Dosage d'un panel d'anticrises de nouvelle génération par LC-MS/MS / Dosing of a New Generation Anti-Seizure Panel by LC-MS/MS

INTRODUCTION: Une demande d'introduction d'une nouvelle analyse au Répertoire québécois et système de mesure des procédures de biologie médicale (ci-après nommé « Répertoire ¼) a été effectuée par le Centre hospitalier de l'Université de Montréal (CHUM) et transmise à l'Institut national d'excellence en santé et en services sociaux (INESSS) selon le mécanisme d'évaluation des nouvelles analyses de biologie médicale. Le mandat confié vise à évaluer le dosage d'un panel d'anticrises de nouvelle génération par chromatographie liquide couplée à la spectrométrie de masse en tandem (LC-MS/MS) dans le cadre du suivi thérapeutique de l'épilepsie. Étant donné que ce test ne figure pas dans le Répertoire, le ministère de la Santé et des Services sociaux (MSSS) juge nécessaire que la pertinence de cette analyse soit évaluée. MÉTHODOLOGIE: La démarche d'évaluation comprend une revue de la documentation scientifique, une recherche de la littérature grise et des consultations menées auprès de cliniciens et d'autres parties prenantes. La méthodologie a été déployée autour de sept questions d'évaluation, portant notamment sur les dimensions socioculturelle, populationnelle, clinique (validité clinique et utilité clinique), organisationnelle et économique (efficience et impact budgétaire). Une revue de la littérature économique a été réalisée ainsi qu'une évaluation de la possibilité d'effectuer une modélisation économique pour mesurer l'efficience du dosage des anticrises de nouvelle génération par LC-MS/MS. Une analyse d'impact budgétaire considérant les coûts liés à l'introduction du dosage des anticrises de nouvelle génération par LC-MS/MS au Répertoire a été réalisée. Les coûts ont été projetés sur un horizon temporel de trois ans selon la perspective du système de soins de santé. L'ensemble des données scientifiques, contextuelles et expérientielles a été interprété et synthétisé sous la forme de constats afin de guider le processus de délibération du Comité délibératif permanent (CDP) - Approches diagnostiques et dépistage en vue de l'élaboration de recommandations. CONTEXTE DE L'ÉVALUATION: L'épilepsie entraîne des conséquences neurologiques, cognitives, psychologiques et sociales importantes pour les personnes qui en sont atteintes. Le traitement de l'épilepsie est essentiellement pharmacologique. Selon les individus, les médicaments peuvent avoir une efficacité, une innocuité et des effets indésirables variables. Il s'avère donc nécessaire de surveiller l'évolution de cette maladie et d'adapter la prise en charge adéquatement. Un recours au suivi thérapeutique par dosage des anticrises est de plus en plus recommandé. Toutefois, de nombreux autres anticrises largement utilisés ne bénéficient d'aucune procédure de dosage officiellement inscrite au Répertoire. À ce jour, au Québec, le Répertoire ne contient que deux tests correspondant aux dosages des anticrises de nouvelle génération, soit la lamotrigine (30690) et le clobazam (30660). DIMENSION SOCIOCULTURELLE: Le Guide de pratique clinique du gouvernement de l'Ontario sur la prise en charge de l'épilepsie et d'autres documents similaires issus de sociétés savantes à l'international mentionnent que le suivi thérapeutique des anticrises repose sur le jugement clinique du médecin traitant. Bien qu'il ne soit pas recommandé de le faire systématiquement pour tous les patients, le suivi thérapeutique devrait être considéré lorsque les crises ne sont pas contrôlées, qu'une condition altérant la pharmacocinétique comme une grossesse est présente ou encore lorsqu'une toxicité ou une non-observance est suspectée. DIMENSION POPULATIONNELLE: L'épilepsie touche environ 300 000 personnes au Canada et est diagnostiquée à tout âge. L'épilepsie augmente les risques de blessures et de décès prématuré, peut perturber le sommeil, affecter le choix de carrière, limiter la pratique d'activité physique et restreindre le droit de conduire. La stigmatisation liée à l'épilepsie est un défi considérable pour certains patients, ce qui a des répercussions sur leur qualité de vie globale. Les médicaments anticrises demeurent la base du traitement de l'épilepsie. Ils permettent de réduire la fréquence des crises tout en offrant une meilleure qualité de vie aux patients. La concentration plasmatique efficace varie d'un individu à l'autre et ne se retrouve pas nécessairement à l'intérieur d'une plage de référence. Dans ce contexte, l'identification d'une concentration individuelle plasmatique pourrait être souhaitée. Les anticrises ont des effets indésirables qui peuvent gêner la vie quotidienne et doivent être considérés dans la prise en charge. Au Québec, l'offre actuelle de tests pour effectuer le suivi thérapeutique des anticrises de nouvelle génération ne répond pas à la demande des cliniciens. En effet, plusieurs de ces médicaments ne sont pas dosés et le temps réponse pour obtenir le résultat du dosage de ceux qui le sont est jugé inacceptable. DIMENSION CLINIQUE: Malgré un niveau de preuve généralement faible, les études sélectionnées ont indiqué que le dosage des anticrises de nouvelle génération dans le cadre du suivi thérapeutique offrirait quelques avantages cliniques, notamment un meilleur contrôle des crises ou une diminution des effets indésirables. Cela pourrait être particulièrement avantageux pour les patients présentant une variabilité pharmacocinétique accrue, comme les enfants, les personnes âgées, les femmes enceintes et les patients atteints de comorbidités. À la lumière de la littérature scientifique repérée et de l'opinion des experts, la LC-MS/MS est considérée comme une méthode de référence pour effectuer le dosage des anticrises de nouvelle génération à partir d'échantillons de sérum ou de plasma. DIMENSION ORGANISATIONNELLE: La LC-MS/MS offre la possibilité d'analyser à la chaîne un lot d'échantillons provenant de différents patients traités avec un ou plusieurs anticrises, ce qui facilite la centralisation et l'optimisation des procédures. Certains laboratoires détiennent les ressources nécessaires pour doser les anticrises de nouvelle génération selon une approche multiplex en LC-MS/MS. Les cliniciens estiment que le temps réponse de trois semaines est long, ce qui risque de compromettre l'utilité clinique du suivi thérapeutique des anticrises. Un délai plus court prenant en considération le temps nécessaire pour acheminer l'échantillon au laboratoire devrait être visé. DIMENSION ÉCONOMIQUE: Efficience: Aucune étude évaluant l'efficience du suivi thérapeutique des anticrises de nouvelle génération par LC-MS/MS chez les patients atteints d'épilepsie n'a été repérée. Étant donné l'incertitude concernant les bénéfices de santé liés au suivi thérapeutique des anticrises de nouvelle génération par LC-MS/MS, l'INESSS ne peut pas évaluer l'efficience du panel proposé, par rapport aux dosages présentement effectués au Québec. L'analyse de coûts réalisée montre que son utilisation pourrait permettre une réduction des coûts de 12 $ à 103 $, par rapport aux analyses présentement au Répertoire. Analyse d'impact budgétaire: Vu l'incertitude entourant certains paramètres de l'analyse d'impact budgétaire, une approche par scénario a été privilégiée. Selon le scénario considéré, l'ajout du panel proposé pourrait engendrer des coûts de 55 k$ à 821 k$ au cours des trois premières années, pour la réalisation de 12 900 à 33 900 analyses. Ces résultats sont toutefois empreints d'incertitude, puisqu'il est difficile d'évaluer avec précision le nombre d'analyses anticipées. CONCLUSIONS: Afin de maximiser l'utilité clinique anticipée et de limiter le risque d'usage non optimal, l'INESSS préciseb que les conditions suivantes sont nécessaires à l'implantation de l'analyse proposée: Le temps réponse clinique devrait être au maximum de dix jours (incluant le temps requis pour acheminer l'échantillon au laboratoire). Il faudra assurer un suivi d'implantation du test au cours des prochaines années afin de documenter, notamment, les indications cliniques, les temps réponse, la volumétrie et les coûts d'analyse. Le formulaire de requête devrait permettre de sélectionner l'indication clinique pour laquelle le test est demandé, soit: - suspicion de toxicités; - crises épileptiques non contrôlées; - grossesse; - maladie hépatique ou rénale; - interactions médicamenteuses; - altération pharmacocinétique autre; - suspicion de non-observance thérapeutique; - pédiatrie. Les analyses réalisées par une trousse commerciale ou une méthode développée en laboratoire devraient satisfaire aux exigences de la norme ISO 15189. L'offre de service devrait être disponible dans plusieurs laboratoires à travers la province.

INTRODUCTION: The Centre hospitalier de l'Université de Montréal (CHUM) has submitted a request to introduce a new assay to the Répertoire québécois et système de mesure des procédures de biologie médicale (hereinafter referred to as the "Répertoire"), and has forwarded it to the Institut national d'excellence en santé et en services sociaux (INESSS) in accordance with the evaluation mechanism for new medical biology assays. The mandate given was to evaluate the new-generation anti-seizure panel assay by liquid chromatography combined with tandem mass spectrometry (LC-MS/MS) as part of the therapeutic follow-up of epilepsy. As this assay is not listed in the Répertoire, the Ministère de la Santé et des Services sociaux (MSSS) considers it necessary to evaluate its relevance. METHODOLOGY: The evaluation approach included a review of the scientific literature, a search of the grey literature, and consultations with clinicians and other stakeholders. The methodology was structured around seven evaluation questions, covering socio-cultural, population, clinical (clinical validity and clinical utility), organizational and economic (efficacy and budgetary impact) dimensions. A review of the economic literature was conducted, along with a feasibility evaluation of economic modeling to measure the effectiveness of LC-MS/MS dosing of new-generation anti-seizure agents. A budgetary impact analysis was conducted, considering the costs associated with the introduction of new-generation LCMS/MS anti-seizure assays to the Repertoire. Costs were projected over a three-year time horizon from a healthcare system perspective. All scientific, contextual, and experiential data were interpreted and synthesized into findings to guide the deliberative process of the Standing Deliberative Committee (SDC) - Diagnostic Approaches and Screening, in order to develop recommendations. EVALUATION CONTEXT: Epilepsy has significant neurological, cognitive, psychological, and social consequences for sufferers. The treatment of epilepsy is essentially pharmacological. Depending on the individual, drugs may have varying degrees of efficacy, safety, and side effects. It is therefore essential to monitor the progression of this disease and adapt management accordingly. The use of anti-seizure monitoring is increasingly recommended. However, many other widely used anti-seizure drugs do not benefit from an officially listed dosing procedure in the Répertoire. To date, only two assays for the new-generation anti-seizure drugs lamotrigine (30690) and clobazam (30660) are listed in the Répertoire. SOCIOCULTURAL DIMENSION: The Government of Ontario's Clinical Practice Guidelines for the Management of Epilepsy, and similar documents from international learned societies, state that antiseizure therapy is based on the clinical judgment of the treating physician. Although it is not recommended to do so systematically for all patients, therapeutic follow-up should be considered when seizures are uncontrolled, when a condition altering pharmacokinetics such as pregnancy is present, or when toxicity or non-adherence is suspected. Population Dimension Epilepsy affects some 300,000 people in Canada and is diagnosed at all ages. Epilepsy increases the risk of injury and premature death, can disrupt sleep, affect career choices, limit physical activity, and restrict driving privileges. The stigma associated with epilepsy is a considerable challenge for some patients, impacting on their overall quality of life. Anti-seizure medication remains the mainstay of epilepsy treatment. They reduce the frequency of seizures while improving patients' quality of life. Effective plasma concentrations vary from one individual to another, and do not necessarily fall within a reference range. Identifying an individual plasma concentration may therefore be desirable. Anti-seizure medications have adverse effects that can interfere with daily life and must be considered in their management. In Quebec, the current supply of assays for therapeutic monitoring of new-generation anti-seizure drugs (TDM) does not meet clinicians' needs. In fact, many of these drugs are not assayed, and the response time to obtain assay results for those that are is deemed unacceptable. CLINICAL DIMENSION: Despite a generally low body of evidence, the selected studies indicated that administering new-generation anti-seizure drugs as part of follow-up therapy would offer some clinical benefits, such as better seizure control or fewer adverse effects. This could be particularly advantageous for patients with increased pharmacokinetic variability, such as children, the elderly, pregnant women, and patients with comorbidities. In light of the identified scientific literature and expert opinion, LC MS/MS is considered a reference method for assaying new-generation anti-seizures from serum or plasma samples. ORGANIZATIONAL DIMENSION. LC-MS/MS offers the possibility of analyzing a batch of samples from different patients treated with one or more anti-seizures, making it easier to centralize and optimize procedures. Some laboratories have the resources needed to assay new-generation anti-seizures using a multiplex LC-MS/MS approach. Clinicians consider the three-week response time to be long, which may compromise the clinical usefulness of anti-seiz follow-up therapy. A shorter response time, considering the time needed to get the sample to the laboratory, should be targeted. ECONOMIC DIMENSION: Effectiveness: No studies evaluating the cost-effectiveness of therapeutic monitoring of new-generation anti-seizure assays by LC-MS/MS in patients with epilepsy have been identified. Given the uncertainty surrounding the health benefits associated with therapeutic monitoring of new-generation anti-seizure assays by LC-MS/MS, the INESSS is unable to evaluate the effectiveness of the proposed panel, compared with the assays currently performed in Quebec. The cost analysis conducted shows that its use could result in a cost reduction of $12 to $103, compared with assays currently in the Répertoire. BUDGET IMPACT ANALYSIS: Given the uncertainty surrounding certain parameters of the budget impact analysis, a scenario-based approach was adopted. Depending on the scenario considered, the addition of the proposed panel could generate costs of between $55k and $821k over the first three years for the completion of between 12,900 and 33,900 assays. However, these results are subject to uncertainty, since it is difficult to accurately estimate the number of anticipated assays. CONCLUSIONS: In order to maximize anticipated clinical utility and limit the risk of sub-optimal use, the INESSS stipulates that the following conditions are necessary for the implementation of the proposed assay: Clinical response time should be a maximum of ten days (including the time required to transport the sample to the laboratory). Implementation of the assay will have to be monitored over the next few years, in order to document clinical indications, response times, volumetry, and analysis costs. The request form should make it possible to select the clinical indication for which the assay is requested, i.e., suspected toxicity; uncontrolled epileptic seizures; pregnancy; liver or kidney disease; drug interactions; other pharmacokinetic alterations; suspected non-compliance; pediatrics. Assays conducted using either a commercial kit or a laboratory-developed method should meet ISO 15189 requirements. The service should be available in several laboratories across the province.

Coupling immuno-magnetic capture with LC-MS/MS(MRM) as a sensitive, reliable, and specific assay for SARS-CoV-2 identification from clinical samples.

Recently, numerous diagnostic approaches from different disciplines have been developed for SARS-CoV-2 diagnosis to monitor and control the COVID-19 pandemic. These include MS-based assays, which provide analytical information on viral proteins. However, their sensitivity is limited, estimated to be 5 × 104 PFU/ml in clinical samples. Here, we present a reliable, specific, and rapid method for the identification of SARS-CoV-2 from nasopharyngeal (NP) specimens, which combines virus capture followed by LC-MS/MS(MRM) analysis of unique peptide markers. The capture of SARS-CoV-2 from the challenging matrix, prior to its tryptic digestion, was accomplished by magnetic beads coated with polyclonal IgG-α-SARS-CoV-2 antibodies, enabling sample concentration while significantly reducing background noise interrupting with LC-MS analysis. A sensitive and specific LC-MS/MS(MRM) analysis method was developed for the identification of selected tryptic peptide markers. The combined assay, which resulted in S/N ratio enhancement, achieved an improved sensitivity of more than 10-fold compared with previously described MS methods. The assay was validated in 29 naive NP specimens, 19 samples were spiked with SARS-CoV-2 and 10 were used as negative controls. Finally, the assay was successfully applied to clinical NP samples (n = 26) pre-determined as either positive or negative by RT-qPCR. This work describes for the first time a combined approach for immuno-magnetic viral isolation coupled with MS analysis. This method is highly reliable, specific, and sensitive; thus, it may potentially serve as a complementary assay to RT-qPCR, the gold standard test. This methodology can be applied to other viruses as well.

Differentiation of leucine and isoleucine residues in peptides using charge transfer dissociation mass spectrometry (CTD-MS).

RATIONALE: The function of a protein or the binding affinity of an antibody can be substantially altered by the replacement of leucine (Leu) with isoleucine (Ile), and vice versa, so the ability to identify the correct isomer using mass spectrometry can help resolve important biological questions. Tandem mass spectrometry approaches for Leu/Ile (Xle) discrimination have been developed, but they all have certain limitations. METHODS: Four model peptides and two wild-type peptide sequences containing either Leu or Ile residues were subjected to charge transfer dissociation (CTD) mass spectrometry on a modified three-dimensional ion trap. The peptides were analyzed in both the 1+ and 2+ charge states, and the results were compared to conventional collision-induced dissociation spectra of the same peptides obtained using the same instrument. RESULTS: CTD resulted in 100% sequence coverage for each of the studied peptides and provided a variety of side-chain cleavages, including d, w and v ions. Using CTD, reliable d and w ions of Xle residues were observed more than 80% of the time. When present, d ions are typically greater than 10% of the abundance of the corresponding a ions from which they derive, and w ions are typically more abundant than the z ions from which they derive. CONCLUSIONS: CTD has the benefit of being applicable to both 1+ and 2+ precursor ions, and the overall performance is comparable to that of other high-energy activation techniques like hot electron capture dissociation and UV photodissociation. CTD does not require chemical modifications of the precursor peptides, nor does it require additional levels of isolation and fragmentation.

Development and Validation of a LC-MS/MS Technique for the Analysis of Short Chain Fatty Acids in Tissues and Biological Fluids without Derivatisation Using Isotope Labelled Internal Standards.

The gut microbiota is critical to the maintenance of physiological homeostasis and as such is implicated in a range of diseases such as colon cancer, ulcerative colitis, diabetes, cardiovascular diseases, and neurodegenerative diseases. Short chain fatty acids (SCFAs) are key metabolites produced by the gut microbiota from the fermentation of dietary fibre. Here we present a novel, sensitive, and direct LC-MS/MS technique using isotopically labelled internal standards without derivatisation for the analysis of SCFAs in different biological matrices. The technique has significant advantages over the current widely used techniques based on sample derivatization and GC-MS analysis, including fast and simple sample preparation and short LC runtime (10 min). The technique is specific and sensitive for the quantification of acetate, butyrate, isobutyrate, isovalerate, lactate, propionate and valerate. The limits of detection were all 0.001 mM except for acetate which was 0.003 mM. The calibration curves for all the analytes were linear with correlation coefficients r2 > 0.998. The intra- and inter-day precisions in three levels of known concentrations were <12% and <20%, respectively. The quantification accuracy ranged from 92% to 120%. The technique reported here offers a valuable analytical tool for use in studies of SCFA production in the gut and their distribution to host tissues.

Development of an immobilized-trypsin reactor coupled to liquid chromatography and tandem mass spectrometry for the analysis of human hemoglobin adducts with sulfur mustard.

Sulfur mustard reacts with blood proteins, such as hemoglobin, to form stable adducts that can be used as long-lived biomarkers of exposure. These adducts can be analyzed by liquid chromatography coupled to tandem mass-spectrometry (LC-MS/MS) after an enzymatic digestion step. The objective of this study was to develop trypsin-based immobilized enzyme reactors (IMERs) in order to obtain a faster digestion of hemoglobin than the conventional in-solution digestion. Trypsin IMERs were synthetized by grafting the enzyme on a CNBr-Sepharose gel and the influence of several parameters on the digestion yields, such as the transfer volume between the injection loop and the IMER, the temperature and the digestion time was studied. The repeatability of the digestion on three laboratory-made IMERs was demonstrated for pure hemoglobin and hemoglobin previously exposed to different concentrations of sulfur mustard (RSD inferior to 13% and 21% respectively) and was better than that obtained for in-solution digestions (RSD inferior to 28% and up to 53% respectively). A preferential adduction of sulfur mustard on the histidine residues of hemoglobin was confirmed, for both in-solution and IMER digestion results. On a quantitative point of view, the performances of in-solution and IMER digestions were similar, with the theoretical possibility to detect peptides resulting from the in vitro incubation of hemoglobin in pure water with sulfur mustard at 7.5 ng⋅mL-1. However, digestion on IMER proved to be more repeatable and 32 times faster than in-solution digestion, and a given IMER could be reused at least 60 times.

High-throughput and trace analysis of diazepam in plasma using DART-MS/MS and its pharmacokinetic application.

A high-throughput quantitative analytical method based on Direct Analysis in Real Time tandem mass spectrometry (DART-MS/MS) has been developed and validated for the determination of diazepam in rat plasma, whereby analyzing of each sample needs merely 25 µL plasma, simple solid phase extraction sample preparation and 15 s acquisition time. The multiple reaction monitoring (MRM) transitions at m/z 285.2 â†’ 193.1 and 316.0 â†’ 270.0 were selected for the monitoring of diazepam and its internal standard clonazepam respectively. A good linearity within the range of 10-2000 ng/mL, an intra- and inter-day precisions within <7.78% as to an accuracy ranging from 1.04% to 7.92% have been achieved. The method has been successfully applied to the pharmacokinetic study of diazepam in rats' plasma after a single intragastric administration at a dose of 10 mg/kg. The results indicate that this method fulfills the requirements of the bioanalysis in sensitivity and accuracy. It shows considerable promise for application of DART-MS to the quantitative investigation of other drugs.

Dissociation of Biomolecules by an Intense Low-Energy Electron Beam in a High Sensitivity Time-of-Flight Mass Spectrometer.

We report the progress on an electron-activated dissociation (EAD) device coupled to a quadrupole TOF mass spectrometer (QqTOF MS) developed in our group. This device features a new electron beam optics design allowing up to 100 times stronger electron currents in the reaction cell. The electron beam current reached the space-charge limit of 0.5 µA at near-zero electron kinetic energies. These advances enable fast and efficient dissociation of various analytes ranging from singly charged small molecules to multiply protonated proteins. Tunable electron energy provides access to different fragmentation regimes: ECD, hot ECD, and electron-impact excitation of ions from organics (EIEIO). The efficiency of the device was tested on a wide range of precursor charge states. The EAD device was installed in a QqTOF MS employing a novel trap-and-release strategy facilitating spatial mass focusing of ions at the center of the TOF accelerator. This technique increased the sensitivity 6-10 times and allows for the first time comprehensive structural lipidomics on an LC time scale. The system was evaluated for other compound classes such as intact proteins and glycopeptides. Application of hot ECD for the analysis of glycopeptides resulted in rich fragmentation with predominantly peptide backbone fragments; however, glycan fragments attributed to the ECD process were also observed. A standard small protein ubiquitin (8.6 kDa) was sequenced with 90% cleavage coverage at spectrum accumulation times of 100 ms and 98% at 800 ms. Comparable cleavage coverage for a medium-size protein (carbonic anhydrase: 29 kDa) could be achieved, albeit with longer accumulation times.

High-throughput determination of flavanone-O-glycosides in citrus beverages by paper spray tandem mass spectrometry.

A fast and accurate methodology for the quantification of the most abundant flavanone glycosides in citrus beverages has been developed. The approach relies on the use of paper spray mass spectrometry, which allows to record data in few minutes and without sample pre-treatment. The experiments have been carried out in Multiple Reaction Monitoring scan mode, in order to obtain the best specificity and sensitivity. The analytical parameters were all satisfactory. The results coming from the analysis of real samples were compared to the data obtained by the commonly used chromatographic method, proving the robustness of the proposed approach.

A New Workflow for Drug Metabolite Profiling by Utilizing Advanced Tribrid Mass Spectrometry and Data-Processing Techniques.

Drug metabolite profiling utilizes liquid chromatography with tandem mass spectrometry (LC/MS/MS) to acquire ample information for metabolite identification and structural elucidation. However, there are still challenges in detecting and characterizing all potential metabolites that can be masked by a high biological background, especially the unknown and uncommon ones. In this work, a novel metabolite profiling workflow was established on a platform using a state-of-the-art tribrid high-resolution mass spectrometry (HRMS) system. Primarily, an instrumental method was developed based on the novel design of the tribrid system that facilitates in-depth MSn scans with two fragmentation devices. Additionally, different advanced data acquisition techniques were assessed and compared, and automatic background exclusion and deep-scan approaches were adopted to promote assay efficiency and metabolite coverage. Finally, different data-analysis techniques were explored to fully extract metabolite data from the information-rich MS/MS data sets. Overall, a workflow combining tribrid mass spectrometry and advanced acquisition methodology has been developed for metabolite characterization in drug discovery and development. It maximizes the tribrid HRMS platform's utility and enhances the coverage, efficiency, quality, and speed of metabolite profiling assays.

Capillary Zone Electrophoresis-Electron-Capture Collision-Induced Dissociation on a Quadrupole Time-of-Flight Mass Spectrometer for Top-Down Characterization of Intact Proteins.

Mass spectrometry (MS)-based denaturing top-down proteomics (dTDP) requires high-capacity separation and extensive gas-phase fragmentation of proteoforms. Herein, we coupled capillary zone electrophoresis (CZE) to electron-capture collision-induced dissociation (ECciD) on an Agilent 6545 XT quadrupole time-of-flight (Q-TOF) mass spectrometer for dTDP for the first time. During ECciD, the protein ions were first fragmented using ECD, followed by further activation and fragmentation by applying a CID potential. In this pilot study, we optimized the CZE-ECciD method for small proteins (lower than 20 kDa) regarding the charge state of protein parent ions for fragmentation and the CID potential applied to maximize the protein backbone cleavage coverage and the number of sequence-informative fragment ions. The CZE-ECciD Q-TOF platform provided extensive backbone cleavage coverage for three standard proteins lower than 20 kDa from only single charge states in a single CZE-MS/MS run in the targeted MS/MS mode, including ubiquitin (97%, +7, 8.6 kDa), superoxide dismutase (SOD, 87%, +17, 16 kDa), and myoglobin (90%, +16, 17 kDa). The CZE-ECciD method produced comparable cleavage coverage of small proteins (i.e., myoglobin) with direct-infusion MS studies using electron transfer dissociation (ETD), activated ion-ETD, and combinations of ETD and collision-based fragmentation on high-end orbitrap mass spectrometers. The results render CZE-ECciD a new tool for dTDP to enhance both separation and gas-phase fragmentation of proteoforms.

Comparison of QuEChERS and "dilute and shoot" extraction methods for multi-mycotoxin analysis of samples from button mushroom (Agaricus bisporus) cultivation.

Several components of mushroom compost (wheat straw, chicken manure) can be contaminated with mycotoxins posing food health risks to mushroom consumers. To assess the relevance of such contaminations high-throughput analytical methods are needed. In this study, two sample preparation approaches, dilute & shoot (D&S) and modified citrate buffered Quick, Easy, Cheap, Effective, Rugged, Safe (QuEChERS) were compared in terms of extraction efficiency and matrix effect in case of 13 mycotoxins in complex matrices-wheat straw, the growing media and button mushrooms (Agaricus bisporus)-of mushroom cultivation using high-performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS). D&S method resulted in recoveries of LB medium, button mushroom and compost for ≥60% in case of all investigated mycotoxins except for DON-3G. However, using modified citrate buffered QuEChERS with 2% acidification of the extraction solvent showed the complete loss of strongly polar DON-3G and fumonisin B1 (FB1). The investigated matrices had suppressive effect on ionization in all target mycotoxins except for FB1. Regarding the use of isotopologues to compensate matrix effect, even U-[13C15]-DON and U-[13C24]-T-2 can also be used to quantify their related metabolites in the studied matrices, using internal standard method.

Pharmacokinetics and Safety of Zidovudine, Lamivudine, and Lopinavir/Ritonavir in HIV-infected Children With Severe Acute Malnutrition in Sub-Saharan Africa: IMPAACT Protocol P1092.

BACKGROUND: Severe acute malnutrition (SAM) may alter the pharmacokinetics (PK), efficacy, and safety of antiretroviral therapy. The phase IV study, IMPAACT P1092, compared PK, safety, and tolerability of zidovudine (ZDV), lamivudine (3TC), and lopinavir/ritonavir (LPV/r) in children with and without SAM. MATERIALS AND METHODS: Children living with HIV 6 to <36 months of age with or without World Health Organization (WHO)-defined SAM received ZDV, 3TC, and LPV/r syrup for 48 weeks according to WHO weight band dosing. Intensive PK sampling was performed at weeks 1, 12, and 24. Plasma drug concentrations were measured using liquid chromatography tandem mass spectrometry. Steady-state mean area under the curve (AUC0-12h) and clearance (CL/F) for each drug were compared. Grade ≥3 adverse events were compared between cohorts. RESULTS: Fifty-two children were enrolled across 5 sites in Africa with 44% (23/52) female, median age 19 months (Q1, Q3: 13, 25). Twenty-five children had SAM with entry median weight-for-height Z-score (WHZ) -3.4 (IQR -4.0, -3.0) and 27 non-SAM had median WHZ -1.0 (IQR -1.8, -0.1). No significant differences in mean AUC0-12h or CL/F were observed (P ≥ 0.09) except for lower 3TC AUC0-12h (GMR, 0.60; 95% CI, 0.4-1.0; P = 0.047) at week 12, higher ZDV AUC0-12h (GMR, 1.52; 1.2-2.0; P = 0.003) at week 24 in the SAM cohort compared with non-SAM cohort. Treatment-related grade ≥3 events did not differ significantly between cohorts (24.0% vs. 25.9%). CONCLUSION: PK and safety findings for ZDV, 3TC, and LPV/r support current WHO weight band dosing of syrup formulations in children with SAM.

Free Open Source Software for Protein and Peptide Mass Spectrometry- based Science.

In the field of biology, and specifically in protein and peptide science, the power of mass spectrometry is that it is applicable to a vast spectrum of applications. Mass spectrometry can be applied to identify proteins and peptides in complex mixtures, to identify and locate post-translational modifications, to characterize the structure of proteins and peptides to the most detailed level or to detect protein-ligand non-covalent interactions. Thanks to the Free and Open Source Software (FOSS) movement, scientists have limitless opportunities to deepen their skills in software development to code software that solves mass spectrometric data analysis problems. After the conversion of raw data files into open standard format files, the entire spectrum of data analysis tasks can now be performed integrally on FOSS platforms, like GNU/Linux, and only with FOSS solutions. This review presents a brief history of mass spectrometry open file formats and goes on with the description of FOSS projects that are commonly used in protein and peptide mass spectrometry fields of endeavor: identification projects that involve mostly automated pipelines, like proteomics and peptidomics, and bio-structural characterization projects that most often involve manual scrutiny of the mass data. Projects of the last kind usually involve software that allows the user to delve into the mass data in an interactive graphics-oriented manner. Software projects are thus categorized on the basis of these criteria: software libraries for software developers vs desktop-based graphical user interface, software for the end-user and automated pipeline-based data processing vs interactive graphics-based mass data scrutiny.

Mass Spectrometry Techniques: Principles and Practices for Quantitative Proteomics.

In the current omics-age of research, major developments have been made in technologies that attempt to survey the entire repertoire of genes, transcripts, proteins, and metabolites present within a cell. While genomics has led to a dramatic increase in our understanding of such things as disease morphology and how organisms respond to medications, it is critical to obtain information at the proteome level since proteins carry out most of the functions within the cell. The primary tool for obtaining proteome-wide information on proteins within the cell is mass spectrometry (MS). While it has historically been associated with the protein identification, developments over the past couple of decades have made MS a robust technology for protein quantitation as well. Identifying quantitative changes in proteomes is complicated by its dynamic nature and the inability of any technique to guarantee complete coverage of every protein within a proteome sample. Fortunately, the combined development of sample preparation and MS methods have made it capable of quantitatively comparing many thousands of proteins obtained from cells and organisms.

Identification-Free Control over the Precursor Isotopic Mass Misassignment in Orbitrap-Based Proteomics.

Selection of a precursor ion from a peptide isotopic cluster to obtain a fragmentation mass spectrum is a crucial step in data-dependent proteome analysis. However, the monoisotopic mass assignment performed in this step is often an issue confronted by the data acquisition software of hybrid Orbitrap FTMS that is most widely used in proteomics. To address the problem, many data processing tools, such as raw data converters and search engines, have optional accounting for the precursor mass shift due to the isotopic error. These solutions require additional data preprocessing steps and lead to an increase in the search space, thus making the analysis longer and/or less reliable. In this work, we processed 100 Orbitrap-based LC-MS/MS runs from 10 publicly available data sets to examine the rate of precursor isotope misassignment. The effect from taking the isotope error into account during the search on the number of identified peptides varied in a wide range from 0 to 33%. Thus, it may be tempting to spend extra time before or during a search to account for the mass assignment issue. Alternatively, this effect can be predicted a priori using an identification-free metric, which can be a part of data quality control software. Based on the results obtained in this work, we propose such a metric be further added into the visual and intuitive quality control software, viQC, developed previously and available at https://github.com/lisavetasol/viQC. It takes about a minute to calculate and plot nine quality metrics, including the proposed one for typical proteome analysis.

Matrix-Assisted Ionization and Tandem Mass Spectrometry Capabilities in Protein Biomarker Characterization-An Initial Study Using the Small Cell Lung Cancer Biomarker Progastrin Releasing Peptide as a Model Compound.

This initial study evaluates vacuum matrix-assisted ionization (vMAI) mass spectrometry (MS) for identification and determination of tryptic peptides from the biomarker protein progastrin releasing peptide (ProGRP). Similar peptides and charge states were observed as in liquid chromatography (LC) electrospray ionization (ESI) MS. The prolonged ion duration in vMAI with similar charge states as in ESI was advantageous for determining the MS/MS fragmentation conditions compared to MAI. It is assumed that the vacuum ionization conditions lower the detection limits of the experiment. This may be the reason vMAI combined with high resolution MS enabled detection of tryptic peptides from more digested proteins than MAI selected reaction monitoring MS. Additionally, MAI ion mobility spectrometry MS (MAI-IMS-MS) was evaluated for differentiation of intact protein isoforms, successfully enabling differentiation of the isoforms by drift time selection. Examples are both shown for model proteins bovine serum albumin, cytochrome C, and lysozyme and the clinically relevant small cell lung cancer protein biomarker ProGRP, which exists in three isoforms. Coupling with the vacuum ionization conditions using a dedicated vacuum-probe source MAI enables information to be extracted readily as with conventional approaches, just faster.

Collision energies on QTof and Orbitrap instruments: How to make proteomics measurements comparable?

Quadrupole time-of-flight (QTof) collision-induced dissociation (CID) and Orbitrap higher-energy collisional dissociation (HCD) are the most commonly used fragmentation techniques in mass spectrometry-based proteomics workflows. The information content of the MS/MS spectra is first and foremost determined by the applied collision energy. How can we set up the two instrument types to achieve maximum transferability? To answer this question, we compared MS/MS spectra obtained on a Bruker QTof CID and a Thermo Q-Exactive Focus Orbitrap HCD instrument as a function of collision energy using the similarity index. Results show that with a few eV lower collision energy setting on HCD (Orbitrap-specific CID) than on QTof CID, nearly identical MS/MS spectra can be obtained for leucine enkephalin pentapeptide standard, for selected +2 and +3 enolase tryptic peptides and for a large number of peptides in a HeLa protein digest. The Bruker QTof was able to produce colder ions, which may be significant to study inherently labile compounds. Further, we examined energy dependence of peptide identification confidence, as characterized by Mascot scores, on the HeLa peptides. In line with earlier QTof results, this dependence shows one or two maxima (unimodal or bimodal behavior) on Orbitrap. The fraction of bimodal peptides is lower on Orbitrap. Optimal energies as a function of m/z show a similar linear trend on both instruments, which suggests that with appropriate collision energy adjustment, matching conditions for proteomics can be achieved. Data have been deposited in the MassIVE repository (MSV000086434).

Metabolomics Analysis of Viral Therapeutics.

Virotherapy, enabled by recent advances in the transdisciplinary field of biotechnology, has emerged as a powerful tool for use in anticancer treatment, gene therapy, immunotherapy, etc. Examining the effects of viruses and virus-derived immune-modulating therapeutics is of great fundamental and clinical interest. Here we describe a sample preparation protocol for metabolite extraction from virus-infected tissue, in addition to liquid chromatography-mass spectrometry conditions essential for subsequent analysis. This metabolomics approach delivers highly sensitive and specific metabolite information on various biospecimens. Such an approach may be adopted to monitor biological changes in over 30 relevant metabolic pathways in response to viral infection and also viral therapeutics.

Developments in tandem ion mobility mass spectrometry.

Ion Mobility (IM) coupled to mass spectrometry (MS) is a useful tool for separating species of interest out of small quantities of heterogenous mixtures via a combination of m/z and molecular shape. While tandem MS instruments are common, instruments which employ tandem IM are less so with the first commercial IM-MS instrument capable of multiple IM selection rounds being released in 2019. Here we explore the history of tandem IM instruments, recent developments, the applications to biological systems and expected future directions.

Rapid Analysis of Reduced Antibody Drug Conjugate by Online LC-MS/MS with Fourier Transform Ion Cyclotron Resonance Mass Spectrometry.

Antibody drug conjugates (ADCs), which harness the high targeting specificity of monoclonal antibodies (mAb) with the potency of small molecule therapeutics, are one of the fastest growing pharmaceutical classes. Nevertheless, ADC conjugation techniques and processes may introduce intrinsic heterogeneity including primary sequence variants, varied drug-to-antibody ratio (DAR) species, and drug positional isomers, which must be monitored to ensure the safety and efficacy of ADCs. Liquid chromatography coupled to mass spectrometry (LC-MS) is a powerful tool for characterization of ADCs. However, the conventional bottom-up MS analysis workflows require an enzymatic digestion step which can be time consuming and may introduce artifactual modifications. Herein, we develop an online LC-MS/MS method for rapid analysis of reduced ADCs without digestion, enabling determination of DAR, characterization of the primary sequence, and localization of the drug conjugation site of the ADC using high-resolution Fourier transform ion cyclotron resonance (FTICR) MS. Specifically, a model cysteine-linked ADC was reduced to generate six unique subunits: light chain (Lc) without drug (Lc0), Lc with 1 drug (Lc1), heavy chain (Hc) without drug (Hc0), and Hc with 1-3 drugs (Hc1-3, respectively). A concurrent reduction strategy is applied to assess ADC subunits in both the partially reduced (intrachain disulfide bonds remain intact) and fully reduced (all disulfide bonds are cleaved) forms. The entire procedure including the sample preparation and LC-MS/MS takes less than 55 min, enabling rapid multiattribute analysis of ADCs.