veterinary consumption, pharmaceuticals can be excreted in unchanged form, as the parent compound, and/or as free or conjugated metabolites. Determination of most pharmaceuticals and metabolites in the environment is commonly made by liquid chromatography (LC) coupled to mass spectrometry (MS). LC coupled to tandem MS is the technique of choice nowadays in this field. The acquisition of two selected reaction monitoring (SRM) transitions together with the retention time is the most widely accepted criterion for a safe quantification and confirmation assay. However, scarce attention is normally paid to the selectivity of the selected transitions as well as to the chromatographic separation. In this work, the importance of full spectrum acquisition high-resolution MS data using a hybrid quadrupole time-of-flight analyser and/or a suitable chromatographic separation (to reduce the possibility of co-eluting interferences) is highlighted when investigating pharmaceutical metabolites that share common fragment ions. For this purpose, the analytical challenge associated to the determination of metabolites of the widely used analgesic dipyrone (also known as metamizol) in urban wastewater is discussed. Examples are given on the possibilities of reporting false positives of dypirone metabolites by LC-MS/MS under SRM mode due to a wrong assignment of identity of the compounds detected.

A universal surrogate peptide to enable LC-MS/MS bioanalysis of a diversity of human monoclonal antibody and human Fc-fusion protein drug candidates in pre-clinical animal studies

For the development of human antibody Fc (fraction crystallizable) region-containing therapeutic protein candidates, which can be either monoclonal antibodies (mAbs) or pharmacologically active proteins/peptides fused to the Fc region of human Immunoglobulin G (IgG), reliable quantification of these proteins in animal pharmacokinetic study plasma samples is critical. LC-MS/MS has emerged as a promising assay platform for this purpose. LC-MS/MS assays used for bioanalysis of human antibody Fc region-containing therapeutic protein candidates frequently rely upon quantification of a 'signature' surrogate peptide whose sequence is unique to the protein analyte of interest. One drawback of the signature peptide approach is that a new LC-MS/MS assay must be developed for each new human Fc region-containing therapeutic protein. To address this issue, we propose an alternative 'universal surrogate peptide' approach for the quantification of human antibody Fc region-containing therapeutic protein candidates in plasma samples from all nonclinical species. A single surrogate tryptic peptide was identified in the Fc region of most human antibody Fc-containing therapeutic protein candidates. An LC-MS-MS method based upon this peptide was shown to be capable of supporting bioanalysis of a diversity of human Fc region-containing therapeutic protein candidates in plasma samples of all commonly used animal species.

Recent advances in metabolite identification and quantitative bioanalysis by LC–Q-TOF MS

The need for rapid, sensitive and effective identification and quantitation of drugs and metabolites to accelerate drug discovery and development has given MS its central position in drug metabolism and pharmacokinetic research. This review attempts to orient the readers with respect to hybrid Q-TOF MS, which enables accurate mass measurement and generates information-rich datasets. The key properties of the Q-TOF MS system, including mass accuracy, resolution, scan speed and dynamic range, are herein discussed. Developments on tandem separation techniques (e.g., UHPLC® and ion mobility spectrometry), data acquisition and data-mining methods (e.g., mass defect, product/neutral loss, isotope pattern filters and background subtraction) that facilitate qualitative and quantitative analysis are then examined. The performance and versatility of LC–Q-TOF MS are thoroughly illustrated by its applications in metabolite identification and quantitative bioanalysis. Future perspectives are also discussed.

High-throughput quantitation of large molecules using multiplexed chromatography and high-resolution/accurate mass LC–MS

Background: High-throughput screening with LC–MS has been routinely implemented to various degrees throughout the entire drug-discovery process. One of the major advantages of utilizing LC–MS earlier at the lead discovery stage is reducing the cost of sample analysis while increasing assay selectivity. Avoiding labeling agents and other non-native species in an assay environment can reduce costly sample preparation, while chromatographic separation of the analyte of interest from interferences in the sample matrix has been shown to increase selectivity and sensitivity. Method: In this paper, we utilize high-resolution MS–LC multiplexing to analyze phosphorylated peptides as part of a screening assay. Commonly used enzyme buffers were used to prepare phosphorylated peptide standards of varying concentrations and these were plated into a 96-well plate format for LC–MS analysis. The overall cycle time for analysis from sample to sample, LLOQ, Z’ and coefficient of variance were determined. Conclusion: High-resolution MS coupled with LC multiplexing provides high-quality sample analysis at sampling rates of up to 18 s per sample. Samples analyzed in both simple and complex sample matrixes demonstrated an LOQ of 5 nM with linear response across the working range of the assay. Overall statistical analysis of the large samples produced Z’ = 0.85 for sample sets in sodium citrate solution and Z’ = 0.66 for sample sets in HEPES solution indicating a robust analytical method.