Retention time and peak width in the combined pH/organic modifier gradient high performance liquid chromatography

The purpose of this work was to test the applicability of the current theory to predict the peak retention time and the peak width in the combined pH/organic modifier gradient reversed phase high performance liquid chromatography (RP HPLC). A series of 38 isocratic measurements have been conducted for a wide range of pH and methanol contents for ketoprofen (weak acid) and papaverine (weak base). It served to find the model describing dependence of retention factor and the height equivalent of a theoretical plate (HETP) on pH and organic modifier content. The information gathered in the isocratic mode was used to simulate retention times and peak widths for 30 various methanol gradients, 25 pH gradients, and 3 combined pH/methanol gradients. The simulations were compared with the experimental data. We also proposed a simplified version of this model that was parameterized based on 12 initial organic modifier gradients carried out for different pHs and for the 20 min and 60 min gradient development times. The full and the simplified model described the experimental data very well. In conclusion, the proposed modeling approach allowed predicting analyte retention times and peak width for various pH and organic modifier changes. Its simplified version required only 12 initial experiments and seems to be very promising in the optimization RP HPLC separations for complex samples and for conditions providing peak compression.     

Immobilized pH gradients (IPG) simulator--an additional step in pH gradient engineering: I. Linear pH gradients.

A new computer program, called immobilized pH gradients (IPG) simulator, is proposed for calculating and optimizing any recipe for use in isoelectric focusing in immobilized pH gradients. Unlike our previous monoprotic electrolyte gradient simulation (MGS) and polyelectrolyte gradient simulation (PGS) programs, based on minimizing CV(beta), the present program has a target function the minimization of the quadratic moment around zero of the residuals (mu 2). With this algorithm it is possible to formulate IPG recipes which have deviations from linearity well below 1% of the given pH interval (a limit set with the previous MGS and PGS programs), in fact, as small as 0.1-0.2% (in pH units). The new simulator performs 2-3 times better than the previous ones in the pH 4-10 range, and is absolutely necessary when working outside this range, at extreme pH values, where CV(beta) cannot work against the buffering power of bulk water, thus generating pH recipes with huge deviations from linearity. In the latter cases, mu 2 performs 10 times better than CV(beta). When utilizing strong titrants for extended pH intervals, the "all or none" rule has been discovered: such titrants should always be used in tandem, since omission of one of the two at either the acidic or basic extremes produces strongly distorted pH profiles. Our new, most powerful simulator also contains equations for creating nonlinear gradients, notably: concave and convex exponentials and sigmoidal (see the companion paper: Righetti, P. G. and Tonani, C., Electrophoresis 1991, 12, 1021-1027).     

pH gradient simulator for electrophoretic techniques in a windows environment

A new program is presented for optimizing mixtures of buffers and titrants for creating pH gradients for isoelectric focusing in immobilized pH gradients and in general for chromatographic processes. The program is written on a windows platform and it includes several novel features compared with previous simulators. First, the estimation of a pH gradient (a non-linear problem) has been transformed into a linear programming problem, thus allowing the use of the simplex as an optimization algorithm. Second, several types of pH gradients can be simulated and optimized, including linear, exponential, logarithmic and sigmoidal. Finally, an equation has been implemented in the program that accounts for the variation of the activity coefficients of ions as a function of the prevailing ionic strength in solution. This simulator was checked experimentally by eluting solutions from a two-vessel gradient mixer and verifying the shape of the various pH gradients. An excellent correlation was found between simulated and experimental data. The program allows the calculation and optimization of pH profiles (including the accompanying ionic strength and buffering power values) for mixtures of up to 50 different monoprotic or oligoprotic buffers and titrants. Calculations and optimizations are performed in a fraction of the time required by previous programs (often in less than 1 min, even for highly complex mixtures).     

Steady state electrolysis and isoelectric focusing

The properties of pH gradients formed by stationary electrolysis of weak mobile or fixed electrolytes are analyzed. The model uses the appropriate balance equations and those of chemical equilibria. It is shown how the equation of the current density has to be modified for considering that fraction of current that is associated with the diffusion of neutral buffer molecules within a pH gradient. Furthermore it is shown that the pH gradients themselves give rise to water production within the gradient and that essential properties of the steady state are related to chemical reactions between the electrolyte constituents. The differential equations describing the gradients of the concentration of a given component, the pH, conductivity and potential are explicitly formulated in relation to those reactions. The equations are solved numerically and the significance of the results for isoelectric focusing is discussed. The experimental conditions to reach shallow and smooth pH gradients exhibiting sufficient ionic strength are formulated.     

Photoprotective compounds in cyanobacteria, phytoplankton and macroalgae--a database

A database on photoprotective compounds in cyanobacteria, phytoplankton and macroalgae has been developed. It contains information on photoprotective compounds such as mycosporine-like amino acids (MAAs), scytonemin and other not yet identified compounds reported in aquatic organisms, their habitat, the collection site and date and the reference. Further information on the absorption maxima and extinction coefficients of different photoprotective compounds as well as experimental procedures are provided (see http:/ /www.biologie.uni-erlangen.de/botanik1/index.html). The database answers the urgent need for a library on these substances and provides scientists in the field with the necessary information to identify and quantify screening pigments in different aquatic organisms from various growing sites and different collection dates.     

Protein separations with induced pH gradients using cation-exchange chromatographic columns containing weak acid groups

The behavior of chromatographic columns packed with resins containing both weak and strong cation-exchange groups is investigated in order to obtain protein separations by means of internally generated pH gradients in response to step changes in buffer composition. A local equilibrium model is developed to predict pH transitions using non-adsorbed buffers, i.e. containing neutral and negatively charged buffering species, based exclusively on the resin titration curve. In agreement with experimental results, the model predicts practical, fairly linear gradients between pH 5 and 7, which are formed using suitable mixtures of acetate and phosphate buffers. The separation of mixtures of ovalbumin, albumin, and transferrin is used as a model system, but, unlike most previous work, we consider preparative conditions. Near baseline resolution is obtained with protein loads as high as 10mg/mL and mobile phase velocities at high as 460 cm/h using porous, 70-microm diameter particles. The peaks obtained with this approach are much sharper than could be obtained isocratically or using externally generated, unretained gradients as a result of the peak compression caused by the axial pH gradient formed along the column. Moreover, separation is obtained at very low ionic strengths (2-3 mS/cm). The effects of flow velocity, mobile phase composition, time of injection, and protein load on retention and elution pH are investigated systematically demonstrating a range of ways in which the separation can be controlled and optimized.     

UTAB: a computer database on residues of xenobiotic organic chemicals and heavy metals in plants.

The UTAB Database contains information concerned with the uptake/accumulation, translocation, adhesion, and biotransformation of both xenobiotic organic chemicals and heavy metals by vascular plants. UTAB can be used to estimate the accumulation of chemicals in vegetation and their subsequent movement through the food chain. The database contains actual data from papers in the published literature dating from 1926 for organic chemicals and from 1976 for heavy metals. At present the database is comprised of more than 37,000 records pertaining to 900 different organic chemicals, 21 heavy metals, and over 350 plant species. Each record contains information on a single combination of species, chemical, and dose. Other information includes the application and destination sites, amount accumulated, rates of uptake or translocation, products and sites of biotransformation, experimental condition parameters, and the source paper. Thus, the database can be used to quickly obtain specific data pertaining to a chemical, plant species, mine spoil, etc. or it can be used for the comparative analysis of a set of data pertaining to groups of chemicals and plants.     

A database of 660 peptide ion cross sections: Use of intrinsic size parameters for bona fide predictions of cross sections

An ion trap/ion mobility/time-of-flight mass spectrometry technique has been used to measure collision cross sections for 660 peptide ions generated by tryptic digestion of 34 common proteins. Measured cross sections have been compiled into a database that contains peptide molecular weight and sequence information. The database is used to generate average intrinsic contributions to cross section (size parameters) for different amino acid residues by solving systems of equations that relate the unknown contributions of individual residues to the sequences and cross sections of database peptides. Size parameters are combined with information about amino acid composition to calculate cross sections for database peptides. Bona fide cross section predictions (made prior to measurement) for peptides observed in tryptic digests of sperm whale myoglobin and yeast enolase are made. Eight of 10 predicted cross sections are within 2% of the experimental values and all 10 are within 3.2%. The utility of size parameters for cross section prediction is explored and discussed.     

The application of gradient reversed-phase high-performance liquid chromatography to the pK(a) and log k(w) determination of polyprotic analytes

The purpose of this work was to propose a theoretical model of the combined pH/organic modifier gradient in reversed-phase high-performance liquid chromatography (RP HPLC) with special emphasis on its applicability to polyprotic analytes. The model was developed and approximated to be useful for a data set comprising organic modifier gradients obtained at different pH changes and different gradient durations. It was evaluated regarding its ability to describe experimental data. The chromatographic pK(a) and lipophilicity parameter, log k(w), were obtained by fitting to the proposed model and comparing to the literature values.     

Modeling of salt and pH gradient elution in ion‐exchange chromatography

The separation of proteins by internally and externally generated pH gradients in chromatofocusing on ion‐exchange columns is a well‐established analytical method with a large number of applications. In this work, a stoichiometric displacement model was used to describe the retention behavior of lysozyme on SP Sepharose FF and a monoclonal antibody on Fractogel SO₃ (S) in linear salt and pH gradient elution. The pH dependence of the binding charge B in the linear gradient elution model is introduced using a protein net charge model, while the pH dependence of the equilibrium constant is based on a thermodynamic approach. The model parameter and pH dependences are calculated from linear salt gradient elutions at different pH values as well as from linear pH gradient elutions at different fixed salt concentrations. The application of the model for the well‐characterized protein lysozyme resulted in almost identical model parameters based on either linear salt or pH gradient elution data. For the antibody, only the approach based on linear pH gradients is feasible because of the limited pH range useful for salt gradient elution. The application of the model for the separation of an acid variant of the antibody from the major monomeric form is discussed.     

A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships

The rapid expansion of structural information for protein-ligand binding sites is potentially an important source of information in structure-based drug design and in understanding ligand cross reactivity and toxicity. We have developed a large database of ligand binding sites extracted automatically from the Protein Data Bank. This has been combined with a method for calculating binding site similarity based on geometric hashing to create a relational database for the retrieval of site similarity and binding site superposition. It contains an all-against-all comparison of binding sites and holds known protein-ligand binding sites, which are made accessible to data mining. Here we demonstrate its utility in two structure-based applications: in determining site similarity and in aiding the derivation of a receptor-based pharmacophore model. The database is available from http://www.bioinformatics.leeds.ac.uk/sb/.     

A database of lipid phase transition temperatures and enthalpy changes

The systematic study of the mesomorphic phase properties of synthetic and biologically derived lipids began some 30 years ago. In the past decade, interest in this area has grown enormously. As a result, there exists a wealth of information on lipid phase behavior, but unfortunately, these data have, until now, been scattered throughout the literature in a variety of books, proceedings, and journals. The data have recently been compiled in a centralized database with a view to providing ready access to the same and to the appropriate literature. The compilation facilitates review of what has thus far been accomplished and highlights what remains to be done in this active research area. As such, it represents a convenient summary of the existing data which, when evaluated, will enable us to identify where deficits exist in the data, to reveal the fundamental physicochemical principles upon which lipid phase behavior is based, and to understand more completely lipid phase relations in biological, reconstituted, and formulated systems. The compilation consists of a tabulation of all known mesomorphic and polymorphic phase transition temperatures and enthalpy changes for synthetic and biologically derived lipids in the dry and in the partially and fully hydrated states. Also included is the effect on these thermodynamic values of pH, and of salt and metal ion concentration and other additives such as proteins, drugs, etc. The methods used in making the measurements and the experimental conditions are reported. Bibliographic information includes complete literature referencing and list of authors. As of this writing, the database is current through June 1990 and contains 9500 records. Each record contains 28 fields. Here, we describe how the database originated, its scope and contents, data abstraction procedures, and issues relating to mesophase and lipid nomenclature, data analysis, and evaluation, and database maintenance and distribution.     

Preparative isoelectric focusing of proteins using binary buffers in a vortex-stabilized, free-flow apparatus

Recombinant proteins are often produced as isoforms with different kinds and amounts of post-translational modifications that alter their function. Isoelectric focusing in shallow pH gradients, less than 0.5 pH/cm, might be capable of fractionating these isoforms. The synthetic carrier ampholyte mixtures typically used to generate these pH gradients are expensive and may adversely interact with proteins. Using defined buffers instead of synthetic carrier ampholytes reduces these problems. We tested two defined buffer systems in a vortex-stabilized electrophoresis device to see if they could form shallow pH gradients useful for separating isoforms. These pH gradients were formed by pouring a two-component concentration gradient. The poured gradients were smooth, reproducible, and stable for at least 1.5 h at 5 kV. One poured gradient focused 20 mg of cytochrome c. A second poured gradient separated glucose oxidase from amyloglucosidase. The breadth of the amyloglucosidase band indicates that the shallow, poured pH gradients can only partially separate protein isoforms at 10 kV. Proteins with pI < 0.2 pH units apart will have overlapping bands in these shallow, poured pH gradients.     

Electrophoresis in gel channels

We describe a novel approach to generate dynamic pH gradients suited to fractionate or purify samples of biomolecules or particles such as proteins and viruses in tiny volumes. The method combines diffusion and electromigration between micro-scaled channels embedded in hydrogel. For the used geometry and in accordance with numerical calculations the gel-channel system reaches a tuneable, steady-state pH gradient after a few minutes. For quantification of experimentally generated pH-profiles, the concentration independent extinction ratio of phenol red at two wavelengths is used. The proposed electrophoretic flow-cell is simple and flexible since no Immobilines are required to establish the pH gradient.     

A database for inventory of proteoform profiles: “2DE-pattern”

The human proteome is composed of a diverse and heterogeneous range of gene products/proteoforms/protein species. Because of the growing amount of information about proteoforms generated by different methods, we need a convenient approach to make an inventory of the data. Here, we present a database of proteoforms that is based on information obtained by separation of proteoforms using 2DE followed by shotgun ESI–LC–MS/MS. The database's principles and structure are described. The database is called “2DE-pattern” as it contains multiple isoform-centric patterns of proteoforms separated according to 2DE principles. The database can be freely used at http://2de-pattern.pnpi.nrcki.ru .     

The impact of boundary conditions in free flow field step electrophoresis

The impact of the type of membrane used to separate the electrolyte compartments from the separation cell for continuous flow field step electrophoresis is examined using both experimental and computer simulation data. It is shown that the distinct transport characteristics of ion exchange membranes and dialysis membranes may have an effect on the stability of the pH and conductivity gradients created by the buffer system. These effects are interpreted using computer simulation data. The limitations of the model used to portray the transport characteristics of ion exchange membranes are discussed as are the experimental conditions which provide the greatest stability for field step electrophoresis.     

Model based robustness analysis of an ion-exchange chromatography step

Process development, optimization and robustness analysis for chromatographic separation are often entirely based on experimental work and generic knowledge. This paper describes a model-based approach that can be used to gain process knowledge and assist in the robustness analysis of an ion-exchange chromatography step using a model-based approach. A kinetic dispersive model, where the steric mass action model accounts for the adsorption is used to describe column performance. Model calibration is based solely on gradient elution experiments at different gradients, flow rates, pH and column loads. The position and shape of the peaks provide enough information to calibrate the model and thus single-component experiments can be avoided. The model is calibrated to the experiments and the confidence intervals for the estimated parameters are used to account for the model error throughout the analysis. The model is used to predict the result of a robustness analysis conducted as a factorial experiment and to design a robust pooling approach. The confidence intervals are used in a "worst case" approach where the parameters for the components are set at the edge of their confidence intervals to create a worst case for the removal of impurities at each point in the factorial experiment. The pooling limit was changed to ensure product quality at every point in the factorial analysis. The predicted purities and yields were compared to the experimental results to ensure that the prediction intervals cover the experimental results.