1.5 Proteinanalytik
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Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly
(2023)
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.
An airborne high repetition rate laser-induced plasma was applied as a versatile ambient ionization source for mass-spectrometric determinations of polar and nonpolar analytes in solution. The laser plasma was sustained between a home-built pneumatic nebulizer and the inlet capillary of an Orbitrap mass spectrometer. To maintain stable conditions in the droplet-rich spray environment, the plasma was directly fed by the fundamental output (λ = 1064 nm) of a current state-of-the-art diode-pumped solid-state laser. Ionization by the laser-driven plasma resulted in signals of intact analyte ions of several chemical categories. The analyte ions were found to be fully desolvated since no further increase in ion signal was observed upon heating of the inlet capillary. Due to the electroneutrality of the plasma, both positive and negative analyte ions could be formed simultaneously without altering the operational parameters of the ion source. While, typically, polar analytes with pronounced gas phase basicities worked best, nonpolar and amphoteric compounds were also detected. The latter were detected with lower ion signals and were prone to a certain degree of fragmentation induced during the ionization process. All the described attests the laser-induced microplasma by a good performance in terms of stability, robustness, sensitivity, and general applicability as a self-contained ion source for the liquid sample introduction.
Synthetic peptide pools are used in antigen-specific T-cell assays, which are an important part in vaccine and immunotherapeutic clinical trials. As the analytical characterization is challenging due to the similarity of the single peptides or is expensive due to isotope labeled standards, usually only a pre-characterization of the single peptides is performed. However, a regular quality control of the peptide mix would be highly desirable. Therefore, a cost-efficient high performance liquid chromatography-high resolution mass spectrometry (HPLC-HRMS) method for quality control of a model peptide pool is developed.
Peptides were synthesized using peptides&elephants proprietary libraries of individual peptides (LIPS) technology and purified by reversed-phase chromatography to > 90% each. The lyophilized single peptides were combined to a model peptide pool and analyzed by reversed-phase high-performance capillary liquid chromatography coupled to an orbitrap mass spectrometer. Separation was performed on a capillary reversed phase column (2 μm, ID x L 300 μm x 150 mm) with a linear gradient of acetonitrile + 0,05% trifluoroacetic acid.
After optimizing the injection mode, the gradient elution, the temperature and the additives a model peptide pool was separated. The extracted ion chromatogram (XIC) was studied to confirm the exact masses.
By combination of capillary HPLC and HRMS a new cost-efficient quality control method could be developed for the separation and identification of complex synthetic peptide pools.
Synthetic peptide pools are used in antigen-specific T-cell assays, which are an important part in vaccine and immunotherapeutic clinical trials. As the analytical characterization is challenging due to the similarity of the single peptides or is expensive due to isotope labeled standards, usually only a pre-characterization of the single peptides is performed. However, a regular quality control of the peptide mix would be highly desirable. Therefore, a cost-efficient high performance liquid chromatography-high resolution mass spectrometry (HPLC-HRMS) method for quality control of a model peptide pool is developed.
Peptides were synthesized using peptides&elephants proprietary libraries of individual peptides (LIPS) technology and purified by reversed-phase chromatography to > 90% each. The lyophilized single peptides were combined to a model peptide pool and analyzed by reversed-phase high-performance capillary liquid chromatography coupled to an orbitrap mass spectrometer. Separation was performed on a capillary reversed phase column (2 μm, ID x L 300 μm x 150 mm) with a linear gradient of acetonitrile + 0,05% trifluoroacetic acid.
For the separation of a model peptide pool the additive, additive concentration, the gradient elution and the temperature were optimized. Different quantification approaches were tested. Identification was performed by high resolution mass spectrometry in which extracted ion chromatograms (XIC) were used to confirm exact masses.
In line with the development of a new cost-efficient quality control method for the separation and identification of complex synthetic peptide pools, varied HPLC parameters highlighted their influence on chromatographic resolution and peptides were identified with high mass accuracy.
Peptide pools consist of short amino acid sequences and have proven to be versatile tools in various research areas in immunology and clinical applications. They are commercially available in many different compositions and variants. However, unlike other reagents that consist of only one or a few compounds, peptide pools are highly complex products which makes their quality control a major challenge. Quantitative peptide analysis usually requires sophisticated methods, in most cases isotope-labeled standards and reference materials. Usually, this would be prohibitively laborious and expensive. Therefore, an approach is needed to provide a practical and feasible method for quality control of peptide pools. With insufficient quality control, the use of such products could lead to incorrect experimental results, worsening the well-known reproducibility crisis in the biomedical sciences. Here we propose the use of ultra-high performance liquid chromatography (UHPLC) with two detectors, a standard UV detector at 214 nm for quantitative analysis and a high-resolution mass spectrometer (HRMS) for identity confirmation. To be cost-efficient and fast, quantification and identification are performed in one chromatographic run. An optimized protocol is shown, and different peak integration methods are compared and discussed. This work was performed using a peptide pool known as CEF advanced, which consists of 32 peptides derived from cytomegalovirus (CMV), Epstein–Barr virus (EBV) and influenza virus, ranging from 8 to 12 amino acids in length.
This study demonstrates the potential of the concurrent assessment of inflammatory activity and ECM degradation by dual-probe molecular MRI in an experimental mouse model of AAA. Based on the combined information from both molecular probes the rupture of AAAs could reliably be predicted, with higher accuracy compared with each probe alone. The combined in vivo quantification of these biomarkers in 1 imaging session may be useful to improve the in vivo characterization of AAAs.
Background:
Molecular-MRI is a promising imaging modality for the assessment of abdominal aortic aneurysms (AAAs). Interleukin-1β (IL-1β) represents a new therapeutic tool for AAA-treatment, since pro-inflammatory cytokines are key-mediators of inflammation. This study investigates the potential of molecular-MRI to evaluate therapeutic effects of an anti-IL-1β-therapy on AAA-formation in a mouse-model.
Methods:
Osmotic-minipumps were implanted in apolipoprotein-deficient-mice (N = 27). One group (Ang-II+01BSUR group, n = 9) was infused with angiotensin-II (Ang-II) for 4 weeks and received an anti-murine IL-1β-antibody (01BSUR) 3 times. One group (Ang-II-group, n = 9) was infused with Ang-II for 4 weeks but received no treatment. Control-group (n = 9) was infused with saline and received no treatment. MR-imaging was performed using an elastin-specific gadolinium-based-probe (0.2 mmol/kg).
Results:
Mice of the Ang-II+01BSUR-group showed a lower aortic-diameter compared to mice of the Ang-II-group and control mice (p < 0.05). Using the elastin-specific-probe, a significant decrease in elastin-destruction was observed in mice of the Ang-II+01BSUR-group. In vivo MR-measurements correlated well with histopathology (y = 0.34x-13.81, R2 = 0.84, p < 0.05), ICP-MS (y = 0.02x+2.39; R2 = 0.81, p < 0.05) and LA-ICP-MS. Immunofluorescence and western-blotting confirmed a reduced IL-1β-expression.
Conclusions:
Molecular-MRI enables the early visualization and quantification of the anti-inflammatory-effects of an IL-1β-inhibitor in a mouse-model of AAAs. Responders and non-responders could be identified early after the initiation of the therapy using molecular-MRI.
Spheriplex multiplexed immunoassays: A practical tool for environmental, food and bioanalysis
(2019)
Clinical, environmental, and food analysis, require efficient and accurate quantitative analysis. Immunoassays take advantage of highly selective and affine binding of an antibody towards an antigen, being easy-to-use and allowing for high sample throughput. However, common immunoassays, e. g. ELISA are not capable of multiplexed analysis, thus limiting possible applications. On the other hand, multi-analyte methods, e.g. liquid chromatographytandem mass spectrometry requires expensive equipment, trained analysts and the time of analysis usually limits sample throughput. This bottleneck can be overcome combining the suspension array technology, where particles are encoded to allow multiplexed detection, with fluorescence immunoassays to create suspension array fluorescence immunoassays (SAFIA).
Polystyrene core/silica shell microparticles serve as platform for SAFIA. While an encoding dye is introduced in the polystyrene core, the silica shell is used for immobilization: For competitive hapten immunoassays small molecules are immobilized on the surface, serving as a competitive binding site for selective antibodies. For quantification of proteins, antibodies can be immobilized on the surface and the sandwich immunoassay format can be employed. All mentioned immunoassays can be executed wash-free and highly parallelized, allowing up to 500 determinations within three hours. In contrast to ELISA, short incubation times, a wash-free mix-and-read procedure and automated flow-cytometric read-out makes SAFIA applicable for even non-trained personal.
SAFIA showed excellent performance in studies on the origin and fate of drug residues in waste water, which is important to assess clearance rates of wastewater treatment plants. Furthermore, SAFIA can be employed in environmental screenings, detecting pollution of natural river waters by tracking anthropogenic marker substances. It was successfully employed in clinical and food analysis applications, e.g. the quantification of the anti-inflammatory drug diclofenac in breast milk or the quantification of caffeine in beverages. Due to multiplexing capacities, SAFIA can significantly improve biotechnological processes, as in the screening of hybridoma cells for selective and efficient antibody production. For small molecule analytes, limits of detection down to 4 ng/L and for proteins below 25 ng/mL (IgG) were observed, which makes SAFIA applicable to all addressed analytical issues. Moreover, in the analysis of real-world samples, SAFIA shows higher accuracy in contrast to ELISA, indicating higher matrix stability and thus higher robustness in analysis.
Functional sequences of precision polymers based on thiolactone/Michael chemistry are identified from a large one-bead one-compound library. Single-bead readout by MALDI-TOF MS/MS identifies sequences that host m-THPC that is a second Generation photo-sensitizer drug. The corresponding Tla/Michael-PEG conjugates make m-THPC available in solution and drug payload as well as drug release kinetics can be fine-tuned by the precision segment.
Zeolitic imidazolate framework (ZIF) hybrid fluorescent nanoparticles and ZIF antibody conjugates have been synthesized, characterized, and employed in lateral-flow immunoassay (LFIA). The bright fluorescence of the conjugates and the possibility to tailor their mobility gives a huge potential for diagnostic assays. An enzyme-linked immunosorbent assay (ELISA) with horseradish peroxidase (HRP) as label, proved the integrity, stability, and dispersibility of the antibody conjugates, LC-MS/MS provided evidence that a covalent link was established between these metal-organic frameworks and lysine residues in IgG antibodies.