Multidimensional LC-MS with 1D multi-method option and parallel middle-up and bottom-up MS acquisition for in-depth characterization of antibodies.

Monoclonal antibodies (mAbs) are large and highly heterogeneous species typically characterized using a plethora of analytical methodologies. There is a trend within the biopharmaceutical industry to combine several of these methods in one analytical platform to simultaneously assess multiple structural attributes. Here, a protein analyzer for the fully automated middle-up and bottom-up liquid chromatography-mass spectrometry (LC-MS) analysis of charge, size and hydrophobic variants is described. The multidimensional set-up combines a multi-method option in the first dimension (1D) (choice between size exclusion - SEC, cation exchange - CEX or hydrophobic interaction chromatography - HIC) with second dimension (2D) on-column reversed-phase (RPLC) based desalting, denaturation and reduction prior to middle-up LC-MS analysis of collected 1D peaks and parallel on-column trypsin digestion of denatured and reduced peaks in the third dimension (3D) followed by bottom-up LC-MS analysis in the fourth dimension (4D). The versatile and comprehensive workflow is applied to the characterization of charge, hydrophobic and size heterogeneities associated with an engineered Fc fragment and is complemented with hydrogen-deuterium exchange (HDX) MS and FcRn affinity chromatography - native MS to explain observations in a structural/functional context.

Evaluation of size-exclusion chromatography, multi-angle light scattering detection and mass photometry for the characterization of mRNA.

The recent approval of messenger ribonucleic acid (mRNA) as vaccine to combat the COVID-19 pandemic has been a scientific turning point. Today, the applicability of mRNA is being demonstrated beyond infectious diseases, for example in cancer immunotherapy, protein replacement therapy and gene editing. mRNA is produced by in vitro transcription (IVT) from a linear DNA template and modified at the 3' and 5' ends to improve translational efficiency and stability. Co-existing impurities such as RNA fragments and double-stranded RNA (dsRNA), amongst others, can drastically impact mRNA quality and efficacy. In this study, size-exclusion chromatography (SEC) is evaluated for the characterization of IVT-mRNA. The effect of mobile phase composition (ionic strength and organic modifier), pH, column temperature and pore size (300 Å, 1000 Å, and 2000 Å) on the separation performance and structural integrity of IVT-mRNA varying in size is described. Non-replicating, self-amplifying (saRNA), temperature degraded, and ribonuclease (RNase) digested mRNA, the latter to characterize the 3' poly(A) tail, were included in the study. Beyond ultraviolet (UV) detection, refractive index (RI) and multi-angle light scattering (MALS) detection were implemented to accurately determine molecular weight (MW) of mRNA. Finally, mass photometry is introduced as a complementary methodology to study mRNA under native conditions.

Characterization of mAb size heterogeneity originating from a cysteine to tyrosine substitution using denaturing and native LC-MS.

Upon assessing the comparability between a biosimilar mAb and its reference product by non-reducing CE-SDS, increased levels of a heavy-heavy-light chain (HHL) variant, present as a low molecular weight (LMW) peak, were observed. RPLC-MS applied at top, middle-up and bottom-up level revealed the existence of Cys-to-Tyr substitutions, predominantly at position HC226 involved in connecting LC and HC, explaining the abundant HHL levels. Antigen binding was not impacted by the presence of this size variant suggesting a non-covalent association of Tyr substituted HHL and LC. The latter complex is not maintained in the denaturing conditions associated with CE-SDS and RPLC-MS. Its existence could, nevertheless, be confirmed by native SEC-MS which preserves non-covalent protein interactions during separation and electrospray ionization. Amino acid analysis furthermore demonstrated a depletion of Cys during the fed-batch process indicating that the observed size/sequence variant is not of genetic but rather of metabolic origin. Native SEC-MS showed that supplementing the cell culture medium with Cys halts misincorporation of Tyr and promotes the formation of the desired mAb structure. To the best of our knowledge, Cys-to-Tyr substitutions preventing interchain disulfide bridge formation have not been described earlier. This observation adds to the impressive structural heterogeneity reported to date for mAbs.

3D-LC-MS with 2D Multimethod Option for Fully Automated Assessment of Multiple Attributes of Monoclonal Antibodies Directly from Cell Culture Supernatants.

Fully automated analysis of multiple structural attributes of monoclonal antibodies (mAbs) using three-dimensional liquid chromatography-mass spectrometry (3D-LC-MS) is described. The analyzer combines Protein A affinity chromatography in the first dimension (1D) with a multimethod option in the second dimension (2D) (choice between size exclusion (SEC), cation exchange (CEX), and hydrophobic interaction chromatography (HIC)) and desalting SEC-MS in the third dimension (3D). This innovative 3D-LC-MS setup allows simultaneous and sequential assessment of mAb titer, size/charge/hydrophobic variants, molecular weight (MW), amino acid (AA) sequence, and post-translational modifications (PTMs) directly from cell culture supernatants. The reported methodology that finds multiple uses throughout the biopharmaceutical development trajectory was successfully challenged by the analysis of different trastuzumab and tocilizumab samples originating from biosimilar development programs.

Monoclonal antibody charge variant characterization by fully automated four-dimensional liquid chromatography-mass spectrometry.

Fully automated characterization of monoclonal antibody (mAb) charge variants using four-dimensional liquid chromatography-mass spectrometry (4D-LC-MS) is reported and illustrated. Charge variants resolved by cation-exchange chromatography (CEX) using a salt- or pH-gradient are collected in loops installed on a multiple heart-cutting valve and consequently subjected to online desalting, denaturation, reduction and trypsin digestion prior to LC-MS based peptide mapping. This innovation which substantially reduces turnaround time, sample manipulation, loss and artefacts and increases information gathering, is described in great technical detail, and applied to characterize the charge heterogeneity associated with three therapeutic mAbs. Sequence coverages > 95% are obtained for major and minor charge variants (> 1.0%). Post-translational modifications (PTMs) and modification sites are readily revealed in a repeatable manner including unstable succinimide intermediates which are not maintained when performing classical in-solution overnight digestion of offline collected CEX peaks.

Untargeted flavor profiling of lager beers by stir bar sorptive extraction -capillary gas chromatography - time-of-flight mass spectrometry: High analytical performance with a green touch.

Beer is one of the most popular beverages in the world and its complex flavor is widely appreciated. Beer flavor profiling is important for brewers to optimize beer production and to guarantee odor quality and taste stability of the final products. This is especially the case for pale lager beers that represent the beer type with the largest worldwide production volume. In this study, the combination of stir bar sorptive extraction (SBSE) with capillary gas chromatography (GC) hyphenated to time-of-flight mass spectrometry (TOFMS) was used to perform a detailed aroma profiling of lager beer samples originating from Belgium, The Netherlands, and France. A generic SBSE method was applied resulting in a very broad extraction coverage of odor solutes, while the extraction process is miniaturized, unattended and solventless, meeting green analytical chemistry requirements. Using GC-TOFMS analysis operated in untargeted mode, MS deconvolution and statistical data analysis, with principal component and hierarchical clustering analysis, it was possible to clearly differentiate brands and origins of the beer samples and to identify marker compounds for flavor profiling of these closely related beer samples. An extended database of beer aroma compounds was created. The developed method can be applied in beer quality optimization and quality control in routine laboratories.

Middle-up characterization of monoclonal antibodies by online reduction liquid chromatography-mass spectrometry.

This study describes the fully automated middle-up characterization of monoclonal antibodies (mAbs) and next-generation variants by online reduction liquid chromatography-mass spectrometry (LC-MS). Proteins were trapped on-column and subjected to online desalting, denaturation and reduction prior to reversed phase elution of the created subunits in the MS. The evaluation of more than 20 different therapeutic proteins including full length mAbs (subclasses IgG1, IgG2 and IgG4), bispecific antibodies, antibody fragments, fusion proteins and antibody-drug conjugates (ADC) revealed that the online reduction method is as powerful as the widely applied offline sample preparation with dithiothreitol (DTT) as reducing agent and guanidine hydrochloride (Gnd.HCl) as denaturant and tackles some major disadvantages associated with the latter method, i.e. corrosion of stainless steel components, adduct formation impacting spectral quality and sample stability. The value of the online reduction LC-MS method is also enforced by its ability to reveal unstable antibody variants such as succinimide intermediates of asparagine deamidation and aspartic acid isomerization which are often lost when using the offline sample preparation method. The performance of the online reduction LC-MS set-up was verified and it was revealed that the method is precise with RSD values below 0.25% and 3.0% for retention time and area, respectively. Carry-over is within acceptable limits (< 0.5%) and the reducing buffer is stable up to 24 hours.

Fractionated stir bar sorptive extraction using conventional and solvent-assisted approaches for enhanced identification capabilities of aroma compounds in beverages.

For successful profiling of aroma carriers in food samples, a highly efficient extraction method is mandatory. A two-step stir bar sorptive extraction (SBSE) approach, namely fractionated SBSE (Fr-SBSE), was developed to improve both the organoleptic and the chemical identification of aroma compounds in beverages. Fr-SBSE consists of two multi-SBSE procedures (mSBSE) performed sequentially on the same sample. The first extraction consists of a conventional mSBSE using three polydimethylsiloxane (PDMS) stir bars (1stmSBSE). This is followed by a solvent-assisted mSBSE performed on the same sample using three solvent-swollen PDMS stir bars (2nd SA-mSBSE). The 1stmSBSE mainly extracts apolar/medium polar solutes with log Kow values >2, while the 2nd SA-mSBSE mainly extracts polar solutes with log Kow values <2. After this two-step fractionation procedure, either thermal desorption (TD) or liquid desorption - large volume injection (LD-LVI), followed by GC-MS is performed on each set of three stir bars. A real-life sample of roasted green tea was used for method development. The performance of the Fr-SBSE method is further illustrated with sensory evaluations and GC-MS analysis for a stout beer sample. Compared to an extraction procedure with SA-mSBSE only, Fr-SBSE including a 1stmSBSE and a 2nd SA-mSBSE reduced co-elution of aroma compounds in the chromatograms and was capable of providing improved mass spectral quality for identification of 17 additional compounds in roasted green tea, and 12 additional compounds in stout beer, respectively. Moreover, odor description and characterization were clearly improved.

Recent Developments of Stir Bar Sorptive Extraction for Food Applications: Extension to Polar Solutes.

Stir bar sorptive extraction (SBSE) is a miniaturized and solvent-less sample preparation method for extraction and concentration of organic compounds from aqueous samples. The method is based on sorptive extraction, whereby the solutes are extracted into a polymer, such as polydimethylsiloxane (PDMS), coated on a stir bar. Using an apolar PDMS coating, SBSE provides high recoveries for apolar solutes; however, SBSE recoveries for polar solutes are low. Although several more polar coatings for SBSE were developed, these extraction phases are mostly not compatible with thermal desorption (TD) and/or have inferior performance characteristics related to robustness, bleeding, stability, etc. compared to PDMS. In this perspective, two recently introduced SBSE approaches are described that can be used to extend the applicability of a PDMS coating to more polar solutes: (1) SBSE with freeze concentration [ice concentration linked with extractive stirrer (ICECLES)], which is based on the concentration of analytes by gradually reducing the phase ratio (sample/extraction phase), and (2) SBSE using a solvent-swollen PDMS [solvent-assisted SBSE (SA-SBSE)], which is based on a combination of polarity modification and volume increase by PDMS phase swelling using certain types of solvents while maintaining the original characteristics of the PDMS phase.

The versatility of heart-cutting and comprehensive two-dimensional liquid chromatography in monoclonal antibody clone selection.

In recent years, two-dimensional liquid chromatography (2D-LC) has seen an enormous evolution and one of the fields where it is being widely adopted is in the analysis of therapeutic monoclonal antibodies (mAbs). We here further add to the many flavours of this powerful technology. Workflows based on heart-cutting (LC-LC) and comprehensive (LC×LC) 2D-LC are described that allow to guide the clone selection process in mAb and biosimilar development. Combining Protein A affinity chromatography in the first dimension with size exclusion (SEC), cation exchange (CEX) or reversed-phase liquid chromatography-mass spectrometry (RPLC-MS) in the second dimension simultaneously allows to assess mAb titer and critical structural aspects such as aggregation, fragmentation, charge heterogeneity, molecular weight (MW), amino acid sequence and glycosylation. Complementing the LC-LC measurements at intact protein level with LC×LC based peptide mapping provides the necessary information to make clear decisions on which clones to take further into development.

Determination of pesticides in fatty matrices using gel permeation clean-up followed by GC-MS/MS and LC-MS/MS analysis: A comparison of low- and high-pressure gel permeation columns.

Two low-pressure columns (Bio-Beads SX-3) and three high-pressure GPC columns were compared for clean-up of a wide range of pesticides in fatty matrices of vegetable or animal origin. The GPC fractions were analyzed by GC-MS/MS and LC-MS/MS without additional clean-up. The performance of the GPC clean-up on the five column types was compared in terms of solvent consumption, lipid removal, pesticide recovery and repeatability. It was found that for fatty matrices, mainly consisting of high molecular weight triglycerides i.e. most vegetable oils and animal fats, good fractionation is obtained for the majority of the pesticides. On the other hand, for fats and oils containing relatively high amounts of low molecular weight triglycerides, i.e. butter fat and palm kernel oil, none of the columns provided sufficient clean-up and cause interferences and system contamination, especially in the case of GC-MS/MS analysis. For the latter case, best results in terms of lipid removal and pesticide recovery were obtained on a set (2×300mmlength) of narrow bore (7.5mm ID) columns packed with 5µm PL Gel material. Column loadability is, however, much lower on that set of columns compared the other evaluated GPC columns, impairing overall method sensitivity.

Enantioselective comprehensive two-dimensional gas chromatography of lavender essential oil.

The enantiomeric composition of several chiral markers in lavender essential oil was studied by flow modulated comprehensive two-dimensional gas chromatography operated in the reverse flow mode and hyphenated to flame ionization and quadrupole mass spectrometric detection. Two capillary column series were used in this study, 2,3-di-O-ethyl-6-O-tert-butyldimethylsilyl-ß-cyclodextrin or 2,3,6-tri-O-methyl-ß-cyclodextrin, as the chiral column in the first dimension and α polyethylene glycol column in the second dimension. Combining the chromatographic data obtained on these column series, the enantiomeric and excess ratios for α-pinene, ß-pinene, camphor, lavandulol, borneol, and terpinen-4-ol were determined. This maybe a possible route to assess the authenticity of lavender essential oil.

Comparison of the performance of forward fill/flush and reverse fill/flush flow modulation in comprehensive two-dimensional gas chromatography.

The performances of forward flow fill and flush (FFF) and of reverse flow fill and flush (RFF) in flow modulated comprehensive two-dimensional gas chromatography (GC×GC) using the same volume of the sampling channel have been studied and compared. Sample models include a reference mixture of hydrocarbons at low concentration, a petroleum reformate product and the essential oil of Rosa damascena Miller. The latter samples contain solutes in different concentrations but some up to 30% allowing to study overloading phenomena in detail. For solutes injected at low quantity, the performance of FFF and RFF is similar. For solutes present in a sample at high quantity, RFF guarantees less broadening and spreading resulting in better quantitation.

Solvent-assisted stir bar sorptive extraction by using swollen polydimethylsiloxane for enhanced recovery of polar solutes in aqueous samples: Application to aroma compounds in beer and pesticides in wine.

A novel solvent-assisted stir bar sorptive extraction (SA-SBSE) technique was developed for enhanced recovery of polar solutes in aqueous samples. A conventional PDMS stir bar was swollen in several solvents with log Kow ranging from 1.0 to 3.5 while stirring for 30min prior to extraction. After extraction, thermal desorption - gas chromatography - (tandem) mass spectrometry (TD-GC-(MS/)MS) or liquid desorption - large volume injection (LD-LVI)-GC-MS were performed. An initial study involved investigation of potential solvents for SA-SBSE by weighing of the residual solvent in the swollen PDMS stir bar before and after extraction. Compared to conventional SBSE, SA-SBSE using diethyl ether, methyl isobutyl ketone, dichloromethane, diisopropyl ether and toluene provided higher recoveries from water samples for test solutes with log Kow<2.5. For SA-SBSE using dichloromethane, recoveries were improved by factors of 1.4-4.1, while maintaining or even improving the recoveries for test solutes with log Kow>2.5. The performance of the SA-SBSE method using dichloromethane, diisopropyl ether, and cyclohexane is illustrated with analyses of aroma compounds in beer and of pesticides in wine.

Multiple heart-cutting and comprehensive two-dimensional liquid chromatography hyphenated to mass spectrometry for the characterization of the antibody-drug conjugate ado-trastuzumab emtansine.

Antibody-drug conjugates might be the magic bullets referred to by Paul Ehrlich over 100 years ago. Together with a huge therapeutic potential, these molecules come with a structural complexity that drives state-of-the-art chromatography and mass spectrometry to its limits. The use of multiple heart-cutting (mLC-LC) and comprehensive (LC×LC) multidimensional LC in combination with high resolution mass spectrometry for the characterization of the lysine conjugated antibody-drug conjugate ado-trastuzumab emtansine, commercialized as Kadcyla, is presented. By combining protein and peptide measurements, attributes such as drug loading, drug distribution and drug conjugation sites can be assessed in an elegant manner.

Lipidomics of tobacco leaf and cigarette smoke.

Detailed lipidomics experiments were performed on the extracts of cured tobacco leaf and of cigarette smoke condensate (CSC) using high-resolution liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (LC-Q-TOF MS). Following automated solid-phase extraction (SPE) fractionation of the lipid extracts, over 350 lipids could be annotated. From a large-scale study on 22 different leaf samples, it was determined that differentiation based on curing type was possible for both the tobacco leaf and the CSC extracts. Lipids responsible for the classification were identified and the findings were correlated to proteomics data acquired from the same tobacco leaf samples. Prediction models were constructed based on the lipid profiles observed in the 22 leaf samples and successfully allowed for curing type classification of new tobacco leaves. A comparison of the leaf and CSC data provided insight into the lipidome changes that occur during the smoking process. It was determined that lipids which survive the smoking process retain the same curing type trends in both the tobacco leaf and CSC data.

Analysis of the reaction products from micro-vial pyrolysis of the mixture glucose/proline and of a tobacco leaf extract:Search for Amadori intermediates.

Micro-vial pyrolysis (PyroVial) was used to study the production of compounds important for the aroma of heat-treated natural products such as tobacco. Firstly, a mixture of glucose and proline was pyrolyzed as model, as this sugar and amino acid are also abundant in tobacco leaf (Nicotiana tobacum L.). The pyrolysate was analyzed using headspace-GC­MS, liquid injection GC­MS and LC­MS. Next, micro-vial pyrolysis in combination with LC­MS was applied to tobacco leaf extract. Using MS deconvolution, molecular feature extraction and differential analysis it was possible to identify Amadori intermediates of the Maillard reaction in the tobacco leaf extract. The intermediate disappeared as was the case for 1-deoxy-1-prolino-ß-d-fructose or the concentration decreased in the pyrolysate compared to the original extract such as for the 1-deoxy-1-[2-(3-pyridyl)-1-pyrrolidinyl]-ß-d-fructose isomers indicating that Amadori intermediates are important precursors for aroma compound formation.

Enantioselective comprehensive two-dimensional gas chromatography. A route to elucidate the authenticity and origin of Rosa damascena Miller essential oils.

The analysis of Bulgarian and Turkish Rosa damascena Miller essential oils was performed by flow-modulated comprehensive two-dimensional gas chromatography using simultaneous detection of the second column effluent by flame ionization and quadrupole mass spectrometric detection. Enantioselective separations were obtained by running the samples on 2,3-di-O-ethyl-6-O-tert-butyldimethylsilyl-ß-cyclodextrin column as the first column and on polyethylene glycol as the second column. The determination of enantiomeric or diastereomeric excess of some terpenoic solutes is a possible route for quality or authenticity control as well as for the elucidation of the country of origin.