LC/MS applications in drug development

MaRiMba: a software application for spectral library-based MRM transition list assembly

Multiple reaction monitoring mass spectrometry (MRM-MS) is a targeted analysis method that has been increasingly viewed as an avenue to explore proteomes with unprecedented sensitivity and throughput. We have developed a software tool, called MaRiMba, to automate the creation of explicitly defined MRM transition lists required to program triple quadrupole mass spectrometers in such analyses. MaRiMba creates MRM transition lists from downloaded or custom-built spectral libraries, restricts output to specified proteins or peptides, and filters based on precursor peptide and product ion properties. MaRiMba can also create MRM lists containing corresponding transitions for isotopically heavy peptides, for which the precursor and product ions are adjusted according to user specifications. This open-source application is operated through a graphical user interface incorporated into the Trans-Proteomic Pipeline, and it outputs the final MRM list to a text file for upload to MS instruments. To illustrate the use of MaRiMba, we used the tool to design and execute an MRM-MS experiment in which we targeted the proteins of a well-defined and previously published standard mixture.

Intracellular adaptation of Brucella abortus

Macrophages were infected with virulent Brucella abortus strain 2308 or attenuated strain 19. Intracellular bacteria were recovered at different times after infection and their proteomes compared. The virulent strain initially reduced most biosynthesis and altered its respiration; adaptations reversed later in infection. The attenuated strain was unable to match the magnitude of the virulent strain's adjustments. The results provide insight into mechanisms utilized by Brucella to establish intracellular infections.

Rapid optimization of MRM-MS instrument parameters by subtle alteration of precursor and product m/z targets

Multiple reaction monitoring (MRM) is a highly sensitive method of targeted mass spectrometry (MS) that can be used to selectively detect and quantify peptides based on the screening of specified precursor peptide-to-fragment ion transitions. MRM-MS sensitivity depends critically on the tuning of instrument parameters, such as collision energy and cone voltage, for the generation of maximal product ion signal. Although generalized equations and values exist for such instrument parameters, there is no clear indication that optimal signal can be reliably produced for all types of MRM transitions using such an algorithmic approach. To address this issue, we have devised a workflow functional on both Waters Quattro Premier and ABI 4000 QTRAP triple quadrupole instruments that allows rapid determination of the optimal value of any programmable instrument parameter for each MRM transition. Here, we demonstrate the strategy for the optimizations of collision energy and cone voltage, but the method could be applied to other instrument parameters, such as declustering potential, as well. The workflow makes use of the incremental adjustment of the precursor and product m/z values at the hundredth decimal place to create a series of MRM targets at different collision energies that can be cycled through in rapid succession within a single run, avoiding any run-to-run variability in execution or comparison. Results are easily visualized and quantified using the MRM software package Mr. M to determine the optimal instrument parameters for each transition.

Determination of ion structures in structurally related compounds using precursor ion fingerprinting

Structurally-related alkaloids were analyzed by electrospray ionization/multiple stage mass spectrometry (ESI/MS(n)) at varying collision energies to demonstrate a conceptual algorithm, precursor ion fingerprinting (PIF). PIF is a new approach for interpreting and library-searching ESI mass spectra predicated on the precursor ions of structurally-related compounds and their matching product ion spectra. Multiple-stage mass spectra were compiled and constructed into "spectral trees" that illustrated the compounds' product ion spectra in their respective mass spectral stages. The precursor ions of these alkaloids were characterized and their spectral trees incorporated into an MS(n) library. These data will be used to construct a universal, searchable, and transferable library of MS(n) spectra. In addition, PIF will generate a proposed structural arrangement utilizing previously characterized ion structures, which will assist in the identification of unknown compounds.

Cell surface biomarkers of embryonic stem cells

Embryonic stem cells (ESCs) can give rise to any adult cell type and thus offer enormous potential for regenerative medicine and drug discovery. Molecular biomarkers serve as valuable tools to classify and isolate ESCs and to monitor their differentiation state by antibody-based techniques. A number of biomarkers, such as certain cell surface antigens, are used to assign pluripotent ESCs; however, accumulating evidence suggests that ESCs are heterogeneous in morphology, phenotype and function, and are thereby classified into subpopulations characterized by multiple sets of molecular biomarkers. Biomarker discovery is also important for ESC biology to elucidate the molecular mechanisms that regulate pluripotency and differentiation. This review summarizes studies of ESC biomarker discovery. "Genome-wide" expression profiling of ESC mRNAs and proteins and direct analyses of the cell surface subproteome have demonstrated that ESCs express a diverse range of biomarkers, cell surface antigens, and signaling molecules found in different cell lineages, as well as a number of key molecules that assure "stemness". Clearly, future quantitative proteomics approaches will enhance our knowledge of the stage- and lineage-specific expression of the proteome and its temporal changes upon differentiation, and provide a more detailed view of nascent and clonally amplified ESCs.

Liquid chromatography-mass spectrometry in in vitro drug metabolite screening

A combination of high performance liquid chromatography (HPLC) and mass spectrometry (LC/MS) has proven its status as the most powerful analytical tool for screening and identifying drug metabolites in modern drug discovery. These techniques have become irreplaceable for drug metabolism laboratories, providing high amounts of information from a wide variety of samples. This review focuses on the most common and useful applications of these techniques when working on in vitro metabolism, more specifically with screening and identification of chemically stable or reactive metabolites formed via biotransformation reactions. Matching specific tasks and suitable instruments is a recurring consideration; for many reasons, the time-of-flight or orbitrap mass spectrometry provides clearly increased efficiency in metabolite profiling compared to other types of mass spectrometry.

Cassette analysis of eight beta-blockers in bovine eye sclera, choroid-RPE, retina, and vitreous by liquid chromatography-tandem mass spectrometry

A simple, selective, and sensitive LC-MS/MS method was developed for the simultaneous extraction and determination of eight beta-blockers (atenolol, sotalol, nadolol, pindolol, timolol, metoprolol, betaxolol and propranolol) in various bovine eye tissues including sclera, choroid-RPE, retina, and vitreous. The analytes were extracted by liquid-liquid extraction after samples were alkalinized with 2% NaOH solution in water. The chromatographic separation was performed on a Hypersil-ODS C18 column (100 mm x 2.1 mm, 3.9 microm) using a gradient mixture of (A) 5 mM ammonium formate in water (pH 3.5 adjusted with formic acid) and (B) acetonitrile:methanol (75:25) containing 0.02% triethyl amine (pH 4.0; adjusted with formic acid) as mobile phase at a flow rate of 0.4 ml/min. The compounds were ionized in the positive electrospray ionization (ESI) mode and detected in the multiple reaction monitoring (MRM) mode. The average recoveries in all four eye tissues for all beta-blockers were >82%, except for sotalol (>51%). The matrix effect for beta-blockers ranged from 81 to 110% in the four eye tissues. This analytical method was validated and applied successfully for simultaneous quantification of the beta-blockers in sclera after tissue exposure using cassette dosing method. The calibration curve was linear in the range of 10-2000 ng/ml for all analytes, with the correlation coefficient >0.996. Intra-day and inter-day precision (% CV) was less than 15%, and accuracy ranged from 85 to 110% for all analytes. Scleral uptake was the lowest for sotalol and atenolol, two hydrophilic beta-blockers, and the highest for propranolol, a lipophilic beta-blocker.

Metabolite profiling of blood from individuals undergoing planned myocardial infarction reveals early markers of myocardial injury

Emerging metabolomic tools have created the opportunity to establish metabolic signatures of myocardial injury. We applied a mass spectrometry-based metabolite profiling platform to 36 patients undergoing alcohol septal ablation treatment for hypertrophic obstructive cardiomyopathy, a human model of planned myocardial infarction (PMI). Serial blood samples were obtained before and at various intervals after PMI, with patients undergoing elective diagnostic coronary angiography and patients with spontaneous myocardial infarction (SMI) serving as negative and positive controls, respectively. We identified changes in circulating levels of metabolites participating in pyrimidine metabolism, the tricarboxylic acid cycle and its upstream contributors, and the pentose phosphate pathway. Alterations in levels of multiple metabolites were detected as early as 10 minutes after PMI in an initial derivation group and were validated in a second, independent group of PMI patients. A PMI-derived metabolic signature consisting of aconitic acid, hypoxanthine, trimethylamine N-oxide, and threonine differentiated patients with SMI from those undergoing diagnostic coronary angiography with high accuracy, and coronary sinus sampling distinguished cardiac-derived from peripheral metabolic changes. Our results identify a role for metabolic profiling in the early detection of myocardial injury and suggest that similar approaches may be used for detection or prediction of other disease states.

Investigation of double-stranded DNA/drug interaction by ESI/FT ICR: orientation of dissociations relates to stabilizing salt bridges

Noncovalent complexes of DNA and Hoechst 33258 were investigated by ESI-FT/ICR MS in various activation modes (collision-induced dissociation (CID), sustained off-resonance irradiation collision-induced dissociation (SORI-CID), infrared multiphoton dissociation (IRMPD) and electron detachment dissociation (EDD)). The binding selectivity of Hoechst 33258 was confirmed by the comparative study of its noncovalent association with different DNA sequences. The CID spectra of [ds + HO - 5H](5-) obtained with a linear hexapole ion trap resulted in unzipping of the strands. This outcome is a clue to the drug-binding mode, shading light on the localization of the binding sites of Hoechst 33258 to the DNA sequence. The IRMPD and SORI-CID experiments mainly gave DNA backbone cleavages and internal fragment ions. From this result, information on the localization of the binding sites of Hoechst 33258 in the DNA sequence was obtained. No sodium cationization was observed on the DNA sequence ions although they were present on fragmentation of the duplex, indicating that the backbone cleavages were generated from the single strand associated with the Hoechst 33258 where the number of alkali cation is restricted. Under electron detachment (ED) conditions, multiple EDs were achieved for the [ds + HO - 5H](5-) ion without any significant dissociation. The presence of drug appears to enhance the stability of the multiply charged system. It was proposed that the studied noncovalent complex involved the formation of zwitterions and consequently strong salt-bridge interactions between DNA and drug.

MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments

Multiple reaction monitoring (MRM) mass spectrometry identifies and quantifies specific peptides in a complex mixture with very high sensitivity and speed and thus has promise for the high throughput screening of clinical samples for candidate biomarkers. We have developed an interactive software platform, called MRMer, for managing highly complex MRM-MS experiments, including quantitative analyses using heavy/light isotopic peptide pairs. MRMer parses and extracts information from MS files encoded in the platform-independent mzXML data format. It extracts and infers precursor-product ion transition pairings, computes integrated ion intensities, and permits rapid visual curation for analyses exceeding 1000 precursor-product pairs. Results can be easily output for quantitative comparison of consecutive runs. Additionally MRMer incorporates features that permit the quantitative analysis experiments including heavy and light isotopic peptide pairs. MRMer is open source and provided under the Apache 2.0 license.

Characterization of impurities in the bulk drug lisinopril by liquid chromatography/ion trap spectrometry

Two trace impurities in the bulk drug lisinopril were detected by means of high-performance liquid chromatography coupled with mass spectrometry (HPLC/MS) with a simple and sensitive method suitable for HPLC/MSn analysis. The fragmentation behavior of lisinopril and the impurities was investigated, and two unknown impurities were elucidated as 2-(6-amino-1-(1-carboxyethylamino)-1-oxohexan-2-ylamino)-4-phenylbutanoic acid and 6-amino-2-(1-carboxy-3-phenylpro-pylamino)-hexanoic acid on the basis of the multi-stage mass spectrometry and exact mass evidence. The proposed structures of the two unknown impurities were further confirmed by nuclear magnetic resonance (NMR) experiments after preparative isolation.

Current applications of liquid chromatography/mass spectrometry in pharmaceutical discovery after a decade of innovation

Current drug discovery involves a highly iterative process pertaining to three core disciplines: biology, chemistry, and drug disposition. For most pharmaceutical companies the path to a drug candidate comprises similar stages: target identification, biological screening, lead generation, lead optimization, and candidate selection. Over the past decade, the overall efficiency of drug discovery has been greatly improved by a single instrumental technique, liquid chromatography/mass spectrometry (LC/MS). Transformed by the commercial introduction of the atmospheric pressure ionization interface in the mid-1990s, LC/MS has expanded into almost every area of drug discovery. In many cases, drug discovery workflow has been changed owing to vastly improved efficiency. This review examines recent trends for these three core disciplines and presents seminal examples where LC/MS has altered the current approach to drug discovery.

The application of cassette dosing for pharmacokinetic screening in small-molecule cancer drug discovery

Pharmacokinetic evaluation is an essential component of drug discovery and should be conducted early in the process so that those compounds with the best chance of success are prioritized and progressed. However, pharmacokinetic analysis has become a serious bottleneck during the 'hit-to-lead' and lead optimization phases due to the availability of new targets and the large numbers of compounds resulting from advances in synthesis and screening technologies. Cassette dosing, which involves the simultaneous administration of several compounds to a single animal followed by rapid sample analysis by liquid chromatography/tandem mass spectrometry, was developed to increase the throughput of in vivo pharmacokinetic screening. Although cassette dosing is advantageous in terms of resources and throughput, there are possible complications associated with this approach, such as the potential for compound interactions. Following an overview of the cassette dosing literature, this article focuses on the application of the technique in anticancer drug discovery. Specific examples are discussed, including the evaluation of cassette dosing to assess pharmacokinetic properties in the development of cyclin-dependent kinase and heat shock protein 90 inhibitors. Subject to critical analysis and validation in each case, the use of cassette dosing is recommended in appropriate chemical series to enhance the efficiency of drug discovery and reduce animal usage.

Nature's bounty - drug discovery from the sea

With ∼ 40 years of research completed after the development of self-contained underwater breathing apparatus, drug discovery opportunities in the sea are still too numerous to count. Since the FDA approval of the direct-from-the-sea calcium channel blocker ziconotide, marine natural products have been validated as a source for new medicines. However, the demand for natural products is extremely high due to the development of high-throughput assays and this bottleneck has created the need for an intense focus on increasing the rate of isolating and elucidating the structures of new bioactive secondary metabolites. In addition to highlighting the drug discovery potential of the marine environment, this review discusses several of the pressing needs to increase the rate of drug discovery in marine natural products, and describes some of the work and new technologies that are contributing in this regard.

Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution

Biomarker discovery produces lists of candidate markers whose presence and level must be subsequently verified in serum or plasma. Verification represents a paradigm shift from unbiased discovery approaches to targeted, hypothesis-driven methods and relies upon specific, quantitative assays optimized for the selective detection of target proteins. Many protein biomarkers of clinical currency are present at or below the nanogram/milliliter range in plasma and have been inaccessible to date by MS-based methods. Using multiple reaction monitoring coupled with stable isotope dilution mass spectrometry, we describe here the development of quantitative, multiplexed assays for six proteins in plasma that achieve limits of quantitation in the 1-10 ng/ml range with percent coefficients of variation from 3 to 15% without immunoaffinity enrichment of either proteins or peptides. Sample processing methods with sufficient throughput, recovery, and reproducibility to enable robust detection and quantitation of candidate biomarker proteins were developed and optimized by addition of exogenous proteins to immunoaffinity depleted plasma from a healthy donor. Quantitative multiple reaction monitoring assays were designed and optimized for signature peptides derived from the test proteins. Based upon calibration curves using known concentrations of spiked protein in plasma, we determined that each target protein had at least one signature peptide with a limit of quantitation in the 1-10 ng/ml range and linearity typically over 2 orders of magnitude in the measurement range of interest. Limits of detection were frequently in the high picogram/milliliter range. These levels of assay performance represent up to a 1000-fold improvement compared with direct analysis of proteins in plasma by MS and were achieved by simple, robust sample processing involving abundant protein depletion and minimal fractionation by strong cation exchange chromatography at the peptide level prior to LC-multiple reaction monitoring/MS. The methods presented here provide a solid basis for developing quantitative MS-based assays of low level proteins in blood.

Identification of an unknown extraneous contaminant in pharmaceutical product analysis

During the content uniformity test of a drug product (tablet formulation), an unknown peak was observed in the HPLC chromatograms. Upon further investigation, it was determined that the unknown peak was originated from an external source and, therefore, the drug product is free of this unknown peak. The next step was to identify the structure of this unknown peak in order to determine the source of this contaminant species. In this paper, we wish to present the strategy and the results of the experiments that led to the identification of this unknown peak. LC-PDA/UV and LC-MS(n) analyses were conducted to obtain the UV spectrum, molecular weight and MS(n) fragmentation pathways of the unknown peak. The MS analysis revealed certain structural features of the unknown species and a number of model compounds that contain such features were then examined for their UV absorbance profiles in an attempt to establish the functional group connectivity within the unknown species. A careful examination of these results in conjunction with the determination of the high-resolution molecular weight led to a short list of potential candidates for the unknown species, among which the most likely one was 1,3-diphenylguanidine. The identification of the unknown contaminant was confirmed by spiking experiments using the authentic compound. The potential source of this contaminant was also identified as derived from the safety filler of the pipette bulb used to prepare the sample solutions during the drug analysis.

Recent applications in nanoliquid chromatography

Since its first introduction by Karlsson and Novotny in 1988 nano-LC has emerged as a complementary and/or competitive separation method to conventional HPLC, offering several advantages such as higher efficiency, ability to work with minute sample sizes and lower consumption of mobile phases, and better compatibility with MS, etc. Although its use was not so extended initially, in the last years new and interesting applications have appeared which deserve to be carefully considered. The aim of this review is therefore to provide an updated and critical survey of different nano-LC applications in analytical chemistry.

Analytical strategies for identifying drug metabolites

With the dramatic increase in the number of new chemical entities (NCEs) arising from combinatorial chemistry and modern high-throughput bioassays, novel bioanalytical techniques are required for the rapid determination of the metabolic stability and metabolites of these NCEs. Knowledge of the metabolic site(s) of the NCEs in early drug discovery is essential for selecting compounds with favorable pharmacokinetic credentials and aiding medicinal chemists in modifying metabolic "soft spots". In development, elucidation of biotransformation pathways of a drug candidate by identifying its circulatory and excretory metabolites is vitally important to understand its physiological effects. Mass spectrometry (MS) and nuclear magnetic resonance (NMR) have played an invaluable role in the structural characterization and quantification of drug metabolites. Indeed, liquid chromatography (LC) coupled with atmospheric pressure ionization (API) MS has now become the most powerful tool for the rapid detection, structure elucidation, and quantification of drug-derived material within various biological fluids. Often, however, MS alone is insufficient to identify the exact position of oxidation, to differentiate isomers, or to provide the precise structure of unusual and/or unstable metabolites. In addition, an excess of endogenous material in biological samples often suppress the ionization of drug-related material complicating metabolite identification by MS. In these cases, multiple analytical and wet chemistry techniques, such as LC-NMR, enzymatic hydrolysis, chemical derivatization, and hydrogen/deuterium-exchange (H/D-exchange) combined with MS are used to characterize the novel and isomeric metabolites of drug candidates. This review describes sample preparation and introduction strategies to minimize ion suppression by biological matrices for metabolite identification studies, the application of various LC-tandem MS (LC-MS/MS) techniques for the rapid quantification and identification of drug metabolites, and future trends in this field.

Evaluation of high-field asymmetric waveform ion mobility spectrometry coupled to nanoelectrospray ionization for bioanalysis in drug discovery

The potential of high-field asymmetric waveform ion mobility spectrometry (FAIMS) coupled to nanoelectrospray ionization (nanoESI) as a method to improve sample throughput for bioanalysis in a discovery pharmaceutical setting was explored in this work. The ability of FAIMS to separate gas-phase ions in the millisecond timescale was exploited to eliminate the need for liquid chromatography. Samples were introduced into the FAIMS electrodes/mass spectrometer using offline nanoESI at 20 nL/min and 1.5 kV. Signals were averaged for 30 s after which the next sample could be analyzed. The separation of simple mixtures, e.g., the removal of metabolite and endogenous interferences from parent drug, was demonstrated. Moreover, the application of nanoESI attenuated the ion suppression effects that normally plague conventional electrospray. On average, approximately two-thirds of the neat sample signal intensity was preserved in extracted plasma samples. Standard curves were prepared for several compounds and linearity was obtained over approximately two to three orders of magnitude. This methodology was further tested with the analysis of plasma samples from a mouse pharmacokinetic study. Concentration values determined using nanoESI-FAIMS were comparable to those determined using conventional LC/MS as demonstrated by percent differences of less than 30%. This work demonstrated the proof of concept that the combination of FAIMS and nanospray ionization can be a potentially useful tool to improve the throughput of discovery bioanalysis.

Liquid chromatography/electrospray ionization tandem mass spectrometry profiling of compounds from the infusion of Byrsonima fagifolia Niedenzu

A rapid analytical approach suitable to achieve a comprehensive characterization of the compounds present in the infusion prepared from the leaves of Byrsonima fagifolia Niedenzu (Malpighiaceae), a Brazilian plant used as an infusion to treat gastric disorders, was developed. The method was based on high-performance liquid chromatography coupled to electrospray negative ionisation multistage ion trap mass spectrometry (HPLC/ESI-ITMSn). The main ions in the ESI-ITMS spectra were attributed to a quinic acid core containing from one to five galloyl units. Quercetin derivatives containing one and two sugar moieties as well as galloyl esterification were also detected. These results indicated that HPLC/ESI-ITMSn is easily applicable to infusions of this plant and allows the rapid and direct identification of these compounds in crude plant extracts.

Simultaneous determination of desloratadine and pseudoephedrine in human plasma using micro solid-phase extraction tips and aqueous normal-phase liquid chromatography/tandem mass spectrometry

Cation-exchange micro solid-phase extraction (SPE) tips and aqueous normal-phase (ANP) chromatography coupled with tandem mass spectrometry were explored for the rapid, selective and sensitive quantitation of desloratadine and pseudoephedrine in human plasma. A novel micro-SPE device was evaluated for analyte capacity, extraction efficiency and its ability to maximize recovery of an analyte of interest from bioanalytical matrices by successive replicates of linked extraction steps. Ion suppression using two different methods with micro-SPE tips was negligible when compared to protein precipitation. The use of ANP chromatography eliminated the need for sample reconstitution following extraction and was found to be highly selective. A reliable chromatography system was developed with a short duty cycle of 2 min/sample. The proposed bioanalytical method required 50 microL of plasma for the determination of desloratadine and pseudoephedrine at limits of quantitation of 0.1 and 1.25 ng/mL, respectively. The analytical method was validated in accordance with the FDA guidance on bioanalytical method validation; selectivity, linearity, reproducibility and accuracy were all acceptable.

Two-dimensional liquid chromatography/mass spectrometry set-up for structural elucidation of metabolites in complex biological matrices

For absorption, distribution, metabolism and excretion (ADME) studies of drug candidates, mass spectrometry (MS) has become an indispensable tool for the characterization of biotransformation pathways. Samples from in vivo animal studies such as plasma, tissue extracts or excreta contain vast amounts of endogenous compounds. Therefore, the generation of metabolite patterns requires dedicated sample pre-treatment and sophisticated separation methods. Methodologies used for metabolite separation are often inappropriate for structure elucidation. Therefore, a two-dimensional liquid chromatography (LC) approach in combination with MS was developed. Study samples were analyzed using high-performance liquid chromatography (HPLC) for the generation of a qualitative and quantitative metabolite pattern (first dimension) with high reproducibility and recovery without extensive sample pre-treatment. Selected radioactive metabolite fractions were then applied to micro-HPLC with off-line radioactivity monitoring and subsequent MS detection (second dimension). Applying the two-dimensional HPLC/MS approach not only major metabolites could be identified, even minor and trace metabolites were characterized. The usage of sampled metabolite fractions allowed also the re-analysis of specific metabolites for additional investigations (e.g. H/D exchange experiments or product ion scanning experiments). It could be clearly shown that the two-dimensional HPLC/MS approach showed mass spectra with higher sensitivity and selectivity significantly improving the characterization of minor and trace metabolites in in vivo ADME studies.

Simultaneous determination of gemcitabine, taxol, cyclophosphamide and ifosfamide in wipe samples by high-performance liquid chromatography/tandem mass spectrometry: protocol of validation and uncertainty of measurement

Measurable levels of anticancer agents are still detected on work surfaces in health-care settings. However, application of recent guidelines for the protection of workers' safety and health has resulted in lowered contamination levels. To assess occupational exposure to antineoplastic agents, very sensitive and specific procedures for environmental sampling and analysis are therefore needed. In the present study an assay for simultaneous determination of gemcitabine, taxol, cyclophosphamide, and ifosfamide in wipe samples, using two internal standards (trofosfamide and cephalomannine), was developed and validated by high-performance liquid chromatography/tandem mass spectrometry (HPLC/MS/MS). Solid-phase extraction (SPE) was used for sample concentration and cleanup. The assay was found to be linear up to 1000 ng/wipe, with limits of quantitation of 25.0 ng/wipe for gemcitabine and taxol, and 12.5 ng/wipe for cyclophosphamide and ifosfamide. In order to investigate the effectiveness of the surface sampling, removal efficiency tests were repeated on different types of surfaces. Recovery rates of between 62 and 81% were obtained at two contamination levels (50.0 and 250 ng/100 cm2). Precision and trueness were determined on three different days. The within-day precision was found to be always less than 12.1% for all the analytes. The overall precision, expressed as relative standard deviation (RSD), was always less than 9.4%. Recoveries varying from 75.0 (gemcitabine) to 95.0% (taxol) were obtained at three levels. In order to obtain a quantitative indication of the quality of the result, the overall uncertainty of measurement (UOM) was evaluated according to the EURACHEM/CITAC guide. The relative combined uncertainty was found to be always less than 9.5%. The relative expanded uncertainty was also calculated, at three contamination levels.

Liquid chromatography/atmospheric pressure ionization mass spectrometry with post-column liquid mixing for the efficient determination of partially oxidized polycyclic aromatic hydrocarbons

The analytical hyphenation of micro-flow high-performance liquid chromatography (LC), with post-column liquid mixing and mass spectrometric detection (MS) was established to detect partially oxidized polycyclic aromatic hydrocarbons (oxy-PAHs) for low quantity samples. 100pmol injections of 30 reference standards could be detected in good sensitivity using either atmospheric pressure chemical ionization (APCI) and/or atmospheric pressure photoionization (APPI). The connected mass spectrometer was a single quadrupol analyzer realizing simultaneous registration of positive and negative ions in scan range width of 200 - 300Da. The ionization efficiency was compared using three ionization sources (incl. electrospray ionization (ESI)) for several oxy-PAHs. According to the mass spectra, the analytes behave differently in ionization properties. Ionization mechanism (e.g. deprotonated ions and electron captured ions) could be discussed with new inside views. Finally, the hyphenated system was applied to an exemplary aerosol extract and thus highlighting the expedient utilization of this downscaled method for real samples.

Protein biomarker discovery and validation: the long and uncertain path to clinical utility

Better biomarkers are urgently needed to improve diagnosis, guide molecularly targeted therapy and monitor activity and therapeutic response across a wide spectrum of disease. Proteomics methods based on mass spectrometry hold special promise for the discovery of novel biomarkers that might form the foundation for new clinical blood tests, but to date their contribution to the diagnostic armamentarium has been disappointing. This is due in part to the lack of a coherent pipeline connecting marker discovery with well-established methods for validation. Advances in methods and technology now enable construction of a comprehensive biomarker pipeline from six essential process components: candidate discovery, qualification, verification, research assay optimization, biomarker validation and commercialization. Better understanding of the overall process of biomarker discovery and validation and of the challenges and strategies inherent in each phase should improve experimental study design, in turn increasing the efficiency of biomarker development and facilitating the delivery and deployment of novel clinical tests.

Detection and quantification of unbound phytochelatin 2 in plant extracts of Brassica napus grown with different levels of mercury

The mercury (Hg) accumulation mechanism was studied in rape (Brassica napus) plants grown under a Hg concentration gradient (0 microm-1,000 microm). Hg mainly accumulated in roots. Therefore, the presence of phytochelatins (PCs) was studied in the roots of the plants. The high stability of the PC-Hg multicomplexes (mPC-nHg) seems to be the main reason for the lack of previous Hg-PC characterization studies. We propose a modification of the method to detect and quantify unbound PC of Hg in plant extracts via high-performance liquid chromatography coupled to electrospray tandem mass spectrometry and inductively coupled plasma mass spectrometry in parallel. We separated the PC from the Hg by adding the chelating agent sodium 2,3-dimercaptopropanesulfonate monohydrate. We only detected the presence of PC after the addition of the chelating agent. Some multicomplexes mPC-nHg could be formed but, due to their large sizes, could not be detected. In this study, only PC(2) was observed in plant samples. Hg accumulation was correlated with PC(2) concentration (r(2) = 0.98).

Validation and application of a high-performance liquid chromatography–tandem mass spectrometric method for simultaneous quantification of lopinavir and ritonavir in human plasma using semi-automated 96-well liquid–liquid extraction

Kaletra is an important antiretroviral drug, which has been developed by Abbott Laboratories. It is composed of lopinavir (low-pin-a-veer) and ritonavir (ri-toe-na-veer). Both have been proved to be human immunodeficiency virus (HIV) protease inhibitors and have substantially reduced the morbidity and mortality associated with HIV-1 infection. We have developed and validated an assay, using liquid chromatography coupled with atmospheric pressure chemical ionization tandem mass spectrometry (LC/MS/MS), for the routine quantification of lopinavir and ritonavir in human plasma, in which lopinavir and ritonavir can be simultaneously analyzed with high throughput. The sample preparation consisted of liquid-liquid extraction with a mixture of hexane: ethyl acetate (1:1, v/v), using 100 microL of plasma. Chromatographic separation was performed on a Waters Symmetry C(18) column (150 mm x 3.9 mm, particle size 5 microm) with reverse-phase isocratic using mobile phase of 70:30 (v/v) acetonitrile: 2 mM ammonium acetate aqueous solution containing 0.01% formic acid (v/v) at a flow rate of 1.0 mL/min. A Waters symmetry C(18) guard column (20 mm x 3.9 mm, particle size 5 microm) was connected prior to the analytical column, and a guard column back wash was performed to reduce the analytical column contamination using a mixture of tetrahydrofuran (THF), methanol and water (45:45:10, v/v/v). The analytical run was 4 min. The use of a 96-well plate autosampler allowed a batch size up to 73 study samples. A triple-quadrupole mass spectrometer was operated in a positive ion mode and multiple reaction monitoring (MRM) was used for drug quantification. The method was validated over the concentration ranges of 19-5,300 ng/mL for lopinavir and 11-3,100 ng/mL for ritonavir. A-86093 was used as an internal standard (I.S.). The relative standard deviation (RSD) were <6% for both lopinavir and ritonavir. Mean accuracies were between the designed limits (+/-15%). The robust and rapid LC/MS/MS assay has been successfully applied for routine assay to support bioavailability, bioequivalence, and pharmacokinetics studies.

Principles and applications of LC-MS in new drug discovery

The use of high-performance liquid chromatography combined with mass spectrometry (HPLC-MS) or tandem mass spectrometry (HPLC-MS-MS) has proven to be the analytical technique of choice for most assays used in various stages of new drug discovery. A summary of the key components of HPLC-MS systems, as well as an overview of major application areas that use this technique as part of the drug discovery process, will be described here. This review will also provide an introduction into the various types of mass spectrometers that can be selected for the multiple tasks that can be performed using LC-MS as the analytical tool. The strategies for optimizing the use of this technique and also the potential problems and how to avoid them will be highlighted.

Evaluation of LC–MS for the analysis of cleaning verification samples

The cleaning verification of pharmaceutical manufacturing equipment prior to further use is a cGMP requirement. Typically, relevant data are generated by HPLC with UV detection using methods individually developed and validated for each product. This work describes the use of HPLC with mass spectrometry to analyse cleaning verification samples, a novel means of utilising this analytical technology. The initial aim was to produce a single, generic method capable of quantifying a broad range of pharmaceuticals. Ultimately, however, a more effective strategy, in terms of efficiency and reliability, proved to be application of a well-defined approach to the rapid generation of compound specific methods. Results of studies to optimise the sample preparation for a basic compound in drug development (compound 1), together with experimental results for two further compounds are presented. These demonstrated that the combination of a well defined approach to chromatographic method development and mass spectrometric detection provided methodology with advantages in terms of sensitivity. Additionally, and by virtue of its potential for general applicability, the approach proposed has the potential to improve the overall efficiency with which methods for cleaning verification samples can be developed and applied.

Simultaneous quantification of cilostazol and its primary metabolite 3,4-dehydrocilostazol in human plasma by rapid liquid chromatography/tandem mass spectrometry

A simple, rapid, sensitive and selective liquid chromatography/electrospray tandem mass spectrometry method was developed and validated for the simultaneous quantification of cilostazol and its primary metabolite 3,4-dehydrocilostazol in human plasma using mosapride as an internal standard. The method involves a simple one-step liquid-liquid extraction with a diethyl ether and dichloromethane mixture (7:3). The analytes were chromatographed using an isocratic mobile phase on a reversed-phase C18 column and analyzed by mass spectrometry in the multiple reaction monitoring mode using the respective [M+H]+ ions, m/z 370/288 for cilostazol, m/z 368/286 for 3,4-dehydrocilostazol and m/z 422/198 for the internal standard. The assay exhibited a linear dynamic range of 5-2,000 ng/mL for cilostazol and 5-400 ng/mL for 3,4-dehydrocilostazol in human plasma. The lower limit of quantitation was 5 ng/mL for both cilostazol and its metabolite. Acceptable precision and accuracy were obtained for concentrations over the standard curve ranges. A run time of 2.5 min for each sample made it possible to analyze more than 400 human plasma samples per day. The validated method has been successfully used to analyze human plasma samples for application in pharmacokinetics, bioavailability or bioequivalence studies.

Developing multiple high-throughput GLP methods for an investigational drug candidate in various matrices within a 96-well plate

In early pharmaceutical product development, an investigational drug candidate is typically dosed to various species for toxicological and pharmacokinetic studies. Most of these studies require multiple analytical methods that have to be validated with good laboratory practice (GLP) prior to the application in regulated studies. Usually, these analytical methods are developed in either a serial or parallel approach. For either approach, the development of multiple analytical methods takes tremendous work from scientists and instruments, and thus is not cost-effective. In this respect, a new strategy has been developed for simultaneous GLP method development using liquid chromatographic separation and tandem mass spectrometric detection. This high-throughput approach allows system suitability, carryover, calibration curve, accuracy, precision, matrix effect and selectivity to be evaluated in one 96-well plate. The strategy has been successfully implemented for multiple investigational drug candidates at Abbott Laboratories. The methods developed with this strategy are accurate, precise, selective, robust and matrix-independent. As an example, ABT-279 was used to demonstrate the feasibility of this strategy.

Ultra-low flow nanospray for the normalization of conventional liquid chromatography/mass spectrometry through equimolar response: standard-free quantitative estimation of metabolite levels in drug discovery

Nanospray experiments were performed on an ensemble of drug molecules and their commonly known metabolites to compare performance with conventional electrospray ionization (ESI) and to evaluate equimolar response capabilities. Codeine, dextromethorphan, tolbutamide, phenobarbital, cocaine, and morphine were analyzed along with their well-known metabolites that were formed via hydroxylation, dealkylation, hydrolysis, and glucuronidation. Nanospray exhibited a distinct trend toward equimolar response when flow rate was reduced from 25 nL/min to less than 10 nL/min. A more uniform response between the parent drug and the corresponding metabolites was obtained at flow rates of 10 nL/min or lower. The largest discrepancy was within +/-50% for plasma samples. Nanospray was used as a calibrator for conventional ESI liquid chromatography/tandem mass spectrometry (LC/MS/MS) and normalization factors were applied to the quantitation of an acyl-glucuronide metabolite of a proprietary compound in rat plasma. A nanospray calibration method was developed with the standard curve of the parent drug to generate quantitative results for drug metabolites within +/-20% of that obtained with reference standards and conventional ESI. The nanospray method provides a practical solution for the quantitative estimation of drug metabolites in drug discovery when reference standards are not available.

Enhanced mass resolution method development, validation and assay application to support preclinical studies of a new drug candidate

A very highly sensitive and highly selective liquid chromatographic/tandem mass spectrometric (LC/MS/MS) method was developed to evaluate and quantify a new drug candidate in different biological matrices. Following a simple plasma protein precipitation using acetonitrile, the post-treatment samples were analyzed on a C18 column interfaced with a new generation of triple-quadrupole mass spectrometer. The recently introduced triple-quadrupole mass spectrometer, the TSQ Quantum Ultra, with enhanced mass-resolution capability, demonstrated improved sensitivity (0.05 ng/mL), coupled with suitable accuracy and precision, over a broad linear dynamic range (0.05-1000 ng/mL). A comparison of the assay performance data (dynamic range, calibration curve equation, precision and accuracy) of the enhanced resolution method against a unit resolution method under optimized conditions showed the performance improvement of the enhanced mass resolution method for bioanalytical high-throughput applications. The enhanced mass resolution method herein described was successfully applied to the evaluation of the pharmacokinetic profile of a new drug candidate in rat, rabbit and dog plasma samples.

Ultra-performance liquid chromatography coupled to linear ion trap mass spectrometry for the identification of drug metabolites in biological samples

The coupling of ultra-performance liquid chromatography, operating at elevated pressures, to a linear ion trap mass spectrometer provides a high-performance system suitable for drug metabolite characterisation. This system demonstrates improved chromatographic efficiency and sensitivity and at the same time provides diagnostic MSn data often critical for metabolite structural assignment. The linear ion trap was capable of dealing with the high chromatographic efficiencies and hence narrow peak widths associated with 1.7 microm particle-packed column separations. Polarity switching and data-dependent MSn data were generated with ease, and applied to the identification of metabolites found in human plasma.

Method development and validation for zotarolimus concentration determination in stented swine arteries by liquid chromatography/tandem mass spectrometry detection

Drug-eluting stents have attracted significant attention in the medical community and pharmaceutical industry due to their proven success in significantly reducing restenosis. Abbott Laboratories is developing a drug-eluting stent coated with zotarolimus and swine was recently used as an animal model for the pre-clinical study of stent implantation. In this article, we present a detailed experimental design and results for the validation and sample analysis of zotarolimus drug concentration in stented swine artery samples. Introduction of tissue quality control (QC) samples allows evaluation of the entire analytical process as well as the stability of the drug in both original tissue and homogenized tissue samples. In addition, a novel approach using 100% swine blood as the homogenization solution was developed for the consistency of the liquid-liquid extraction recovery and stability of the zotarolimus in tissue homogenates. Standards were prepared by spiking zotarolimus working solution in swine blood and tissue QC samples were used along with the artery samples during the sample analysis. The linear dynamic range of blood standard samples is from 0.61 to 333.20 ng/mL to accommodate the predicted artery homogenate concentrations. Overall tissue QC %CV during the method validation was from 4.4% to 8.6%. The overall %bias of tissue QC samples during the method validation was from -7.3% to 16.6%. The method was successfully applied for the analysis of swine artery samples. A similar approach for method validation and sample analysis has been successfully applied for the analysis of swine myocardium, kidney and liver tissue samples.

Screening for in vivo metabolites of isovalertatin family oligosaccharides in rats by liquid chromatography coupled to electrospray ionization tandem mass spectrometry

Liquid chromatography/electrospray ionization tandem mass spectrometry (LC/MS(n)) was used to identify trace levels of in vivo metabolites after the administration of isovalertatin M23 or isovalertatin D23 to rats. The biosamples of urine, feces, and ileum incubation were pre-treated by solid-phase extraction (SPE), and then chromatographed with a reversed-phase C8 column with acetonitrile/1.5 mM aqueous ammonia (18:82, v/v) as the mobile solvent. The parent drug and the possible metabolites were identified by two independent qualitative parameters, retention time and collision-induced dissociation product ions. Nine and seven metabolites were successfully characterized from biosamples after administration of isovalertatins M23 and D23, respectively, to rats. The metabolism seemed to take place in the rat intestinal tract, and metabolic pathways were identified including isovaleryl de-esterification and hydrolysis of alpha-glucose units located either at the reducing or the non-reducing terminus.

Identification of phenolic constituents in Radix Salvia miltiorrhizae by liquid chromatography/electrospray ionization mass spectrometry

The phenolic components from Radix Salvia miltiorrhizae Bunge, a well-known herbal medicine (Dan-Shen in Chinese), have been investigated by high-performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC/ESI-MS/MS). HPLC analyses were performed on a reversed-phase C18 column using gradient elution. In the ESI mass spectra a predominant [M-H]- ion was observed in negative mode and provided molecular mass information. ESI-MS/MS spectra of the [M-H]- ions were used for structural analysis, based on the spectra of standards. It was found that caffeic acid and its monomeric analogs containing a carboxyl group readily lost CO2, while dimers, trimers and tetramers of caffeic acid expelled successively danshensu or caffeic acid or their esters. Twenty-eight phenolic compounds in S. miltiorrhizae were characterized, of which eight compounds were positively identified by comparison with standards. The remaining twenty phenolics for which standards were not available were tentatively identified based on their UV spectra and MS/MS fragmentation characteristics.

Rapid and reliable determination of illegal adulterant in herbal medicines and dietary supplements by LC/MS/MS

In recent years, dietary supplements and herbal medicines are increasing in popularity all over the world. However, it is problematic that some manufacturers illegally included synthetic drugs in their products. Due to the extremely complex matrices of those products, most existing methods for screening illegal adulterations are time-consuming and liable to false positive. In this paper, a robust LC/MS/MS method for the high-throughput, sensitive and reliable determination of illegal adulterations from herbal medicines and dietary supplements was established. Minimal LC separation was employed and MRM was used to simultaneously monitor the three transitions under their respective optimal collision energy for each compound. Positive results were determined only if well-defined peaks appeared at all of the three transitions and the ratios among the peak areas were within given threshold. In this study, the method had been applied for the screening of nine most commonly adulterated therapeutic substances, such as sildenafil (Viagra) and famotidine, and the lower limits of detection of these compounds ranged from 0.05 to 1.5 ng/ml. Little sample preparation was needed for this method and the analysis time was less than 5 min/sample. The reliability has been demonstrated by the test with blank matrix. Over 200 products that were under suspicion by SDA of China had been assayed and till now no false negative or positive result was found. This method is rapid, simple, reliable and capable of screening multiple adulterants in one run.

Identification of secondary metabolites from Streptomyces violaceoruber TU22 by means of on-flow LC-NMR and LC-DAD-MS

For rapid screening of natural products from Actinomycetes, a combination of on-line couplings LC-NMR, LC-DAD-MS and HPLC-PDA, as well as MALDI-TOF-MS is particularly suitable. Simultaneous use of these coupling techniques provides considerable advantages for the rapid identification of natural compounds in mixtures. The results of our present investigation on secondary metabolite products of Streptomyces violaceoruber TU 22 showed that more than 50% of the identified metabolites are new compounds. The structures of four new polyketides (granaticin C, metenaticin A, B and C) as well as four known ones (granaticin A, granatomycin E, daidzein and genistein) have been elucidated using LC-NMR, LC-MS/MS and -MS(n) techniques in combination with two-dimensional NMR spectroscopy.

Hybrid triple quadrupole-linear ion trap mass spectrometry in fragmentation mechanism studies: application to structure elucidation of buspirone and one of its metabolites

The use of a hybrid triple quadrupole-linear ion trap (QqQ(LIT)) mass spectrometer system for a comprehensive study of fragmentation mechanisms is described. The anxiolytic drug, buspirone, was chosen as a model compound for this study. With the advent of a QqQ(LIT) instrument, both the traditional quadrupole and the new linear ion trap scans (LIT) could be performed in a single LC run. In the past, a sample had to be run on two different instruments, namely, a triple quadrupole instrument (QqQ) and a 3D ion trap (3D IT) to obtain similar information. With the new QqQ(LIT) technology, collision-induced dissociation (CID) occur in a quadrupole collision cell, q2, and fragment ions are trapped and analyzed in Q3 operated in LIT mode. In this work, high-sensitivity product ion spectra of buspirone were obtained from the one-stage 'Enhanced Product Ion' scan (EPI) with rich product ions and no low mass cut-off. Furthermore, detailed fragmentation pathways were elucidated by further dissociation of each of the fragment ions in the EPI spectrum using MS(3) mode in the same run. The MS(3) scan was performed by incorporating CID in q2, and trapping, cooling, isolation, and resonance-excitation in Q3 when operating in LIT mode. This approach allowed unambiguous assignment of all fragment ions quickly with fewer experiments and easier interpretation than the previous approach. The overall sensitivity for obtaining complete fragment ion data was significantly improved for QqQ(LIT) as compared with that of QqQ and 3D IT mass spectrometers. This is beneficial for structure determination of unknown trace components. The method allowed structure determination of metabolites of buspirone in rat microsomes at 1 microM concentration, which was a 10-fold lower concentration than was needed for QqQ or 3D IT instruments. The QqQ(LIT) instrument provided a simple, rapid, sensitive and powerful approach for structure elucidation of trace components.