Open access atmospheric pressure chemical ionization Mass spectrometry for routine sample analysis

Utility of Atmospheric-Pressure Chemical Ionization and Photoionization Mass Spectrometry in Bottom-Up Proteomics

In a typical bottom-up proteomics workflow, proteins are enzymatically cleaved, and the resulting peptides are analyzed by HPLC with electrospray ionization (ESI) tandem mass spectrometry. This approach is practical and widely applied. It has, however, limitations mostly related to less efficient or even inefficient ionization of some peptides in ESI sources. Gas-phase ionization methods like atmospheric-pressure chemical ionization (APCI) or atmospheric-pressure photoionization (APPI) offer alternative ways of detecting various analytes. This work is a systematic study of the ionization efficiencies of peptides in ESI, APCI, and APPI and the applicability of the mentioned ionizations in proteomics. A set of peptide standards and bovine serum albumin digests were examined using a high-resolution mass spectrometer coupled to an ultra HPLC system. Since the ionization efficiency in APCI and APPI depends strongly on experimental conditions, the ion source settings and mobile phase compositions were optimized for each ionization technique. As expected, tryptic peptides were best detected using ESI. The numbers of chymotrypsin peptides successfully detected by ESI, APPI, and APCI were comparable. In the case of Glu-C digest, APPI detected the highest number of peptides. The results suggest that gas-phase ionization techniques, particularly APPI, are an interesting alternative for detecting peptides and delivering complementary data in proteomics.

Towards a generic method for ion chromatography/mass spectrometry of low-molecular-weight amines in pharmaceutical drug discovery and development

RATIONALE

Low-molecular-weight amines are encountered in pharmaceutical analysis, e.g. as reactants in chemical syntheses, but are challenging to analyse using ultrahigh-performance liquid chromatography/mass spectrometry (UHPLC/MS) due to their high polarity causing poor retention. Ion chromatography/mass spectrometry (IC/MS) is an emerging technique for polar molecule analysis that offers better separation. A generic IC/MS method would overcome problems associated with using UHPLC/MS in drug discovery and development environments.

METHODS

Amine standards were analysed using IC/MS with gradient elution (variety of column temperatures evaluated). An electrospray ionisation (ESI) quadrupole mass spectrometer was operated in positive ion polarity in scanning mode. The make-up flow composition was evaluated by assessing the performance of a range of organic modifiers (acetonitrile, ethanol, methanol) and additives (acetic acid, formic acid, methanesulfonic acid). The ESI conditions were optimised to minimise adduct formation and promote generation of protonated molecules.

RESULTS

The performance attributes were investigated and optimised for low-molecular-weight amine analysis. Organic solvents and acidic additives were evaluated as make-up flow components to promote ESI, with 0.05% acetic acid in ethanol optimal for producing protonated molecules. The hydrogen bonding capability of amines led to abundant protonated molecule-solvent complexes; optimisation of source conditions reduced these, with collision-induced dissociation voltage having a strong effect. The detection limit was ≤1.78 ng for the amines analysed, which is fit-for-purpose for an open-access chemistry environment.

CONCLUSIONS

This study demonstrates the value of IC/MS for analysing low-molecular-weight amines. Good chromatographic separation of mixtures was possible without derivatisation. Ionisation efficiency was greatest using a make-up flow of 0.05% acetic acid in ethanol, and optimisation of ESI source conditions promoted protonated molecule generation for easy determination of molecular weight.

Automated open-access liquid chromatography high resolution mass spectrometry to support drug discovery projects

The need of a continuous productivity increases in medicinal chemistry laboratories of the pharmaceutical industry motivated the development, over the years, of new software solutions to enable Open-Access in many analytical techniques such as NMR or LC, among others, to characterize and assess the purity of new molecules. These approaches have been widely spread in LC with low resolution MS systems, but similar automated platforms have been rather less explored with high resolution MS. In this work, an improved Automated Open-Access methodology on an UHPLC with DAD coupled to ESI and quadrupole time-of-flight MS system is described. Detailed reports from standard UHPLC-MS runs containing chromatograms and different spectra (MS with different fragmentation) are automatically sent to the chemists. High resolution MS data is typically achieved within ± 1 mDa mass accuracy regardless of sample concentration. Upon training, chemists log-in samples into the system by selecting appropriate methods, being able to interpret the results by themselves in 95% of the cases. The instrument is working unattended, except for a limited number of samples (5%) which require more complex experiments. To the best of our knowledge, this is the first time a completely automated Open-Access LC-HRMS approach has been implemented for medicinal chemists of a pharmaceutical industry.

Open Access UHPSFC/MS - an additional analytical resource for an academic mass spectrometry facility

RATIONALE

Many compounds submitted for analysis in Chemistry at the University of Southampton do not retain, elute or ionize using open access reversed-phase ultra-high-performance liquid chromatography/mass spectrometry (RP-UHPLC/MS) and require analysis via infusion. An ultra-high-performance supercritical fluid chromatography mass spectrometry approach was implemented to afford high-throughput analysis of these compounds with chromatographic separation.

METHODS

A UPC(2) -TQD MS system has been incorporated into the open access MS provision within Chemistry at the University of Southampton, using an ESCi source (electrospray and atmospheric pressure chemical ionization) and an atmospheric pressure photoionization (APPI) source. Access to instrumentation is enabled via a web-based interface (RemoteAnalyzer™).

RESULTS

Compounds such as fluorosugars, fullerenes, phosphoramidites, porphyrins, and rotaxanes exhibiting properties incompatible with RP-UHPLC/MS have been analyzed using automated chromatography and mass spectrometry methods. The speedy return of data enables research in these areas to progress unhindered by sample type. The provision of an electronic web format enables easy incorporation of chromatograms and mass spectra into electronic files and reports.

CONCLUSIONS

The implementation of UHPSFC/MS increases access to a wide range of chemistries incompatible with reversed-phase chromatography and polar solvents, enabling more than 90% of submitted samples to be analyzed using an open access approach. Further, chromatographic separation is provided where previously flow injection or infusion analyses were the only options. Copyright © 2016 John Wiley & Sons, Ltd.

Size exclusion chromatography coupled to electrospray ionization mass spectrometry for analysis and quantitative characterization of arsenic interactions with peptides and proteins

Arsenic-binding proteins are of toxicological importance since enzymatic activities can be blocked by arsenic interactions. In the present work, a novel methodology based on size exclusion chromatography coupled to electrospray ionization mass spectrometry (SEC-ESI-MS) was developed with special emphasis to preserve the intact proteins and their arsenic bindings. The eluent composition of 25 mMTris/HCl, pH 7.5, with the addition of 100-mM NaCl optimized for SEC with UV detection provided the highest SEC separation efficiency, but was not compatible with the ESI-MS because of the non-volatility of the buffer substance and of the salt additive. In order to find the best compromise between chromatographic separation and ionization of the arsenic-binding proteins, buffer type and concentration, pH value, portion of organic solvent in the SEC eluent as well as the flow rate were varied. In the optimized procedure five different arsenic-binding peptides and proteins (glutathione, oxytocin, aprotinin, alpha-lactalbumin, thioredoxin) covering a molar mass range of 0.3-14 kDa could be analyzed using 75% 10-mM ammonium formate, pH 5.0/25% acetonitrile (v : v) as eluent and a turbo ion spray source operated at 300 degrees C and 5.5 kV. A complete differentiation of all peptides and proteins involved in the arsenic-binding studies as well as of their arsenic-bound forms has become feasible by means of the extracted ion chromatograms (XIC) of the mass spectrometric detection. The new method offered the possibility to estimate equilibrium constants for the reaction of phenylarsine oxide with different thiol-containing biomolecules by means of the XIC peak areas of reactants and products. Limits of detection in the range of 2-10 microM were obtained by SEC-ESI-MS for the individual proteins.

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.

Quantitative evaluation of the binding of phenylarsenic species to glutathione, isotocin, and thioredoxin by means of electrospray ionization time-of-flight mass spectrometry

An attempt was made to quantitatively describe the binding of phenylarsenic species to thiol-containing biomolecules using electrospray ionization mass spectrometry (ESI-MS). The extent of the reactions of phenylarsine oxide (PAO) with the peptides glutathione and isotocin (ITC) and with the protein thioredoxin resulting in covalent As--S bonds were quantified by deriving the dependence of the corresponding ion signal intensities on the concentration of the reaction products. Problems complicating a quantitative evaluation of the mass spectra, such as signal suppression effects, were critically evaluated. Equilibrium constants for condensation reactions as well as formation constants for noncovalent associations were calculated by means of ESI-MS signal intensities. The comparison of the reaction of PAO with different thiol reactants revealed the highest binding affinity for ITC followed by thioredoxin and a lower affinity to glutathione. Possibly, the intramolecular formation of RS-As(C(6)H(5))-SR occurring in case of ITC and thioredoxin is favored over the intermolecular product involving two molecules glutathione even though the molecular mass of glutathione (307 g mol(-1)) is much smaller than that of ITC (966 g mol(-1)) and thioredoxin (11 688 g mol(-1)). A similar binding affinity for trivalent (K approximately 1.6 x 10(-3) l micromol(-1)) and pentavalent (K approximately 1.6 x 10(-3) and 1.0 x 10(-3) l micromol(-1)) arsenic species was found for the formation of a noncovalent complex of glutathione with different phenylarsenic compounds.

Automated mass correction and data interpretation for protein open-access liquid chromatography-mass spectrometry

Characterization of recombinant protein purification fractions and final products by liquid chromatography-mass spectrometry (LC/MS) are requested more frequently each year. A protein open-access (OA) LC/MS system was developed in our laboratory to meet this demand. This paper compares the system that we originally implemented in our facilities in 2003 to the one now in use, and discusses, in more detail, recent enhancements that have improved its robustness, reliability, and data reporting capabilities. The system utilizes instruments equipped with reversed-phase chromatography and an orthogonal accelerated time-of-flight mass spectrometer fitted with an electrospray source. Sample analysis requests are accomplished using a simple form on a web-enabled laboratory information management system (LIMS). This distributed form is accessible from any intranet-connected company desktop computer. Automated data acquisition and processing are performed using a combination of in-house (OA-Self Service, OA-Monitor, and OA-Analysis Engine) and vendor-supplied programs (AutoLynx, and OpenLynx) located on acquisition computers and off-line processing workstations. Analysis results are then reported via the same web-based LIMS. Also presented are solutions to problems not addressed on commercially available, small-molecule OA-LC/MS systems. These include automated transforming of mass-to-charge (m/z) spectra to mass spectra and automated data interpretation that considers minor variants to the protein sequence-such as common post-translational modifications (PTMs). Currently, our protein OA-LC/MS platform runs on five LC/MS instruments located in three separate GlaxoSmithKline R&D sites in the US and UK. To date, more than 8000 protein OA-LC/MS samples have been analyzed. With these user friendly and highly automated OA systems in place, mass spectrometry plays a key role in assessing the quality of recombinant proteins, either produced at our facilities or bought from external sources, without dedicating extensive amounts of analyst resource.

Evolution of an open-access quantitative bioanalytical mass spectrometry service in a drug discovery environment

Increased demand for assays for compounds at the early stages of drug discovery within the pharmaceutical industry has led to the need for open-access mass spectrometry systems for performing quantitative analysis in a variety of biological matrices. The open-access mass spectrometers described here are LC/MS/MS systems operated in 'multiple reaction monitoring' (MRM) mode to obtain the sensitivity and specificity required to quantitate low levels of pharmaceutical compounds in an excess of biological matrix. Instigation of these open-access systems has resulted in mass spectrometers becoming the detectors of choice for non-expert users, drastically reducing analytical method development time and allowing drug discovery scientists to concentrate on their core expertise of pharmacokinetics and drug metabolism. Setting up an open-access facility that effectively allows a user with minimal mass spectral knowledge to exploit the MS/MS capability of triple quadrupole mass spectrometers presents a significantly different challenge from setting up qualitative single stage mass spectrometry systems. Evolution of quantitative open access mass spectrometry within a pharmaceutical drug metabolism and pharmacokinetics group, from its beginnings as a single generic system to a series of specialist fully integrated walk-up facilities, is described.

Protein open-access liquid chromatography/mass spectrometry

Each year increasing numbers of proteins are submitted for routine characterization by liquid chromatography/mass spectrometry (LC/MS). This paper reports a solution that transforms routine LC/MS analysis of proteins into a fully automated process that significantly reduces analyst intervention. The solution developed, protein open-access (OA) LC/MS, consists of web-enabled sample submission and registration, automated data processing, data interpretation, and report generation. Sample submissions and results are recorded in a LIMS that utilizes an Oracle database. The protein sequence is captured during the sample submission process, stored in the database, and utilized to determine the theoretical protein molecular weight. This calculated mass is used to set the parameters for transformation of the mass-to-charge spectra to the mass domain and evaluate the presence or absence of the desired protein. Three protein OA-LC/MS instruments have been deployed in our facility to support protein characterization, purification, and modification efforts.

The automation of a commercial Fourier transform mass spectrometer to provide a quick and robust method for determining exact mass for the synthetic chemist

Automation of a commercially available Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer for the routine analysis of the synthetic products from high-speed chemistry is described. The automation includes software written by the instrument manufacturer and in-house developed software; allowing electronic submission of samples from the chemist and e-mailing of results back to the chemist. The use of samples of relatively high concentration (ca 1 mg x mL(-1)) is possible due to the protocol that has been developed, which includes dilution by the autosampler during sample injection. Though high concentrations are used for speed and convenience the amount of sample consumed is still small ca 15 microg per injection. The results from this method have been shown to be both accurate (average error +/- 0.91 ppm) and precise (-0.70 ppm to 2.26 ppm). The system is capable of analysing up to 800 samples per 24 hours. As high speed chemistry becomes more highly utilised within discovery the number of samples requiring accurate mass analysis will rise, and the method we have described will prevent high resolution mass spectrometry becoming the bottleneck in new chemical entity production. The accuracy and precision demonstrated by this method allows high confidence levels in assigned molecular formulae for expected compounds and reduces the number of possible formulae to consider when working with a compound that is not the desired product of a given reaction.

Open-access liquid chromatography/mass spectrometry in a drug discovery environment

The use of open-access mass spectrometry to monitor synthetic chemistry reactions, and also the integrity and purity of new chemical entities, has been a part of the medicinal chemist's tool-box for more than 5 years. Originally in our group at Wyeth Research there were two open-access methods available to the chemists, flow injection analysis (FIA) and liquid chromatography/mass spectrometry (LC/MS). The FIA method was approximately 3 min long, while the LC/MS method was approximately 20 min long (including an 8 min gradient). Within the first 2 years, the total number of open-access analyses increased by approximately 125%. It is interesting, however, that the number of LC/MS analyses increased by more than 285%. This is attributed to the fact that the chemists began using the LC/MS data to monitor reactions and also to check final product integrity and purity. In addition, the number of chemists performing parallel synthesis reactions has increased; thus, individual chemists can produce sample sets of up to 100 vials. This paper describes the implementation of new methodology, which accommodates the need for much faster run times and also the ability to acquire alternating positive and negative ion spectra within the same run. In addition, the instrument has been configured to e-mail the resulting processed data report to the submitting chemist. Several methods have been developed, including structure elucidation using in-source collision-induced dissociation (CID) and night-time analysis. The LC/MS methods for this system are described herein and are applicable to both industrial and academic synthetic chemistry optimization efforts.

Operation of an academic open access mass spectrometry facility with particular reference to the analysis of synthetic compounds

Open access mass spectrometry now provides the opportunity to move this spectroscopic method to the beginning of the analytical chain, a place formerly the exclusive province of NMR and TLC. To date this transition has been occurring in industrial settings but there has been less change in the academic environment. This paper provides one blueprint for setting up such a facility, primarily in support of organic synthesis but also for the use of biological scientists. The open access format used at UCI utilizes four instruments: an ESI-TOFMS system used in the flow injection mode, two GC/MS systems (one in EI and one in CI) and a MALDI-TOFMS system. The first three instruments have autosamplers and open access software whereas the MALDI system has a fully automated plate handling interface. This level of automation allows access to the instruments by a user community of more than 100 users, day or night. The decisions made in setting up these instruments were based on a 'keep it simple' philosophy, given the fact that the primary type of data of interest is the molecular mass of the analyte and that data are required for a very wide range of structures.

Integration of mass spectrometry into early-phase discovery and development of central nervous system agents

The early-phase discovery and development of useful central nervous system (CNS) agents present ample opportunities to exploit mass spectrometry and provide detailed compound/mixture characterization, or to make the process faster and/or more economic. Neuropeptide FF antagonists and centrally active thyrotropin-releasing hormone analogues were used as specific examples in this work. We evaluated the characterization of focused libraries of peptide derivatives by electrospray ionization, tandem mass spectrometry and liquid chromatography/tandem mass spectrometry on a quadrupole ion trap and nanoelectrospray on a Fourier transform ion cyclotron resonance mass spectrometer. Immobilized artificial-membrane chromatography was employed as a model to predict/rank new agents against lead compounds for their potential to reach the central nervous system in pharmacologically significant amounts. Measuring brain concentrations in rodents after the intravenous administration of test compounds was used as an in vivo approach, and we took advantage of microdialysis sampling that furnished samples without interfering tissue matrix and afforded the estimation of extracellular concentrations in a localized part of the brain. Overall, making atmospheric-pressure ionization mass spectrometry an integral part of the process has played a major role in increasing throughput, selectivity, specificity and detection sensitivity and thereby providing useful information about the extent or mechanism of transport and metabolic activation/inactivation in early-phase discovery and development of CNS agents.

Automated molecular weight assignment of electrospray ionization mass spectra

Process improvements in the synthesis of therapeutic agents and their intermediates are often facilitated by identification of reaction by-products. Analysis by liquid chromatography/mass spectrometry (LC/MS) with electrospray ionization is a powerful approach for obtaining molecular weight information for these compounds. Such analyses are well suited for 'open-access' mass spectrometry using generic chromatographic conditions, provided spectral interpretation for unknown compounds is facile. We have developed a software application (MassAssign) that facilitates automated data processing and molecular weight assignment for chromatographic peaks detected by any standard ultraviolet-visible wavelength detector. The program assigns [M + H](+) ions (and thus molecular weight) in the mass spectra using predetermined criteria. This evaluation process differentiates [M + H](+) ions from other signals in a complex mass spectrum such as those resulting from chromatographic coelution or the presence of multiple species (i.e., fragment ions, singly charged ions, doubly charged ions, adduct ions, proton-bound dimers, etc.). Once the program has evaluated all ions in a mass spectrum that exceed a preset abundance threshold, MassAssign reports either a numeric value-indicating the chromatographic peak consists of a single component having the displayed molecular weight, 'MC'-indicating the peak consisted of multiple components, or 'ND'-that a molecular weight could not be determined unequivocally. The performance of the program was evaluated by comparing mass assignments made by MassAssign against manual interpretation for 55 samples analyzed by positive electrospray ionization using a generic HPLC method. Correct molecular weight assignments were obtained in 90% of the cases.

Exploratory pharmacokinetics and brain distribution study of a neuropeptide FF antagonist by liquid chromatography/atmospheric pressure ionization tandem mass spectrometry

Dansyl-Pro-Gln-Arg-NH(2), an N-terminally modified tripeptide amide and a putative neuropeptide FF antagonist, was amenable to both positive-ion ESI and APCI. The protonated molecule yielded several fragment ions upon collision-induced dissociation in a quadrupole ion trap instrument for the development of LC/MS/MS assay methods. ESI clearly outperformed APCI in limits of detection, and was the method of choice for coupling with narrow-bore reversed-phase liquid chromatography to assess the pharmacokinetic profile and brain concentration of the neuropeptide FF antagonist in experimental animals. While plasma could be analyzed after rapid sample preparation, brain tissue required cleanup (solid phase extraction) and preconcentration before injection, and the assay was prone to matrix interference. This study indicated a rapid disappearance of dansyl-Pro-Gln-Arg-NH(2) from the plasma and the brain, and modest CNS bioavailability after intravenous administration to rats.

LC/MS applications in drug development

The combination of high-performance liquid chromatography and mass spectrometry (LC/MS) has had a significant impact on drug development over the past decade. Continual improvements in LC/MS interface technologies combined with powerful features for structure analysis, qualitative and quantitative, have resulted in a widened scope of application. These improvements coincided with breakthroughs in combinatorial chemistry, molecular biology, and an overall industry trend of accelerated development. New technologies have created a situation where the rate of sample generation far exceeds the rate of sample analysis. As a result, new paradigms for the analysis of drugs and related substances have been developed. The growth in LC/MS applications has been extensive, with retention time and molecular weight emerging as essential analytical features from drug target to product. LC/MS-based methodologies that involve automation, predictive or surrogate models, and open access systems have become a permanent fixture in the drug development landscape. An iterative cycle of "what is it?" and "how much is there?" continues to fuel the tremendous growth of LC/MS in the pharmaceutical industry. During this time, LC/MS has become widely accepted as an integral part of the drug development process. This review describes the utility of LC/MS techniques for accelerated drug development and provides a perspective on the significant changes in strategies for pharmaceutical analysis. Future applications of LC/MS technologies for accelerated drug development and emerging industry trends are also discussed.

Impact of mass spectrometry on combinatorial chemistry

In the past few years, the emergence of combinatorial chemistry has drawn increasing attention and a great deal of analytical research has been centered around this new methodology. These new methods capable of producing vast numbers of samples, which are in many cases highly complex, demand fast and reliable analytical techniques able to provide high quality information concerning sample compositions. Mass spectrometry (MS) is the method of choice to face these analytical challenges. In particular, the introduction of electrospray ionization (ESI and matrix assisted laser desorption/ionization (MALDI) have been the driving forces for many of the recent innovations, not only within the fields of the biosciences, but also in combinatorial chemistry. These ionization techniques are extremely versatile for the characterization of both single compound collections and compound mixture collections. The high-throughput capabilities, as well as many possible couplings with separation techniques (HPLC, CE) have been thus facilitated. However, mass spectrometry is not only limited to use as an instrument for synthesis control, but also plays an increasing role in the identification of active compounds from complex libraries. Recently, new initiatives for library analysis and screening have arisen from the application of the latest developments in mass spectrometry, Fourier transform ion cyclotron resonance (FTICR).