Gas-Phase Proton-Transfer Chemistry Coupled with TOF Mass Spectrometry and Ion Mobility-MS for the Facile Analysis of Poly(ethylene glycols) and PEGylated Polypeptide Conjugates

Streamlining LC-MS Characterization of Pharmaceutical Polymers by Fourier-Transform-Based Deconvolution and Macromolecular Mass Defect Analysis

Polymer conjugation has risen in importance over the past three decades as a means of increasing the in vivo half-life of biotherapeutics, with benefits including better stability, greater drug efficacy, and lower toxicity. However, the intrinsic variability of polymer synthesis results in products with broad distributions in chain length and branching structure, complicating quality control for successful functionalization and downstream conjugation. Frequently, a combination of several analytical techniques is required for comprehensive characterization. While liquid chromatography-mass spectrometry (LC-MS) is a powerful platform that can provide detailed molecular features of polymers, the mass spectra are inherently challenging to interpret due to high mass polydispersity and overlapping charge distributions. Here, by leveraging Fourier transform-based deconvolution and macromolecular mass defect analysis, we demonstrate a new way to streamline pharmaceutical polymer analysis, shedding light on polymer size, composition, branching, and end-group functionalization with the capability for reaction monitoring.

To 200,000 m/z and Beyond: Native Electron Capture Charge Reduction Mass Spectrometry Deconvolves Heterogeneous Signals in Large Biopharmaceutical Analytes

Great progress has been made in the detection of large biomolecular analytes by native mass spectrometry; however, characterizing highly heterogeneous samples remains challenging due to the presence of many overlapping signals from complex ion distributions. Electron-capture charge reduction (ECCR), in which a protein cation captures free electrons without apparent dissociation, can separate overlapping signals by shifting the ions to lower charge states. The concomitant shift to higher m/z also facilitates the exploration of instrument upper m/z limits if large complexes are used. Here we perform native ECCR on the bacterial chaperonin GroEL and megadalton scale adeno-associated virus (AAV) capsid assemblies on a Q Exactive UHMR mass spectrometer. Charge reduction of AAV8 capsids by up to 90% pushes signals well above 100,000 m/z and enables charge state resolution and mean mass determination of these highly heterogeneous samples, even for capsids loaded with genetic cargo. With minor instrument modifications, the UHMR instrument can detect charge-reduced ion signals beyond 200,000 m/z. This work demonstrates the utility of ECCR for deconvolving heterogeneous signals in native mass spectrometry and presents the highest m/z signals ever recorded on an Orbitrap instrument, opening up the use of Orbitrap native mass spectrometry for heavier analytes than ever before.

Mass spectrometry-based methods to characterize highly heterogeneous biopharmaceuticals, vaccines, and nonbiological complex drugs at the intact-mass level

The intact-mass MS measurements are becoming increasingly popular in characterization of a range of biopolymers, especially those of interest to biopharmaceutical industry. However, as the complexity of protein therapeutics and other macromolecular medicines increases, the new challenges arise, one of which is the high levels of structural heterogeneity that are frequently exhibited by such products. The very notion of the molecular mass measurement loses its clear and intuitive meaning when applied to an extremely heterogenous system that cannot be characterized by a unique mass, but instead requires that a mass distribution be considered. Furthermore, convoluted mass distributions frequently give rise to unresolved ionic signal in mass spectra, from which little-to-none meaningful information can be extracted using standard approaches that work well for homogeneous systems. However, a range of technological advances made in the last decade, such as the hyphenation of intact-mass MS measurements with front-end separations, better integration of ion mobility in MS workflows, development of an impressive arsenal of gas-phase ion chemistry tools to supplement MS methods, as well as the revival of the charge detection MS and its triumphant entry into the field of bioanalysis already made impressive contributions towards addressing the structural heterogeneity challenge. An overview of these techniques is accompanied by critical analysis of the strengths and weaknesses of different approaches, and a brief overview of their applications to specific classes of biopharmaceutical products, vaccines, and nonbiological complex drugs.

Ion Mobility Mass Spectrometry Development and Applications

Although as an analytical method with high specificity and high sensitivity, mass spectrometry (MS) has a wide range of applications in many fields, it still needs other technologies as the assist and supplement to enhance the scope and capability of analysis. Coupling with ion mobility (IM) can make an enhancement effect in the field of pharmaceutical analysis as a supplementary method. The two-dimensional mass technology improves the confidence of compounds annotations while increasing peak capacity, with the gradual deepening of theoretical research on IM-MS, it has shown unique advantages in the complex analysis conditions. IM-MS owns great potential for improving the depth, range, dimension of in-depth drug research. In this review, the principle, instruments and methods, applications, advantages and limitations of IM-MS are described. Here, we also elaborate on the prospects in structural evaluation, separation, and identification of complex compounds for the drug discovery and development phase and the great advantages of macromolecules and omics.

Efficient secretory production of proline/alanine/serine (PAS) biopolymers in Corynebacterium glutamicum yielding a monodisperse biological alternative to polyethylene glycol (PEG)

Background

PAS biopolymers are recombinant polypeptides comprising the small uncharged l-amino acids Pro, Ala and/or Ser which resemble the widely used poly-ethylene glycol (PEG) in terms of pronounced hydrophilicity. Likewise, their random chain behaviour in physiological solution results in a strongly expanded hydrodynamic volume. Thus, apart from their use as fusion partner for biopharmaceuticals to achieve prolonged half-life in vivo, PAS biopolymers appear attractive as substitute for PEG—or other poorly degradable chemical polymers—in many areas. As a prerequisite for the wide application of PAS biopolymers at affordable cost, we have established their highly efficient biotechnological production in Corynebacterium glutamicum serving as a well characterized bacterial host organism.

Results

Using the CspA signal sequence, we have secreted two representative PAS biopolymers as polypeptides with ~ 600 and ~ 1200 amino acid residues, respectively. Both PAS biopolymers were purified from the culture supernatant by means of a simple downstream process in a truly monodisperse state as evidenced by ESI–MS. Yields after purification were up to ≥ 4 g per liter culture, with potential for further increase by strain optimization as well as fermentation and bioprocess development. Beyond direct application as hydrocolloids or to exploit their rheological properties, such PAS biopolymers are suitable for site-specific chemical conjugation with pharmacologically active molecules via their unique terminal amino or carboxyl groups. To enable the specific activation of the carboxylate, without interference by the free amino group, we generated a blocked N-terminus for the PAS(1200) polypeptide simply by introducing an N-terminal Gln residue which, after processing of the signal peptide, was cyclised to a chemically inert pyroglutamyl group upon acid treatment. The fact that PAS biopolymers are genetically encoded offers further conjugation strategies via incorporation of amino acids with reactive side chains (e.g., Cys, Lys, Glu/Asp) at defined positions.

Conclusions

Our new PAS expression platform using Corynex^® technology opens the way to applications of PASylation^® technology in multiple areas such as the pharmaceutical industry, cosmetics and food technology.

Approaches to Heterogeneity in Native Mass Spectrometry

Native mass spectrometry (MS) is aimed at preserving and determining the native structure, composition, and stoichiometry of biomolecules and their complexes from solution after they are transferred into the gas phase. Major improvements in native MS instrumentation and experimental methods over the past few decades have led to a concomitant increase in the complexity and heterogeneity of samples that can be analyzed, including protein-ligand complexes, protein complexes with multiple coexisting stoichiometries, and membrane protein-lipid assemblies. Heterogeneous features of these biomolecular samples can be important for understanding structure and function. However, sample heterogeneity can make assignment of ion mass, charge, composition, and structure very challenging due to the overlap of tens or even hundreds of peaks in the mass spectrum. In this review, we cover data analysis, experimental, and instrumental advances and strategies aimed at solving this problem, with an in-depth discussion of theoretical and practical aspects of the use of available deconvolution algorithms and tools. We also reflect upon current challenges and provide a view of the future of this exciting field.

Electrospray Ionization Ion Mobility Mass Spectrometry

Electrospray ionization ion mobility mass spectrometry (ESI-IMS-MS) is a rapidly progressing analytical technique for the examination of complex compounds in the gas phase. ESI-IMS-MS separates isomers, provides structural information, and quantitatively identifies peptides, lipids, carbohydrates, polymers, and metabolites in biological samples. ESI-IMS-MS has pharmaceutical, environmental, and manufacturing applications quickly characterizing drugs, petroleum products, and metal macromolecules. This review provides the history of ESI-IMS-MS development and applications to date.

Denaturing and Native Mass Spectrometric Analytics for Biotherapeutic Drug Discovery Research: Historical, Current, and Future Personal Perspectives

Mass spectrometry (MS) plays a key role throughout all stages of drug development and is now as ubiquitous as other analytical techniques such as surface plasmon resonance, nuclear magnetic resonance, and supercritical fluid chromatography, among others. Herein, we aim to discuss the history of MS, both electrospray and matrix-assisted laser desorption ionization, specifically for the analysis of antibodies, evolving through to denaturing and native-MS analysis of newer biologic moieties such as antibody-drug conjugates, multispecific antibodies, and interfering nucleic acid-based therapies. We discuss challenging therapeutic target characterization such as membrane protein receptors. Importantly, we compare and contrast the MS and hyphenated analytical chromatographic methods used to characterize these therapeutic modalities and targets within biopharmaceutical research and highlight the importance of appropriate MS deconvolution software and its essential contribution to project progression. Finally, we describe emerging applications and MS technologies that are still predominantly within either a development or academic stage of use but are poised to have significant impact on future drug development within the biopharmaceutic industry once matured. The views reflected herein are personal and are not meant to be an exhaustive list of all relevant MS performed within biopharmaceutical research but are what we feel have been historically, are currently, and will be in the future the most impactful for the drug development process.

Pharmacokinetics of 40 kDa Polyethylene glycol (PEG) in mice, rats, cynomolgus monkeys and predicted pharmacokinetics in humans

Conjugation with polyethylene glycol (PEG), PEGylation, has been considered a useful tool to improve drug-like properties of novel small molecules and biologics in drug discovery. PEG40 or 40 kDa PEG is a double-branched PEG, routinely employed to improve the pharmacokinetics (PK) of therapeutics, including successful marketed products such as Pegasys® and Omontys®. However, less is known about the extent of contribution of PEG40 to the overall PK of the PEGylated product. Considering the half-life of PEG40 conjugated PEGylated products ranges from 1 to 14 days in human, this information is immensely valuable. After successfully developing a high sensitivity NMR based analytical method to quantitate PEG40 in mice serum after intravenous (IV) administration (Khandelwal et al., 2019), here, we extend its application to measure PEG40 in serum after IV administration and subcutaneous (SC) absorption in routinely employed non-clinical species in drug discovery, namely, mice, rats and cynomolgus monkeys. We utilized non-compartmental analysis and compartmental modeling to characterize the PK of PEG40 in these non-clinical species. Finally, we employed allometric scaling and Wajima (MRT-Css) method to predict the PK of PEG40 in human after IV administration and SC absorption. In general, our data shows that intrinsic PK parameters of PEG40 in mice, rats and cynomolgus monkeys are in the range of published literature values for PEG40-conjugated products, unless saturable clearance mechanisms are involved. We observed a bioavailability (F) of ~68% in CD-1 mice after SC administration of PEG40. In rats, the clearance (CL) and volume of distribution at steady state (V_ss) after IV infusion of PEG40 were 0.079 mL/min/kg and 0.19 L/kg, respectively; and SC bioavailability was ~20%. In cynomolgus monkeys, after IV infusion, CL and V_ss of PEG40 were 0.037 mL/min/kg and 0.20 L/kg, respectively; and SC bioavailability was ~69%. In addition, our findings indicate flip-flop kinetics of PEG40 in rodents, but not in cynomolgus monkeys. Finally, in human, intrinsic CL and V_ss of PEG40 were projected to be 0.02 mL/min/kg (0.084 L/h) and 0.22 L/kg, respectively. This comprehensive report of PK of PEG40 in non-clinical species and its subsequent prediction in humans is expected to be useful to drug discovery and development scientists for efficient decision-making and optimal resource utilization.

Ion mobility spectrometry - Mass spectrometry coupling for synthetic polymers

This review covers applications of ion mobility spectrometry (IMS) hyphenated to mass spectrometry (MS) in the field of synthetic polymers. MS has become an essential technique in polymer science, but increasingly complex samples produced to provide desirable macroscopic properties of high-performance materials often require separation of species prior to their mass analysis. Similar to liquid chromatography, the IMS dimension introduces shape selectivity but enables separation at a much faster rate (milliseconds vs minutes). As a post-ionization technique, IMS can be hyphenated to MS to perform a double separation dimension of gas-phase ions, first as a function on their mobility (determined by their charge state and collision cross section, CCS), then as a function of their m/z ratio. Implemented with a variety of ionization techniques, such coupling permits the spectral complexity to be reduced, to enhance the dynamic range of detection, or to achieve separation of isobaric ions prior to their activation in MS/MS experiments. Coupling IMS to MS also provides valuable information regarding the 3D structure of polymer ions in the gas phase and regarding how to address the question of how charges are distributed within the structure. Moreover, the ability of IMS to separate multiply charged species generated by electrospray ionization yields typical IMS-MS 2D maps that permit the conformational dynamics of synthetic polymer chains to be described as a function of their length.

Measuring the Kinetics of Neutral Pair Evaporation from Cluster Ions of Ionic Liquid in the Drift Region of a Differential Mobility Analyzer

Singly charged clusters [C⁺A^-]_nC⁺ or [C⁺A^-]_nA^- of two salts [C⁺A^-] are produced by electrospray ionization of alcohol solutions of the ionic liquids 1-ethyl-3-methylimidazolium tris(pentafluoroethyl)trifluorophosphate (EMI-FAP) and 1,2-dimethyl-3-propylimidazolium-methide (DMPI-Me). The rate of neutral pair evaporation into [C⁺A^-] + [C⁺A^-]_n-1C⁺ or [C⁺A^-]_n-1A^- is studied in atmospheric pressure as a function of temperature T for the positive trimer ion (n = 2) of DMPI-Me and the negative trimer ion of EMI-FAP. The trimer is separated from all other electrosprayed ions in a first differential mobility analyzer (DMA₁) and then transferred through a cooled tube to a second DMA whose drift gas is kept at a controlled temperature (25 °C < T < 100 °C). Singular characteristics of the DMA are a residence time τ of ∼0.1 to 1 ms, with essentially uniform temperature and τ. The decomposition occurring within DMA₂ results in a complex mobility spectrum associated with dimer product ions, with apparent mobilities intermediate between those of the dimer and the trimer, depending on the product of the reaction rate k and τ. A theoretical expression yielding k from the shape of the collected mobility spectrum is obtained by accounting for the deterministic reactive, convective, and diffusive evolutions of the parent and product ions within DMA₂. Observed and predicted mobility spectra agree well, yielding the reaction rate k with little ambiguity. Activation energies near 1 eV are determined for both trimer ions. Paradoxically, the evaporation process substantially heats up the cluster ion product. The theory developed enables measuring decay times much smaller and much larger than the residence time in the DMA.

An Analytical Perspective on Protein Analysis and Discovery Proteomics by Ion Mobility-Mass Spectrometry

Ion mobility combined with mass spectrometry (IM-MS) is a powerful technique for the analysis of biomolecules and complex mixtures. This chapter reviews the current state-of-the-art in ion mobility technology and its application to biology, protein analysis, and quantitative discovery proteomics in particular, from an analytical perspective. IM-MS can be used as a technique to separate mixtures, to determine structural information (rotationally averaged cross-sectional area) and to enhance MS duty cycle and sensitivity. Moreover, IM-MS is ideally suited for hyphenating with liquid chromatography, or other front-end separation techniques such as, GC, microcolumn LC, capillary electrophoresis, and direct analysis, including MALDI and DESI, providing an semiorthogonal layer of separation, which affords the more unambiguous and confident detection of a wide range of analytes. To illustrate these enhancements, as well as recent developments, the principle of in-line IM separation and hyphenation to orthogonal acceleration time-of-flight mass spectrometers are discussed, in addition to the enhancement of biophysical MS-based analysis using typical proteomics and related application examples.

Native and Denaturing MS Protein Deconvolution for Biopharma: Monoclonal Antibodies and Antibody-Drug Conjugates to Polydisperse Membrane Proteins and Beyond

Electrospray ionization mass spectrometry (ESI-MS) is a ubiquitously used analytical method applied across multiple departments in biopharma, ranging from early research discovery to process development. Accurate, efficient, and consistent protein MS spectral deconvolution across multiple instrument and detector platforms (time-of-flight, Orbitrap, Fourier-transform ion cyclotron resonance) is essential. When proteins are ionized during the ESI process, a distribution of consecutive multiply charged ions are observed on the m/z scale, either positive [M + nH]n+ or negative [M - nH]n- depending on the ionization polarity. The manual calculation of the neutral molecular weight (MW) of single proteins measured by ESI-MS is simple; however, algorithmic deconvolution is required for more complex protein mixtures to derive accurate MWs. Multiple deconvolution algorithms have evolved over the past two decades, all of which have their advantages and disadvantages, in terms of speed, user-input parameters (or ideally lack thereof), and whether they perform optimally on proteins analyzed under denatured or native-MS and solution conditions. Herein, we describe the utility of a parsimonious deconvolution algorithm (explaining the observed spectra with a minimum number of masses) to process a wide range of highly diverse biopharma relevant and research grade proteins and complexes (PEG-GCSF; an IgG1k; IgG1- and IgG2-biotin covalent conjugates; the membrane protein complex AqpZ; a highly polydisperse empty MSP1D1 nanodisc and the tetradecameric chaperone protein complex GroEL) analyzed under native-MS, denaturing LC-MS, and positive and negative modes of ionization, using multiple instruments and therefore multiple data formats. The implementation of a comb filter and peak sharpening option is also demonstrated to be highly effective for deconvolution of highly polydisperse and enhanced separation of a low level lysine glycation post-translational modification (+162.1 Da), partially processed heavy chain lysine residues (+128.1 Da), and loss of N-acetylglucosamine (GlcNAc; -203.1 Da).

Importance of collision cross section measurements by ion mobility mass spectrometry in structural biology

The field of ion mobility mass spectrometry (IM-MS) has developed rapidly in recent decades, with new fundamental advances underpinning innovative applications. This has been particularly noticeable in the field of biomacromolecular structure determination and structural biology, with pioneering studies revealing new structural insight for complex protein assemblies which control biological function. This perspective offers a review of recent developments in IM-MS which have enabled expanding applications in protein structural biology, principally focusing on the quantitative measurement of collision cross sections and their interpretation to describe higher order protein structures.

Fundamental Studies on Poly(2-oxazoline) Side Chain Isomers Using Tandem Mass Spectrometry and Ion Mobility-Mass Spectrometry

When polymer mixtures become increasingly complex, the conventional analysis techniques become insufficient for complete characterization. Mass spectrometric techniques can satisfy this increasing demand for detailed sample characterization. Even though isobaric polymers are indistinguishable using simple mass spectrometry (MS) analyses, more advanced techniques such as tandem MS (MS/MS) or ion mobility (IM) can be used. Here, we report proof of concept for characterizing isomeric polymers, namely poly(2-n-propyl-2-oxazoline) (Pn-PrOx) and poly(2-isopropyl-2-oxazoline) (Pi-PrOx), using MS/MS and IM-MS. Pi-PrOx ions lose in intensity at higher accelerating voltages than Pn-PrOx ions during collision-induced dissociation (CID) MS/MS experiments. A Pn/i-PrOx mixture could also be titrated using survival yield calculations of either precursor ions or cation ejection species. IM-MS yielded shape differences in the degree of polymerization (DP) regions showing the structural rearrangements. Combined MS techniques are thus able to identify and deconvolute the molar mass distributions of the two isomers in a mixture. Finally, the MS/MS and IM-MS behaviors are compared for interpretation. Graphical Abstract .

Influence of size and charge of unstructured polypeptides on pharmacokinetics and biodistribution of targeted fusion proteins

Alternative non-IgG binding proteins developed for therapy are small in size and, thus, are rapidly cleared from the circulation by renal filtration. To avoid repeated injection or continuous infusion for the maintenance of therapeutic serum concentrations, extensions of unfolded polypeptides have been developed to prolong serum half-life, but systematic, comparative studies investigating the influence of their size and charge on serum half-life, extravasation, tumor localization and excretion mechanisms have so far been lacking. Here we used a high-affinity Designed Ankyrin Repeat Protein (DARPin) targeting the tumor marker epithelial cell adhesion molecule (EpCAM) in a preclinical tumor xenograft model in mice, and fused it with a series of defined unstructured polypeptides. We used three different sizes of two previously described polypeptides, an uncharged one consisting of only Pro, Ala and Ser (termed PAS) and a charged one consisting of Pro, Ala, Ser, Thr, Gly, Glu (termed XTEN) and performed for the first time a precise comparative localization, distribution and extravasation study. Pharmacokinetic analysis showed a clear linear relationship between hydrodynamic radius and serum half-life across both polypeptides, reaching a half-life of up to 21 h in mice. Tumor uptake was EpCAM-dependent and directly proportional to half-life and size, showing an even tumor penetration for all fusion proteins without unspecific accumulation in non-target tissue. Unexpectedly, charge had no influence on any parameter, neither tumor nor tissue accumulation nor kidney elimination kinetics. Thus, both polypeptide types have a very similar potential for precise half-life modification and tumor targeting.

Structural similarity, characterization of Poly Ethylene Glycol linkage and identification of product related variants in biosimilar pegfilgrastim

The approval of biosimilars requires demonstration of biosimilarity, which rests on the base of thorough analytical characterization of the biosimilar product. In addition to demonstration of biosimilarity, the product related impurities need to be thoroughly characterized and controlled at minimal levels. Pegylation of peptides and proteins creates significant challenges for detailed structural characterization, such as PEG (Poly Ethylene Glycol) heterogeneity, site of addition and number of attached pegylated moieties. A combination of several methods including circular dichroism, FTIR (Fourier-transform Infrared Spectroscopy), fluorescence spectroscopy, DSC (Differential Scanning Calorimetry), 1D and 2D NMR (Nuclear Magnetic Resonance), Edman degradation and peptide mapping by LC-MS (Liquid Chromatography Mass Spectrometry) were used for characterization of N-terminally pegylated filgrastim. Product related impurities such as oxidized, reduced, deamidated, dipegylated variants and monopegylated positional isomers have been characterized in detail using various HPLC (High Performance Liquid Chromatography) based methods and LC-MS techniques. The functional characterization in terms of receptor binding and cell proliferation assay was conducted for the similarity assessment and the potential impact of the product variants on the in vitro biological activity has also been assessed. In summary, this study presents, for the first time, a detailed structural and molecular level characterization of a biosimilar pegfilgrastim providing a strong base for the demonstration of overall biosimilarity of the product with the innovator product.

Electrospray ionization-ion mobility spectrometry-high resolution tandem mass spectrometry with collision-induced charge stripping for the analysis of highly multiply charged intact polymers

Polymers with large molecular weight are difficult to interpret using electrospray ionization-mass spectrometry (ESI-MS) due to the generation of various highly multiply charged analytes. Although ESI-ion mobility spectrometry (IMS)-MS is effective in reducing the complexity of the mass spectrum, this approach is insufficient for analyzing highly multiply charged polymers. In this study, we propose a method combining tandem mass spectrometry (quadrupole and high-resolution time-of-flight MS, QMS/TOFMS), IMS, and collision-induced charge stripping (CICS) for analyzing large intact polymers (∼40 kDa), which are highly multiply charged. The number of charges can be estimated from a Fourier transform power spectrum of a mass spectrum when the charge number is less than approximately 20. Interpretations of the spectra of poly(ethylene oxide)s (PEOs) weighing 20 kDa, poly(methyl methacrylate)s weighing 22 kDa, and methoxy-PEO-maleimide weighing 40 kDa were successfully demonstrated with isotope level and polymerization degree level separations, respectively. In the proposed method, a mixture can be analyzed for relatively small (a few kDa) and large (a few tens of kDa) polymers simultaneously without any sample pretreatment.

Extracting Charge and Mass Information from Highly Congested Mass Spectra Using Fourier-Domain Harmonics

Native mass spectra of large, polydisperse biomolecules with repeated subunits, such as lipoprotein Nanodiscs, can often be challenging to analyze by conventional methods. The presence of tens of closely spaced, overlapping peaks in these mass spectra can make charge state, total mass, or subunit mass determinations difficult to measure by traditional methods. Recently, we introduced a Fourier Transform-based algorithm that can be used to deconvolve highly congested mass spectra for polydisperse ion populations with repeated subunits and facilitate identification of the charge states, subunit mass, charge-state-specific, and total mass distributions present in the ion population. Here, we extend this method by investigating the advantages of using overtone peaks in the Fourier spectrum, particularly for mass spectra with low signal-to-noise and poor resolution. This method is illustrated for lipoprotein Nanodisc mass spectra acquired on three common platforms, including the first reported native mass spectrum of empty "large" Nanodiscs assembled with MSP1E3D1 and over 300 noncovalently associated lipids. It is shown that overtone peaks contain nearly identical stoichiometry and charge state information to fundamental peaks but can be significantly better resolved, resulting in more reliable reconstruction of charge-state-specific mass spectra and peak width characterization. We further demonstrate how these parameters can be used to improve results from Bayesian spectral fitting algorithms, such as UniDec. Graphical Abstract ᅟ.

Characterization of singly and multiply PEGylated insulin isomers by reversed-phase ultra-performance liquid chromatography interfaced with ion mobility mass spectrometry

Conjugation of poly(ethylene glycol) (PEG) to protein drugs (PEGylation) is increasingly utilized in the biotherapeutics field because it improves significantly the drugs' circulatory half-life, solubility, and shelf-life. The activity of a PEGylated drug depends on the number, size, and location of the attached PEG chain(s). This study introduces a 2D separation approach, including reversed-phase ultra-performance liquid chromatography (RP-UPLC) and ion mobility mass spectrometry (IM-MS), in order to determine the structural properties of the conjugates, as demonstrated for a PEGylated insulin sample that was prepared by random amine PEGylation. The UPLC dimension allowed separation based on polarity. Electrospray ionization (ESI) of the eluates followed by in-source dissociation (ISD) truncated the PEG chains and created insulin fragments that provided site-specific information based on whether they contained a marker at the potential conjugation sites. Separation of the latter fragments by size and charge in the orthogonal IM dimension (pseudo-4D UPLC-ISD-IM-MS approach) enabled clear detection and identification of the positional isomers formed upon PEGylation. The results showed a highly heterogeneous mixture of singly and multiply conjugated isomers plus unconjugated material. PEGylation was observed on all three possible attachment sites (ε-NH₂ of LysB29, A- and B-chain N-termini). Each PEGylation site was validated by analysis of the same product after disulfide bond cleavage, so that the PEGylated A- and B- chain could be individually characterized with the same pseudo-4D UPLC-ISD-IM-MS method.

Multiple Gas-Phase Conformations of a Synthetic Linear Poly(acrylamide) Polymer Observed Using Ion Mobility-Mass Spectrometry

Ion mobility-mass spectrometry (IM-MS) has emerged as a powerful separation and identification tool to characterize synthetic polymer mixtures and topologies (linear, cyclic, star-shaped,…). Electrospray coupled to IM-MS already revealed the coexistence of several charge state-dependent conformations for a single charge state of biomolecules with strong intramolecular interactions, even when limited resolving power IM-MS instruments were used. For synthetic polymers, the sample's polydispersity allows the observation of several chain lengths. A unique collision cross-section (CCS) trend is usually observed when increasing the degree of polymerization (DP) at constant charge state, allowing the deciphering of different polymer topologies. In this paper, we report multiple coexisting CCS trends when increasing the DP at constant charge state for linear poly(acrylamide) PAAm in the gas phase. This is similar to observations on peptides and proteins. Biomolecules show in addition population changes when collisionally heating the ions. In the case of synthetic PAAm, fragmentation occurred before reaching the energy for conformation conversion. These observations, which were made on two different IM-MS instruments (SYNAPT G2 HDMS and high resolution multi-pass cyclic T-Wave prototype from Waters), limit the use of ion mobility for synthetic polymer topology interpretations to polymers where unique CCS values are observed for each DP at constant charge state. Graphical Abstract ᅟ.

A demonstration of analytical similarity comparing a proposed biosimilar pegfilgrastim and reference pegfilgrastim

BACKGROUND

Recombinant human granulocyte-colony stimulating factor (G-CSF, filgrastim) is used primarily to reduce incidence and duration of severe neutropenia and its associated complications in cancer patients that have received a chemotherapy regimen. The pegylated form of filgrastim, "pegfilgrastim", is a long-acting form that requires only a once-per-cycle administration for the management of chemotherapy-induced neutropenia. Apobiologix, a division of ApoPharma USA, Inc., and Intas Pharmaceuticals Limited have co-developed a proposed pegfilgrastim biosimilar to US-licensed pegfilgrastim.

METHODS

The analytical similarity of Apobiologix pegfilgrastim and US-licensed pegfilgrastim with respect to their physicochemical profile was established using a wide range of rigorous orthogonal analytical techniques. Biological function was compared using receptor binding analyses, in vitro proliferation assays, and in vivo hematopoietic progenitor mobilization.

RESULTS

Apobiologix pegfilgrastim and the US-licensed pegfilgrastim reference product were found to be highly similar analytically with respect to molecular mass, primary, secondary and tertiary protein structures, purity, charge, and hydrophobicity. No differences in receptor binding affinity were observed, and all samples demonstrated similar in vitro and in vivo bioactivity.

CONCLUSION

These studies provide robust evidence supporting the structural and functional similarity between Apobiologix pegfilgrastim and the US-licensed reference pegfilgrastim, and hence their biosimilarity.

Multidimensional Mass Spectrometry of Synthetic Polymers and Advanced Materials

Multidimensional mass spectrometry interfaces a suitable ionization technique and mass analysis (MS) with fragmentation by tandem mass spectrometry (MS² ) and an orthogonal online separation method. Separation choices include liquid chromatography (LC) and ion-mobility spectrometry (IMS), in which separation takes place pre-ionization in the solution state or post-ionization in the gas phase, respectively. The MS step provides elemental composition information, while MS² exploits differences in the bond stabilities of a polymer, yielding connectivity and sequence information. LC conditions can be tuned to separate by polarity, end-group functionality, or hydrodynamic volume, whereas IMS adds selectivity by macromolecular shape and architecture. This Minireview discusses how selected combinations of the MS, MS² , LC, and IMS dimensions can be applied, together with the appropriate ionization method, to determine the constituents, structures, end groups, sequences, and architectures of a wide variety of homo- and copolymeric materials, including multicomponent blends, supramolecular assemblies, novel hybrid materials, and large cross-linked or nonionizable polymers.

Top-down mass spectrometry of hybrid materials with hydrophobic peptide and hydrophilic or hydrophobic polymer blocks

A multidimensional mass spectrometry (MS) methodology is introduced for the molecular level characterization of polymer-peptide (or polymer-protein) copolymers that cannot be crystallized or chromatographically purified. It encompasses electrospray ionization (ESI) or matrix-assisted laser desorption ionization (MALDI) coupled with mass analysis, tandem mass spectrometry (MS(2)) and gas-phase separation by ion mobility mass spectrometry (IM-MS). The entire analysis is performed in the mass spectrometer ("top-down" approach) within milliseconds and with high sensitivity, as demonstrated for hybrid materials composed of hydrophobic poly(tert-butyl acrylate) (PtBA) or hydrophilic poly(acrylic acid) (PAA) blocks tethered to the hydrophobic decapeptide VPGVGVPGVG (VG2) via triazole linkages. The composition of the major products can be rapidly surveyed by MALDI-MS and MS(2). For a more comprehensive characterization, the ESI-IM-MS (and MS(2)) combination is more suitable, as it separates the hybrid materials based on their unique charges and shapes from unconjugated polymer and partially hydrolyzed products. Such separation is essential for reducing spectral congestion, deconvoluting overlapping compositions and enabling straightforward structural assignments, both for the hybrid copolymers as well as the polymer and peptide reactants. The IM dimension also permits the measurement of collision cross-sections (CCSs), which reveal molecular architecture. The MS and MS(2) spectra of the mobility separated ions conclusively showed that [PtBA-VG2]m and [PAA-VG2]m chains with the expected compositions and sequences were formed. Single and double copolymer blocks (m = 1-2) could be detected. Further, the CCSs of the hybrids, which were prepared via azide/alkyne cycloadditions, confirmed the formation of macrocyclic structures. The top-down methodology described would be particularly useful for the detection and identification of peptide/protein-polymer conjugates which are increasingly used in biomedical and pharmaceutical applications.

Peptide antagonists of the calcitonin gene-related peptide (CGRP) receptor with improved pharmacokinetics and pharmacodynamics

Antagonism of the calcitonin gene-related peptide (CGRP) receptor may be a useful approach for migraine treatment. Selective PEGylated peptide antagonists to the CGRP receptor are described, derived from CGRP(8-37) with polymer derivatization at an engineered lysine-25 residue. Potent PEGylated peptides with improved pharmacokinetics were identified through peptide side-chain modification to mitigate metabolic liabilities. PEGylated Ac-Trp-[Cit(11,18),hArg(24),Lys(25),Asp(31),Pro(34),1-Nal(35)]CGRP(8-37)-NH2, 9, elicits a dose-dependent reduction of intradermal CGRP-induced local blood flow in rodents with an ED50 of 0.52 mg kg(-1) without any overt adverse effects.

Extension of in vivo half-life of biologically active molecules by XTEN protein polymers

XTEN™ is a class of unstructured hydrophilic, biodegradable protein polymers designed to increase the half-lives of therapeutic peptides and proteins. XTEN polymers and XTEN fusion proteins are typically expressed in Escherichia coli and purified by conventional protein chromatography as monodisperse polypeptides of exact length and sequence. Unstructured XTEN polypeptides have hydrodynamic volumes significantly larger than typical globular proteins of similar mass, thus imparting a bulking effect to the therapeutic payloads attached to them. Since their invention, XTEN polypeptides have been utilized to extend the half-lives of a variety of peptide- and protein-based therapeutics. Multiple clinical and preclinical studies and related drug discovery and development efforts are in progress. This review details the most current understanding of physicochemical properties and biological behavior of XTEN and XTENylated molecules. Additionally, the development path and status of several advanced drug discovery and development efforts are highlighted.

Investigation of falsified documents via direct analyte-probed nanoextraction coupled to nanospray mass spectrometry, fluorescence microscopy, and Raman spectroscopy

Microscopy with direct analyte-probed nanoextraction coupled to nanospray ionization mass spectrometry (DAPNe-NSI-MS) is a direct extraction technique that extracts ultra-trace amounts of analyte.

Characterization of polylactides with different stereoregularity using electrospray ionization ion mobility mass spectrometry

We investigated the effect of stereoregularity on the gas-phase conformations of linear and cyclic polylactides (PLA) using electrospray ionization ion mobility mass spectrometry (ESI-IM-MS) combined with molecular dynamics simulations. IM-MS analysis of PLA ions shows intriguing difference between the collision cross section (ΩD) value of poly-L-lactide (PLLA) and poly-LD-lactide (PLDLA) ions with respect to their chain architecture and stereoregularity. In the singly sodiated linear PLA (l-PLA∙Na(+)) case, both l-PLLA and l-PLDLA up to 11mer have very similar ΩD values, but the ΩD values of l-PLLA are greater than that of l-PLDLA ions for larger ions. In the case of cyclic PLA (c-PLA), c-PLLA∙Na(+) is more compact than c-PLDLA∙Na(+) for short PLA ions. However, c-PLLA exhibits larger ΩD value than c-PLDLA for PLA ions longer than 13mer. The origin of difference in the ΩD values was investigated using theoretical investigation of PLAs in the gas phase. The gas-phase conformation of PLA ions is influenced by Na(+)-oxygen coordination and the weak intramolecular hydrogen bond interaction, which are more effectively formed in more flexible chains. Therefore, the less flexible PLLA has a larger ΩD value than PLDLA. However, for short c-PLA, concomitant maximization of both Na(+)-oxygen coordination and hydrogen bond interaction is difficult due to the constricted chain freedom, which makes the ΩD value of PLAs in this range show a different trend compared with other PLA ions. Our study facilitates the understanding of correlation between stereoregularity of PLAs and their structure, providing potential utility of IM-MS to characterize stereoisomers of polymers.

Electrospray ionization mechanisms for large polyethylene glycol chains studied through tandem ion mobility spectrometry

Ion mobility mass spectrometry (IMS-MS) is used to investigate the abundance pattern, n(z)(m) of poly-(ethyleneglycol) (PEG) electrosprayed from water/methanol as a function of mass and charge state. We examine n(z)(m) patterns from a diversity of solution cations, primarily dimethylammonium and triethylammonium. The ability of PEG chains to initially attach to various cations in the spraying chamber, and to retain them (or not) on entering the MS, provide valuable clues on the ionization mechanism. Single chains form in highly charged and extended shapes in most buffers. But the high initial charge they hold under atmospheric pressure is lost on transit to the vacuum system for large cations. In contrast, aggregates of two or more chains carry in all buffers at most the Rayleigh charge of a water drop of the same volume. This shows either that they form via Dole's charge residue mechanism, or that highly charged and extended aggregates are ripped apart by Coulombic repulsion. IMS-IMS experiments in He confirm these findings, and provide new mechanistic insights on the stability of aggregates. When collisionally activated, initially globular dimers are stable. However, slightly nonglobular dimers projecting out a linear appendix are segregated into two monomeric chains. The breakup of a charged dimer is therefore a multi-step process, similar to the Fenn-Consta polymer extrusion mechanism. The highest activation barrier is associated to the first step, where a short chain segment carrying a single charge escapes (ion-evaporates) from a charged drop, leading then to gradual field extrusion of the whole chain out of the drop.

A direct-infusion- and HPLC-ESI-Orbitrap-MS approach for the characterization of intact PEGylated proteins

The characterization of proteins modified with poly(ethylene glycol) (PEG), such as recombinant human granulocyte-colony stimulating factor (PEGylated rhG-CSF or pegfilgrastim), by electrospray ionization-mass spectrometry (ESI-MS) constitutes a challenge due to the overlapping protein charge state pattern and PEG polydispersity. In order to minimize spectral overlaps, charge reduction by means of the addition of amine was applied. Method development for direct-infusion measurements, carried out on an ESI-time-of-flight (ESI-TOF) instrument, demonstrated the potential of triethylamine (TEA) for shifting the charge state pattern toward lower-charged species and of formic acid (FA) for causing higher charging. After successful method transfer to the LTQ Orbitrap XL instrument, isotopically resolved mass spectra could be acquired. With a median mass accuracy of 1.26 ppm, a number-average monoisotopic molecular mass of 40074.64 Da was determined for pegfilgrastim. The direct comparison of three Orbitrap mass spectrometers, namely the LTQ Orbitrap XL, the Exactive, and the Q Exactive, demonstrated that online interfacing to high performance liquid chromatography (HPLC) was only feasible with the Q Exactive, which offers adequate spectral quality on a time scale compatible with chromatographic separation (i.e., 0.2 min acquisition time per chromatographic peak). Finally, the applicability of both direct-infusion Orbitrap MS and HPLC interfaced to Orbitrap MS was demonstrated for the detection of methionine oxidation in pegfilgrastim. Singly, doubly, and triply oxidized species were readily resolved in the chromatogram, while their oxidation status was easily determined from the mass shifts observed in the deconvoluted mass spectra.

Extension of in vivo half-life of biologically active peptides via chemical conjugation to XTEN protein polymer

XTEN, unstructured biodegradable proteins, have been used to extend the in vivo half-life of genetically fused therapeutic proteins and peptides. To expand the applications of XTEN technology to half-life extension of other classes of molecules, XTEN protein polymers and methods for chemical XTENylation were developed. Two XTEN precursors were engineered to contain enzymatically removable purification tags. The proteins were readily expressed in bacteria and purified to homogeneity by chromatography techniques. As proof-of-principle, GLP2-2G peptide was chemically conjugated to each of the two XTEN protein polymers using maleimide-thiol chemistry. The monodisperse nature of XTEN protein polymer enabled reaction monitoring as well as the detection of peptide modifications in the conjugated state using reverse phase-high performance liquid chromatography (RP-HPLC) and electrospray ionization mass spectrometry. The resulting GLP2-2G-XTEN conjugates were purified by preparative RP-HPLC to homogeneity. In comparison with recombinantly fused GLP2-2G-XTEN, chemically conjugated GLP2-2G-XTEN molecules exhibited comparable in vitro activity, in vitro plasma stability and pharmacokinetics in rats. These data suggest that chemical XTENylation could effectively extend the half-life of a wide spectrum of biologically active molecules, therefore broadening its applicability.

Method for characterization of PEGylated bioproducts in biological matrixes

PEGylation of peptides and proteins has been widely used to enhance stability and reduce immunogenicity of biotherapeutics. Characterizing the degradation of these PEGylated products in biological fluids can yield essential information to support pharmacokinetic evaluations and provide clues about their in vivo properties useful for further molecular optimization. In this paper, we describe a novel and uncomplicated approach to characterize PEGylated peptides or proteins and their related degradation products in biological matrixes. The method involves direct liquid chromatography/mass spectrometry (LC/MS) analysis of animal sera containing low nanograms to low micrograms per milliliter of PEGylated product with or without an acetonitrile precipitation sample treatment. Applying the methodology to analyze the model PEGylated peptides, 20K PEGylated-Pancreatic Polypeptide analogue (PPA) and 20K PEGylated-glucagon, we elucidated the decomposition pathways occurring in animal sera. The data provided direct evidence of cleavages within the peptide backbone. The identified degradation products were unambiguously confirmed by tandem mass spectrometry with high-energy C-trap dissociation (HCD) analysis, followed with in-source fragmentation. Additional spiking studies demonstrated nearly full recovery of PEGylated products, linear detection when the spiked concentration of PEGylated product was ≤1000 ng/mL, and a low ng/mL limit of quantitation (LOQ).

Emerging mass spectrometry-based approaches to probe protein-receptor interactions: focus on overcoming physiological barriers

Physiological barriers, such as the blood-brain barrier and intestinal epithelial barrier, remain significant obstacles towards wider utilization of biopharmaceutical products. Receptor-mediated transcytosis has long been viewed as an attractive means of crossing such barriers, but successful exploitation of this route requires better understanding of the interactions between the receptors and protein-based therapeutics. Detailed characterization of such processes at the molecular level is challenging due to the very large physical size and heterogeneity of these species, which makes use of many state-of-the art analytical techniques, such as high-resolution NMR and X-ray crystallography impractical. Mass spectrometry has emerged in the past decade as a powerful tool to study protein-receptor interactions, although its applications to investigate interaction of biopharmaceuticals with their physiological partners are still limited. We highlight the potential of this technique by considering several recent examples where it had been instrumental for understanding molecular mechanisms critical for receptor-mediated transcytosis of transferrin-based therapeutics.