Application of sample displacement batch chromatography for fractionation of proteoforms.

Fractionation of proteoforms is currently the most challenging topic in the field of proteoform analysis. The need for considering the existence of proteoforms in experimental approaches is not only important in Life Science research in general but especially in the manufacturing of therapeutic proteins (TPs) like recombinant therapeutic antibodies (mAbs). Some of the proteoforms of TPs have significantly decreased actions or even cause side effects. The identification and removal of proteoforms differing from the main species, having the desired action, is challenging because the difference in the composition of atoms is often very small and their concentration in comparison to the main proteoform can be low. In this study, we demonstrate that sample displacement batch chromatography (SDBC) is an easy-to-handle, economical, and efficient method for fractionating proteoforms. As a model sample a commercial ovalbumin fraction was used, containing many ovalbumin proteoforms. The most promising parameters for the SDBC were determined by a screening approach and applied for a 10-segment fractionation of ovalbumin with cation exchange chromatography resins. Mass spectrometry of intact proteoforms was used for characterizing the SDBC fractionation process. By SDBC, a significant separation of different proteoforms was obtained.

Analysis and experimental demonstration of temperature step gradients in preparative liquid chromatography.

The amount of substance adsorbed on solid surface depends on temperature. Therefore, the migration velocities of the solutes in a chromatographic column can be altered by introducing temperature gradients. Such gradients designed to change retention behaviours can be exploited to improve the separation performances in preparative chromatography. To describe key process features, we used analytical solutions of the equilibrium model with instant stepwise shift of temperature. To achieve a more realistic description, the equilibrium dispersion model was additionally applied to treat finite column efficiencies. The effect of temperature gradients was illustrated experimentally using two identical columns sequentially connected. Temperature of the second column was modulated by thermostats. Wide pulse injections of a single component led to instructive elution profiles in a preliminary investigation. The observations were found to be in qualitative agreement with predictions of the equilibrium dispersion model. Subsequently, the separation of a ternary model mixture was investigated considering a simple two-step temperature gradient. To support the quantitative analysis and to identify suitable switching and cycle times, the temperature dependencies of the Henry constants were determined by short pulse injections. A meaningful variation of the parameters of the temperature gradient is required for adjusting the cycle times, which is the time difference between two consecutive injections that needs to shorten. Decreasing this time is connected with a desirable increase in process productivity. The results achieved revealed that relatively simple to implement stepwise temperature gradients offer an option to improve and fine-tune the performance of repetitive batch chromatography.

Optimization of Single-Column Batch and Multicolumn Continuous Protein A Chromatography and Performance Comparison Based on Mechanistic Model.

Expensive Protein A chromatography resins drive the need to maximize process productivity as well as resin capacity utilization. To this end, two strategies are explored. The first one is termed "super-batch," which utilizes a single short-bed-height column with rapid cycling to increase productivity, combined with variable load flow rates to enhance resin capacity utilization. The second one is multicolumn continuous chromatography, which utilizes multiple columns in the load zone to achieve high resin capacity utilization. The general rate model is used to simulate and optimize single-column super-batch and multicolumn continuous chromatography. Compared to conventional long-bed-height chromatography, both strategies yield productivity enhancements of 2.5-fold at 1, threefold at 5, and fourfold at 15 g L-1 of feed titer. Using the mechanistic model, the performances of conventional batch, single-column super-batch, and multicolumn continuous Protein A chromatography are investigated at a 2000 L scale considering perfusion and fed-batch cell culture processes. Multicolumn continuous chromatography achieves resin capacity utilization >90%, 16% higher than that of the super-batch process for a 15 g L-1 cell culture process, and it does not show any meaningful performance improvement compared to the single-column super-batch process in a low-titer perfusion cell culture process.

Batch chromatography with recycle lag. I-Concept and design.

This is the first of a two-part study in which we explore the concept of batch chromatography with recycle lag, concluding with the design, construction, and experimental validation of a prototype that embodies the physical realization of this concept. Moreover, the apparatus is simple to set up in particular in view of large-scale applications. Here the theory behind batch chromatography with recycle lag is revisited and extended, with emphasis on the mathematical formulation and procedure for deriving the single-column batch analogue of any variant of multicolumn simulated countercurrent chromatography. By resorting to selected examples, namely GE Healthcare Bio-science's three-column periodic countercurrent chromatography, Novasep's sequential multicolumn chromatography, and a few hypothetical multicolumn processes, we discuss how the theory can be operationalized. Finally, we conclude by describing the design of a device or apparatus-an eluate recycling device (ERD)-to physically realize the proposed concept. The ERD implements an approximate "first in, first out" method for organizing and manipulating the to-be-recycled fractions of eluate collected from the chromatography column, where the oldest (first) amount fluid, or 'head' of the fraction, is the first to exit and be recycled to the column.

Batch chromatography with recycle lag. II-Physical realization and experimental validation.

This is the second of a two-part study in which we explore the concept of batch chromatography with recycle lag, concluding with the design, construction, and experimental validation of a prototype-an eluate recycling device (ERD)-that embodies the physical realization of this concept. The ERD implements an approximate "first in, first out" method of organizing and manipulating the to-be-recycled fractions of eluate collected from the chromatography column, where the oldest (first) amount fluid, or 'head' of the fraction, is the first to exit and be recycled back to the column. Moreover, the apparatus is simple to set up in particular in view of large-scale applications. Here we detail the construction of the ERD and assembly of a setup to interconnect the ERD and a chromatography column. Through the coordinated operation of two-way valves and two-position six-port switching valves it is possible to implement a diverse set of configurations or operating modes interconnecting the chromatography column and the ERD. The setup is validated experimentally with success using the separation of a nucleoside mixture by reversed phase chromatography as a model problem. It is also shown that by redesigning the fluid distributor using 3D printing technology the ERD performance can be improved.

Preparation of eicosapentaenoic acid ethyl ester from fish oil ethyl esters by continuous batch chromatography.

Fish oils are rich in eicosapentaenoic acid, which has the wide-ranging biological activities. The rapid and efficient separation of eicosapentaenoic acid ethyl ester from fish oils ethyl ester is still regarded as a challenge. In this study, we described an effective and flexible chromatography for eicosapentaenoic acid ethyl ester preparation, named continuous batch chromatography, which combined the batch chromatography with the continuous chromatographic operation mode. After continuous batch chromatography experiment, the recovery of eicosapentaenoic acid ethyl ester was 82.01%, the average relative purity and the relative highest purity of eicosapentaenoic acid ethyl ester were 97.82 and 98.98%. The productivity of continuous batch chromatography was 5.48 times higher than that of batch chromatography, while the solvent consumption of eicosapentaenoic acid ethyl ester was 78% of the batch chromatography. This study provided a reference for the separation of the targeted chemical component from multi-component mixtures.

Protein identification from the parotoid macrogland secretion of Duttaphrynus melanostictus.

BACKGROUND: Bufonid parotoid macrogland secretion contains several low molecular mass molecules, such as alkaloids and steroids. Nevertheless, its protein content is poorly understood. Herein, we applied a sample preparation methodology that allows the analysis of viscous matrices in order to examine its proteins. METHODS: Duttaphrynus melanostictus parotoid macrogland secretion was submitted to ion-exchange batch sample preparation, yielding two fractions: salt-displaced fraction and acid-displaced fraction. Each sample was then fractionated by anionic-exchange chromatography, followed by in-solution proteomic analysis. RESULTS: Forty-two proteins could be identified, such as acyl-CoA-binding protein, alcohol dehydrogenase, calmodulin, galectin and histone. Moreover, de novo analyses yielded 153 peptides, whereas BLAST analyses corroborated some of the proteomic-identified proteins. Furthermore, the de novo peptide analyses indicate the presence of proteins related to apoptosis, cellular structure, catalysis and transport processes. CONCLUSIONS: Proper sample preparation allowed the proteomic and de novo identification of different proteins in the D. melanostictus parotoid macrogland secretion. These results may increase the knowledge about the universe of molecules that compose amphibian skin secretion, as well as to understand their biological/physiological role in the granular gland.

Protein identification from the parotoid macrogland secretion of Duttaphrynus melanostictus

Bufonid parotoid macrogland secretion contains several low molecular mass molecules, such as alkaloids and steroids. Nevertheless, its protein content is poorly understood. Herein, we applied a sample preparation methodology that allows the analysis of viscous matrices in order to examine its proteins. Methods: Duttaphrynus melanostictus parotoid macrogland secretion was submitted to ion-exchange batch sample preparation, yielding two fractions: salt-displaced fraction and acid-displaced fraction. Each sample was then fractionated by anionic-exchange chromatography, followed by in-solution proteomic analysis. Results: Forty-two proteins could be identified, such as acyl-CoA-binding protein, alcohol dehydrogenase, calmodulin, galectin and histone. Moreover, de novo analyses yielded 153 peptides, whereas BLAST analyses corroborated some of the proteomic-identified proteins. Furthermore, the de novo peptide analyses indicate the presence of proteins related to apoptosis, cellular structure, catalysis and transport processes. Conclusions: Proper sample preparation allowed the proteomic and de novo identification of different proteins in the D. melanostictus parotoid macrogland secretion. These results may increase the knowledge about the universe of molecules that compose amphibian skin secretion, as well as to understand their biological/physiological role in the granular gland.(AU)

Protein identification from the parotoid macrogland secretion of Duttaphrynus melanostictus

Background: Bufonid parotoid macrogland secretion contains several low molecular mass molecules, such as alkaloids and steroids. Nevertheless, its protein content is poorly understood. Herein, we applied a sample preparation methodology that allows the analysis of viscous matrices in order to examine its proteins. Methods: Duttaphrynus melanostictus parotoid macrogland secretion was submitted to ion-exchange batch sample preparation, yielding two fractions: salt-displaced fraction and acid-displaced fraction. Each sample was then fractionated by anionic-exchange chromatography, followed by in-solution proteomic analysis. Results: Forty-two proteins could be identified, such as acyl-CoA-binding protein, alcohol dehydrogenase, calmodulin, galectin and histone. Moreover, de novo analyses yielded 153 peptides, whereas BLAST analyses corroborated some of the proteomic-identified proteins. Furthermore, the de novo peptide analyses indicate the presence of proteins related to apoptosis, cellular structure, catalysis and transport processes. Conclusions: Proper sample preparation allowed the proteomic and de novo identification of different proteins in the D. melanostictus parotoid macrogland secretion. These results may increase the knowledge about the universe of molecules that compose amphibian skin secretion, as well as to understand their biological/physiological role in the granular gland.

Biochemical Analyses of Proteins from Duttaphrynus melanostictus (Bufo melanostictus) Skin Secretion: Soluble Protein Retrieval from a Viscous Matrix by Ion-Exchange Batch Sample Preparation.

A crucial step in scientific analysis can be sample preparation, and its importance increases in the same rate as the sensitivity of the following employed/desired analytical technique does. The need to analyze complex, viscous matrices is not new, and diverse approaches have been employed, with different success rates depending on the intended molecules. Solid-phase extraction, for example, has been successfully used in sample preparation for organic molecules and peptides. However, due to the usual methodological conditions, biologically active proteins are not successfully retrieved by this technique, resulting in a low rate of protein identification reported for the viscous amphibian skin secretion. Here we describe an ion-exchange batch processing sample preparation technique that allows viscous or adhesive materials (as some amphibian skin secretions) to be further processed by classical liquid chromatography approaches. According to our protocol, samples were allowed to equilibrate with a specific resin that was washed with appropriated buffers in order to yield the soluble protein fraction. In order to show the efficiency of our methodology, we have compared our results to classically prepared skin secretion, i.e., by means of filtration and centrifugation. After batch sample preparation, we were able to obtain reproductive resolved protein chromatographic profiles, as revealed by SDS-PAGE, and retrieve some biological activities, namely, hydrolases belonging to serine peptidase family. Not only that, but also the unbound fraction was rich in low molecular mass molecules, such as alkaloids and steroids, making this sample preparation technique also suitable for the enrichment of such molecules.

Biochemical analyses of proteins from Duttaphrynus melanostictus (Bufo melanostictus) skin secretion: soluble protein retrieval from a viscous matrix by ion-exchange batch sample preparation

A crucial step in scientific analysis can be sample preparation, and its importance increases in the same rate as the sensitivity of the following employed/desired analytical technique does. The need to analyze complex, viscous matrices is not new, and diverse approaches have been employed, with different success rates depending on the intended molecules. Solid-phase extraction, for example, has been successfully used in sample preparation for organic molecules and peptides. However, due to the usual methodological conditions, biologically active proteins are not successfully retrieved by this technique, resulting in a low rate of protein identification reported for the viscous amphibian skin secretion. Here we describe an ion-exchange batch processing sample preparation technique that allows viscous or adhesive materials (as some amphibian skin secretions) to be further processed by classical liquid chromatography approaches. According to our protocol, samples were allowed to equilibrate with a specific resin that was washed with appropriated buffers in order to yield the soluble protein fraction. In order to show the efficiency of our methodology, we have compared our results to classically prepared skin secretion, i.e., by means of filtration and centrifugation. After batch sample preparation, we were able to obtain reproductive resolved protein chromatographic profiles, as revealed by SDS-PAGE, and retrieve some biological activities, namely, hydrolases belonging to serine peptidase family. Not only that, but also the unbound fraction was rich in low molecular mass molecules, such as alkaloids and steroids, making this sample preparation technique also suitable for the enrichment of such molecules.

Facile Purification of Milligram to Gram Quantities of Condensed Tannins According to Mean Degree of Polymerization and Flavan-3-ol Subunit Composition.

Unambiguous investigation of condensed tannin (CT) structure-activity relationships in biological systems requires well-characterized, high-purity CTs. Sephadex LH-20 and Toyopearl HW-50F resins were compared for separating CTs from acetone/water extracts, and column fractions analyzed for flavan-3-ol subunits, mean degree of polymerization (mDP), and purity. Toyopearl HW-50F generated fractions with higher mDP values and better separation of procyanidins (PC) and prodelphinidins (PD) but required a prepurification step, needed more time for large scale purifications, and gave poorer recoveries. Therefore, two gradient elution schemes were developed for CT purification on Sephadex LH-20 providing 146-2000 mg/fraction. Fractions were analyzed by thiolysis and NMR spectroscopy. In general, PC/PD ratios decreased and mDP increased during elution. 1H NMR spectroscopy served as a rapid screening tool to qualitatively determine CT enrichment and carbohydrate impurities present, guiding fractionation toward repurification or 1H-13C HSQC NMR spectroscopy and thiolysis. These protocols provide options for preparing highly pure CT samples.

Light extinction and scattering by agarose based resin beads and applications in high-throughput screening.

Optimization of chromatographic processes by high-throughput screening (HTS) methodologies have become a critical part of downstream process development. Nevertheless there are still no non-invasive optical methods to characterize resin as well as protein-resin interaction on liquid-handling platforms available. Several approaches to automated resin screening in microplates are described in literature, yet all those methods involve indirect measurements by removal of, and sample quantification within, supernatant volumes. In this work, we introduce light extinction by light scattering to directly assess resin volume and bead density within microplates. Methods for this novel resin characterization are described for 96 and 384-well microplates. An example application demonstrates ligand concentration measurement in microplates with four commercial SP Sepharose™ Fast Flow batches. Further, direct quantification of adsorbent bound biomolecules is shown in an example with kinetic protein-resin interaction measurement in a batch screening process. This new approach is expected to promote batch-based resin characterization and monitoring on HTS platforms and further miniaturization and increase in throughput of chromatographic HTS processes.

Adaptation to high throughput batch chromatography enhances multivariate screening.

High throughput process development offers unique approaches to explore complex process design spaces with relatively low material consumption. Batch chromatography is one technique that can be used to screen chromatographic conditions in a 96-well plate. Typical batch chromatography workflows examine variations in buffer conditions or comparison of multiple resins in a given process, as opposed to the assessment of protein loading conditions in combination with other factors. A modification to the batch chromatography paradigm is described here where experimental planning, programming, and a staggered loading approach increase the multivariate space that can be explored with a liquid handling system. The iterative batch chromatography (IBC) approach is described, which treats every well in a 96-well plate as an individual experiment, wherein protein loading conditions can be varied alongside other factors such as wash and elution buffer conditions. As all of these factors are explored in the same experiment, the interactions between them are characterized and the number of follow-up confirmatory experiments is reduced. This in turn improves statistical power and throughput. Two examples of the IBC method are shown and the impact of the load conditions are assessed in combination with the other factors explored.