1 mm ID poly(styrene-co -divinylbenzene) monolithic columns for high-peak capacity one- and two-dimensional liquid chromatographic separations of intact proteins

Recent advances in top-down proteome sample processing ahead of MS analysis

Top-down proteomics is emerging as a preferred approach to investigate biological systems, with objectives ranging from the detailed assessment of a single protein therapeutic, to the complete characterization of every possible protein including their modifications, which define the human proteoform. Given the controlling influence of protein modifications on their biological function, understanding how gene products manifest or respond to disease is most precisely achieved by characterization at the intact protein level. Top-down mass spectrometry (MS) analysis of proteins entails unique challenges associated with processing whole proteins while maintaining their integrity throughout the processes of extraction, enrichment, purification, and fractionation. Recent advances in each of these critical front-end preparation processes, including minimalistic workflows, have greatly expanded the capacity of MS for top-down proteome analysis. Acknowledging the many contributions in MS technology and sample processing, the present review aims to highlight the diverse strategies that have forged a pathway for top-down proteomics. We comprehensively discuss the evolution of front-end workflows that today facilitate optimal characterization of proteoform-driven biology, including a brief description of the clinical applications that have motivated these impactful contributions.

Monolith columns for liquid chromatographic separations of intact proteins: A review of recent advances and applications

In this article we survey 256 references (with an emphasis on the papers published in the past decade) on monolithic columns for intact protein separation. Protein enrichment and purification are included in the broadly defined separation. After a brief introduction, we describe the types of monolithic columns and modes of chromatographic separations employed for protein separations. While the majority of the work is still in the research and development phase, papers have been published toward utilizing monolithic columns for practical applications. We survey these papers as well in this review. Characteristics of selected methods along with their pros and cons will also be discussed.

Advances in organic polymer-based monolithic column technology for high-resolution liquid chromatography-mass spectrometry profiling of antibodies, intact proteins, oligonucleotides, and peptides

This review focuses on the preparation of organic polymer-based monolithic stationary phases and their application in the separation of biomolecules, including antibodies, intact proteins and protein isoforms, oligonucleotides, and protein digests. Column and material properties, and the optimization of the macropore structure towards kinetic performance are also discussed. State-of-the-art liquid chromatography-mass spectrometry biomolecule separations are reviewed and practical aspects such as ion-pairing agent selection and carryover are presented. Finally, advances in comprehensive two-dimensional LC separations using monolithic columns, in particular ion-exchange×reversed-phase and reversed-phase×reversed-phase LC separations conducted at high and low pH, are shown.

Different Stationary Phase Selectivities and Morphologies for Intact Protein Separations

The central dogma of biology proposed that one gene encodes for one protein. We now know that this does not reflect reality. The human body has approximately 20,000 protein-encoding genes; each of these genes can encode more than one protein. Proteins expressed from a single gene can vary in terms of their post-translational modifications, which often regulate their function within the body. Understanding the proteins within our bodies is a key step in understanding the cause, and perhaps the solution, to disease. This is one of the application areas of proteomics, which is defined as the study of all proteins expressed within an organism at a given point in time. The human proteome is incredibly complex. The complexity of biological samples requires a combination of technologies to achieve high resolution and high sensitivity analysis. Despite the significant advances in mass spectrometry, separation techniques are still essential in this field. Liquid chromatography is an indispensable tool by which low-abundant proteins in complex samples can be enriched and separated. However, advances in chromatography are not as readily adapted in proteomics compared to advances in mass spectrometry. Biologists in this field still favour reversed-phase chromatography with fully porous particles. The purpose of this review is to highlight alternative selectivities and stationary phase morphologies that show potential for application in top-down proteomics; the study of intact proteins.

1-Butanol absorption in poly(styrene-divinylbenzene) ion exchange resins for catalysis

The swelling behaviour of poly(styrene-co-divinylbenzene), P(S-DVB), ion exchange resins in 1-butanol (BuOH) has been studied by means of atomistic classical molecular dynamics simulations (MD). The topological characteristics reported for the resin in the dry state, which exhibited complex internal loops (macropores), were considered for the starting models used to examine the swelling induced by BuOH contents ranging from 10% to 50% w/w. Experimental measurements using a laser diffraction particle size analyzer indicate that swelling causes a volume variation with respect to the dry resin of 21%. According to MD simulations, such a volume increment corresponds to a BuOH absorption of 31-32% w/w, which is in excellent agreement with the indirect experimental estimation (i.e. 31% w/w). Simulations reveal that, independently of the content of BuOH, the density of the swelled resin is higher than that of the dry resin, evidencing that the alcohol provokes important structural changes in the polymeric matrix. Thus, BuOH molecules cause a collapse of the resin macropores when the content of alcohol is ≤20% w/w. In contrast, when the concentration of BuOH is close to the experimental value (∼30% w/w), P(S-DVB) chains remain separated by pores faciliting the access of the reactants to the reaction centers. On the other hand, evaluation of both bonding and non-bonding interactions indicates that the mixing energy is the most important contribution to the absorption of BuOH into the P(S-DVB) resin. Overall, the results displayed in this work represent a starting point for the theoretical study of the catalytic conversion of BuOH into di-n-butyl ether in P(S-DVB) ion exchange resins using sophisticated electronic methods.

Separation of intact proteins on γ-ray-induced polymethacrylate monolithic columns: A highly permeable stationary phase with high peak capacity for capillary high-performance liquid chromatography with high-resolution mass spectrometry

Polymethacrylate-based monolithic capillary columns, prepared by γ-radiation-induced polymerization, were used to optimize the experimental conditions (nature of the organic modifiers, the content of trifluoroacetic acid and the column temperature) in the separation of nine standard proteins with different hydrophobicities and a wide range of molecular weights. Because of the excellent permeability of the monolithic columns, an ion-pair reversed-phase capillary liquid chromatography with high-resolution mass spectrometry method has been developed by coupling the column directly to the mass spectrometer without a flow-split and using a standard electrospray interface. Additionally, the high working flow and concomitant high efficiency of these columns allowed us to employ a longer column (up to 50 cm) and achieve a peak capacity value superior to 1000. This work is motivated by the need to develop new materials for high-resolution chromatographic separation that combine chemical stability at elevated temperatures (up to 75°C) and a broad pH range, with a high peak capacity value. The advantage of the γ-ray-induced monolithic column lies in the batch-to-batch reproducibility and long-term high-temperature stability. Their proven high loading capacity, recovery, good selectivity and high permeability, moreover, compared well with that of a commercially available poly(styrene-divinylbenzene) monolithic column, which confirms that such monolithic supports might facilitate analysis in proteomics.

Towards ultra-high peak capacities and peak-production rates using spatial three-dimensional liquid chromatography

In order to successfully tackle the truly complex separation problems arising from areas such as proteomics research, the development of ultra-efficient and fast separation technology is required. In spatial three-dimensional chromatography, components are separated in the space domain with each peak being characterized by its coordinates in a three-dimensional separation body. Spatial three-dimensional (3D-)LC has the potential to offer unprecedented resolving power when orthogonal retention mechanisms are applied, since the total peak capacity is the product of the three individual peak capacities. Due to parallel developments during the second- and third-dimension separations, the analysis time is greatly reduced compared to a coupled-column multi-dimensional LC approach. This communication discusses the different design aspects to create a microfluidic chip for spatial 3D-LC. The use of physical barriers to confine the flow between the individual developments, and flow control by the use of (2)D and (3)D flow distributors is discussed. Furthermore, the in situ synthesis of monolithic stationary phases is demonstrated. Finally, the potential performance of a spatial 3D-LC systems is compared with the performance obtained with state-of-the-art 1D-LC and (coupled-column) 2D-LC approaches via a Pareto-optimization approach. The proposed microfluidic device for 3D-LC featuring 16 (2)D channels and 256 (3)D channels can potentially yield a peak capacity of 8000 in a total analysis time of 10 minutes.

Atomistic simulations of the structure of highly crosslinked sulfonated poly(styrene-co-divinylbenzene) ion exchange resins

The microscopic structures of highly crosslinked sulfonated poly(styrene-co-divinylbenzene) resins have been modeled by generating atomistic microstructures using stochastic-like algorithms, which are subsequently relaxed using molecular dynamics. Two different generation algorithms have been tested. The relaxation of the microstructures generated by the first algorithm, which is based on a homogeneous construction of the resin, leads to a significant overestimation of the experimental density as well as to an unsatisfactory description of the porosity. In contrast, the generation approach that combines algorithms for the heterogeneous growing and branching of the chains enables the formation of crosslinks with different topologies. In particular, the intrinsic heterogeneity observed in these resins is efficiently reproduced when the topological loops, which are defined by two or more crosslinks closing a cycle, are present in their microscopic description. Thus, the apparent density, porosity and pore volume estimated using microstructures with these topological loops, called super-crosslinks, are in very good agreement with the experimental results. Although the backbone dihedral angle distribution of the generated and relaxed models is not influenced by the topology, the number and type of crosslinks affect the medium- and long-range atomic disposition of the backbone atoms and the distribution of sulfonic groups. An analysis of the distribution of the local density indicates that super-crosslinks are responsible for the heterogeneous homogenization observed during the MD relaxation. Finally the π-π stacking interactions have been analyzed. Results indicate that those in which the two rings adopt a T-shaped disposition are considerably more abundant as compared to those with the co-facially oriented rings, independently of the resin topology.

Two variables dominating the retention of intact proteins under gradient elution with simultaneous ultrafast high-resolution separation by hydrophobic interaction chromatography

The retention of proteins under gradient elution in HIC is dominated by two variables of steady and migration regions.

Recent advances on multidimensional liquid chromatography-mass spectrometry for proteomics: from qualitative to quantitative analysis--a review

With the acceleration of proteome research, increasing attention has been paid to multidimensional liquid chromatography-mass spectrometry (MDLC-MS) due to its high peak capacity and separation efficiency. Recently, many efforts have been put to improve MDLC-based strategies including "top-down" and "bottom-up" to enable highly sensitive qualitative and quantitative analysis of proteins, as well as accelerate the whole analytical procedure. Integrated platforms with combination of sample pretreatment, multidimensional separations and identification were also developed to achieve high throughput and sensitive detection of proteomes, facilitating highly accurate and reproducible quantification. This review summarized the recent advances of such techniques and their applications in qualitative and quantitative analysis of proteomes.

New trends in reversed-phase liquid chromatographic separations of therapeutic peptides and proteins: theory and applications

In the pharmaceutical field, there is considerable interest in the use of peptides and proteins for therapeutic purposes. There are various ways to characterize such complex samples, but during the last few years, a significant number of technological developments have been brought to the field of RPLC and RPLC-MS. Thus, the present review focuses first on the basics of RPLC for peptides and proteins, including the inherent problems, some possible solutions and some directions for developing a new RPLC method that is dedicated to biomolecules. Then the latest advances in RPLC, such as wide-pore core-shell particles, fully porous sub-2 μm particles, organic monoliths, porous layer open tubular columns and elevated temperature, are described and critically discussed in terms of both kinetic efficiency and selectivity. Numerous applications with real samples are presented that confirm the relevance of these different strategies. Finally, one of the key advantages of RPLC for peptides and proteins over other historical approaches is its inherent compatibility with MS using both MALDI and ESI sources.

Construction and initial evaluation of an apparatus for spatial comprehensive two-dimensional liquid-phase separations

Spatial comprehensive two-dimensional chromatography is discussed as a potentially alternative to the conventional column-based approach. In "spatial" separations each analyte ends up in a specific location, rather than being eluted at a specific time. Ultimately, higher peak-capacity-production rates (peak capacity per unit time) may be attained by spatial two- and three-dimensional separations. While low-pressure planar chromatography is well developed, the high-pressure equivalent is still in its infancy. We discuss the requirements for a device for high-pressure spatial two-dimensional chromatography and we describe a possible design. A prototype instrument has been constructed in-house. The preparation of a polymer monolithic separation body and a valve configuration that allows manual sample injection are described. Initial tests of this study included the investigation of the homogeneity of the monolith and the flow profile through the separation body. Furthermore, in order to evaluate the current chromatographic performance of the device, a mixture of dyes was separated in one dimension within 30 s.