Complementary Methods for de Novo Monoclonal Antibody Sequencing to Achieve Complete Sequence Coverage

CZE-MS peptide mapping: To desalt or not to desalt?

BACKGROUND

In "shotgun" approaches involving high-performance liquid chromatography or capillary zone electrophoresis (CZE), matrix removal prior to sample analysis is considered as an indispensable tool. Despite the fact that CZE offers a high tolerance towards salts, most publications reported on the use of desalting. There seems to be no clear consensus on the utilization of desalting in the CZE-MS community, most probably due to the absence of works addressing the comparison of desalted and non-desalted digests. Our aim was to fill this research gap using protein samples of varying complexity in different sample matrices.

RESULTS

First, standard protein digests were analyzed to build the knowledge on the effect of sample clean-up by solid-phase extraction (SPE) pipette tips and the possible stacking phenomena induced by different sample matrices. Desalting led to a somewhat altered peptide profile, the procedure affected mostly the hydrophilic peptides (although not to a devastating extent). Nevertheless, desalting samples allowed remarkable stacking efficiency owing to their low-conductivity sample background, enabling a so-called field-amplified sample stacking phenomenon. Non-desalted samples also produced a stacking event, the mechanism of which is based on transient-isotachophoresis due to the presence of high-mobility ions in the digestion buffer itself. Adding either extra ammonium ions or acetonitrile into the non-desalted digests enhanced the stacking efficiency. A complex sample (yeast cell lysate) was also analyzed with the optimal conditions, which yielded similar tendencies.

SIGNIFICANCE

Based on these results, we propose that sample clean-up in the bottom-up sample preparation process prior to CZE-MS analysis can be omitted. The preclusion of desalting can even enhance detection sensitivity, separation efficiency or sequence coverage.

Recent advances (2019-2021) of capillary electrophoresis-mass spectrometry for multilevel proteomics

Multilevel proteomics aims to delineate proteins at the peptide (bottom-up proteomics), proteoform (top-down proteomics), and protein complex (native proteomics) levels. Capillary electrophoresis-mass spectrometry (CE-MS) can achieve highly efficient separation and highly sensitive detection of complex mixtures of peptides, proteoforms, and even protein complexes because of its substantial technical progress. CE-MS has become a valuable alternative to the routinely used liquid chromatography-mass spectrometry for multilevel proteomics. This review summarizes the most recent (2019-2021) advances of CE-MS for multilevel proteomics regarding technological progress and biological applications. We also provide brief perspectives on CE-MS for multilevel proteomics at the end, highlighting some future directions and potential challenges.

[Antibody proteomics]

Antibodies represent an essential component of humoral immunity; therefore their study is important for molecular biology and medicine. The unique property of antibodies to specifically recognize and bind a certain molecular target (an antigen) determines their widespread application in treatment and diagnostics of diseases, as well as in laboratory and biotechnological practices. High specificity and affinity of antibodies is determined by the presence of primary structure variable regions, which are not encoded in the human genome and are unique for each antibody-producing B cell clone. Hence, there is little or no information about amino acid sequences of the variable regions in the databases. This differs identification of antibody primary structure from most of the proteomic studies because it requires either B cell genome sequencing or de novo amino acid sequencing of the antibody. The present review demonstrates some examples of proteomic and proteogenomic approaches and the methodological arsenal that proteomics can offer for studying antibodies, in particular, for identification of primary structure, evaluation of posttranslational modifications and application of bioinformatics tools for their decoding.

Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly

Monoclonal antibodies are biotechnologically produced proteins with various applications in research, therapeutics and diagnostics. Their ability to recognize and bind to specific molecule structures makes them essential research tools and therapeutic agents. Sequence information of antibodies is helpful for understanding antibody-antigen interactions and ensuring their affinity and specificity. De novo protein sequencing based on mass spectrometry is a valuable method to obtain the amino acid sequence of peptides and proteins without a priori knowledge. In this study, we evaluated six recently developed de novo peptide sequencing algorithms (Novor, pNovo 3, DeepNovo, SMSNet, PointNovo and Casanovo), which were not specifically designed for antibody data. We validated their ability to identify and assemble antibody sequences on three multi-enzymatic data sets. The deep learning-based tools Casanovo and PointNovo showed an increased peptide recall across different enzymes and data sets compared with spectrum-graph-based approaches. We evaluated different error types of de novo peptide sequencing tools and their performance for different numbers of missing cleavage sites, noisy spectra and peptides of various lengths. We achieved a sequence coverage of 97.69-99.53% on the light chains of three different antibody data sets using the de Bruijn assembler ALPS and the predictions from Casanovo. However, low sequence coverage and accuracy on the heavy chains demonstrate that complete de novo protein sequencing remains a challenging issue in proteomics that requires improved de novo error correction, alternative digestion strategies and hybrid approaches such as homology search to achieve high accuracy on long protein sequences.

Applications of capillary electrophoresis for biopharmaceutical product characterization

Capillary electrophoresis (CE), after being introduced several decades ago, has carved out a niche for itself in the field of analytical characterization of biopharmaceutical products. It does not only offer fast separation, high resolution in miniaturized format, but equally importantly represents an orthogonal separation mechanism to high-performance liquid chromatography. Therefore, it is not surprising that CE-based methods can be found in all major pharmacopoeias and are recommended for the analysis of biopharmaceutical products during process development, characterization, quality control, and release testing. Different separation formats of CE, such as capillary gel electrophoresis, capillary isoelectric focusing, and capillary zone electrophoresis are widely used for size and charge heterogeneity characterization as well as purity and stability testing of therapeutic proteins. Hyphenation of CE with MS is emerging as a promising bioanalytical tool to assess the primary structure of therapeutic proteins along with any impurities. In this review, we confer the latest developments in capillary electrophoresis, used for the characterization of critical quality attributes of biopharmaceutical products covering the past 6 years (2015-2021). Monoclonal antibodies, due to their significant share in the market, have been given prioritized coverage.

Characterization of capillary inner surface conditions with streaming potential

Streaming potential is created when an electrolyte solution is forced to flow pass a charged surface. For an uncoated fused silica capillary, the streaming potential is measured between the inlet and outlet vials while applying a pressure across the capillary. The changes in streaming potential can be used to characterize the properties of the capillary inner surface. In this work, HCl, NaCl, and NaOH solutions ranging from 0.4 to 6 mM were used as the background electrolyte (BGE) at temperatures of 15 to 35 °C for the mesurements. The streaming potential decreases with the increase in BGE concentration, and the trend is amplified at higher temperatures. When buffer solutions in the pH range of 1.5 to 12.7 were used as the BGE, streaming potential was shown to be sensitive to changes in pH but reaches a maximum at around 9.5. At pH < 3.3, no streaming potentials were observed. The pH of zero surface charge (streaming potential equals 0) changes with temperature, and is measured to be 3.3 to 3.1 when the temperature is changed from 15 to 35°C. Zeta potentials can be calculated from the measured streaming potential, conductivity, and the solution viscosity. Surface charge densities were calculated in this work using the zeta potentials obtained. We demonstrated that capillary surface conditions can significantly change the streaming potential, and with three different solutions, we showed that analyte-dependent adsorption can be monitored and mitigated to improve the peak symmetry and migration times reproducibility.

Investigating native capillary zone electrophoresis-mass spectrometry on a high-end quadrupole-time-of-flight mass spectrometer for the characterization of monoclonal antibodies

Native capillary zone electrophoresis-mass spectrometry (CZE-MS) has attracted attentions for the characterization of monoclonal antibodies (mAbs) due to the potential of CZE for highly efficient separations of mAbs under native conditions as well as its compatibility with native electrospray ionization (ESI)-MS. However, the low sample loading capacity and limited separation resolution of native CZE for large proteins and protein complexes (e.g. mAbs) impede the widespread adoption of native CZE-MS. Here, we present a novel native capillary isoelectric focusing (cIEF)-assisted CZE-MS method for the characterization of mAbs with much larger sample loading capacity and significantly better separation resolution than native CZE-MS alone. The native cIEF-assisted CZE-MS employed separation capillaries with a new carbohydrate-based neutral coating, a commercilized electrokinetically pumped sheathflow CE-MS interface, and a high-end quadrupole-time-of-flight (Q-TOF) mass spectrometer. Using the method, we documented the separations of different proteoforms of the SigmaMAb and the detection of its various glyco-proteoforms and homodimer. The native cIEF-assisted CZE-MS separated the NIST mAb into three peaks with a submicroliter sample loading volume, corresponding to its different proteoforms. We observed that both the NIST mAb and its homodimer had eight glyco-proteoforms, four of which had low abundance. The results demonstrate the potential of our native cIEF-assisted CZE-MS method for advancing the characterization of large proteins and protein complexes under native conditions.