Design of optimized high-performance liquid chromatographic gradients for the separation of either small or large molecules

Optimized purification of a fusion protein by reversed-phase high performance liquid chromatography informed by the linear solvent strength model

Fusion protein systems are commonly used for expression of small proteins and peptides. An important criterion for a fusion protein system to be useful is the ability to separate the protein of interest from the tag. Additionally, because no protease cleaves fusion proteins with 100% efficiency, the ability to separate the desired peptide from any remaining uncleaved protein is also necessary. This is likely to be the more difficult task as at least a portion of the sequence of the fusion protein is identical to that of the protein of interest. When a high level of purity is required, gradient elution reversed-phase HPLC is frequently used as a final purification step. Shallow gradients are often advantageous for maximizing both the purity and yield of the final product; however, the relationship between relative retention times at shallow gradients and those at steeper gradients typically used for analytical HPLC are not always straightforward. In this work, we report reversed-phase HPLC results for the fusion protein system consisting of the N-terminal domain of ribosomal protein L9 (NTL9) and the 36-residue villin headpiece subdomain (HP36) linked by a recognition sequence for the protease factor Xa. This system represents an excellent example of the difficulties in purification that may arise from this unexpected elution behavior at shallow gradients. Additionally, we report on the sensitivity of this elution behavior to the concentration of the additive trifluoroacetic acid in the mobile phase and present optimized conditions for separating HP36 from the full fusion protein by reversed-phase HPLC using a shallow gradient. Finally, we suggest that these findings are relevant to the purification of other fusion protein systems, for which similar problems may arise, and support this suggestion using insights from the linear solvent strength model of gradient elution liquid chromatography.

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.

Simple algorithms for fitting and optimisation for multilinear gradient elution in reversed-phase liquid chromatography

The theory of the multilinear gradient elution in reversed-phase liquid chromatography (RP-HPLC) presented in [P. Nikitas, A. Pappa-Louisi, P. Agrafiotou, J. Chromatogr. A 1120 (2006) 299] is modified to increase its flexibility. In addition, it is embodied to simple algorithms for fitting gradient data and especially for resolution optimisation under multilinear gradient conditions. In particular, two new algorithms for fitting and one for optimisation are tested and compared with conventional algorithms. Their performance was examined using 13 o-phthalaldehyde (OPA) derivatives of amino acids with mobile phases modified by acetonitrile. It was found that the new proposed algorithms, a repeated application of the Levenberg-Marquardt (LM) method for fitting (R_LM) and a modified descent algorithm for optimisation (RND_D), in combination with the modified theory of the multilinear gradient elution can lead to high quality predictions of the retention times and optimisation results.

Multilinear gradient elution optimisation in reversed-phase liquid chromatography using genetic algorithms

The treatment presented in a recent paper [P. Nikitas, A. Pappa-Louisi, J. Chromatogr. A, 1068 (2005) 279] is extended to multilinear gradients, i.e. continuous gradients consisting of a certain number of linear portions. Thus, the experimental lnk versus phi curve, where k is the retention factor of a sample solute under isocratic conditions and phi is the volume fraction of the organic modifier in the water-organic mobile phase, is subdivided into a finite number of linear portions resulting in simple analytical expressions for the solute gradient retention time. These expressions of the retention time are directly used in an optimisation technique based on genetic algorithms. This technique involves first the determination of the theoretical dependence of k upon phi by means of gradient measurements, which in turn is used by the genetic algorithm for the prediction of the best gradient profile. The validity of the analytical expressions and the effectiveness of the optimisation technique were tested using fifteen underivatized amino acids and related compounds with mobile phases modified by acetonitrile. It was found that the adopted methodology exhibits significant advantages and it can lead to high quality predictions of the gradient retention times and optimisation results.

New approach to linear gradient elution used for optimisation in reversed-phase liquid chromatography

A new mathematical treatment concerning the gradient elution in reversed-phase liquid chromatography when the volume fraction psi of an organic modifier in the water-organic mobile phase varies linearly with time is presented. The experimental ln k versus psi curve, where k is the retention factor under isocratic conditions in a binary mobile phase, is subdivided into a finite number of linear portions and the solute gradient retention time tR is calculated by means of an analytical expression arising from the fundamental equation of gradient elution. The validity of the proposed analytical expression and the methodology followed for the calculation of tR was tested using eight catechol-related solutes with mobile phases modified by methanol or acetonitrile. It was found that in all cases the accuracy of the predicted gradient retention times is very satisfactory because it is the same with the accuracy of the retention times predicted under isocratic conditions. Finally, the above method for estimating gradient retention times was used in an optimisation algorithm, which determines the best variation pattern of psi that leads to the optimum separation of a mixture of solutes at different values of the total elution time.

Peptide mapping by reversed-phase high-performance liquid chromatography employing silica rod monoliths

In this paper, a general procedure is described for the generation of peptide maps of proteins with monolithic silica-based columns. The peptide fragments were obtained by tryptic digestion of various cytochrome c species with purification of the tryptic fragments achieved by reversed-phase high-performance liquid chromatographic methods. Peak assignment of the various peptides was based on evaluation of the biophysical properties of the individual peptides and via mass spectrometric identification. The performance of several different monolithic sorbents prepared as columns of identical cross-sectional dimensions were investigated as part of these peptide mapping studies and the data evaluated by applying solvent strength theory. These studies revealed curvilinear dependencies in the corresponding relative resolution maps. These findings directly impact on the selection of specific sorbent types or column configurations for peptide separations with silica rod monoliths. Moreover, the influence of variations in the amino acid sequence of the cytochrome cs were evaluated with respect to their effect on intrinsic hydrophobicity, the number of experimental observed tryptic cleavage sites, detection limits of the derived fragments in relation to their molecular size, and the chromatographic selectivity and resolution of the various peptides obtained following enzymatic fragmentation of the parent protein. Finally, the scope of these approaches in method development was examined in terms of robustness and efficiency.

Computerized design of separation strategies by reversed-phase liquid chromatography: development of DryLab software

The development of DryLab software is a special achievement in analytical HPLC which took place in the last 16 years. This paper tries to collect some of the historical mile stones and concepts. DryLab, being always subject to change according to the needs of the user, never stopped being developed. Under the influence of an ever changing science market, the DryLab development team had to consider not just scientific improvements, but also new technological achievements, such as the introduction of Windows 1.0 and 3.1, and later Windows NT and 2000. The recent availability of new 32-bit programming tools allowed calculations of chromatograms to be completed more quickly so as to show peak movements which result for example from slight changes in eluent pH. DryLab is a great success of interdisciplinary and intercontinental cooperation by many scientists.

HPLC of peptides and proteins: preparation and system set-up

The eight basic modes of HPLC currently in use for peptide and protein analysis and purification are presented in this overview. They include: size-exclusion chromatography (HP-SEC), ion-exchange chromatography (HP-IEX), normal phase chromatography (HP-NPC), hydrophobic interaction chromatography (HP-HIC), reversed-phase chromatography (RP-HPLC), hydrophilic interaction chromatography (HP-HILIC), immobilized metal ion affinity chromatography (HP-IMAC), and biospecific/biomimetic affinity chromatography (HP-BAC). In addition, some subsets of these chromatographic modes, e.g., mixed mode chromatography (HP-MMC), charge transfer chromatography (HP-CTC), or ligand-exchange chromatography (HP-LEC) are described. The unit includes overviews of the system requirements and planning strategies for set-up of the systems.

HPLC of peptides and proteins: standard operating conditions

The standard operating conditions for the eight basic modes of HPLC are presented in this unit. They include: size-exclusion chromatography (HP-SEC), ion-exchange chromatography (HP-IEX), normal phase chromatography (HP-NPC), hydrophobic interaction chromatography (HP-HIC), reversed-phase chromatography (RP-HPLC), hydrophilic interaction chromatography (HP-HILIC), immobilized metal ion affinity chromatography (HP-IMAC), and biospecific/biomimetic affinity chromatography (HP-BAC). In addition, some subsets of these chromatographic modes, e.g., mixed mode chromatography (HP-MMC), charge transfer chromatography (HP-CTC), or ligand-exchange chromatography (HP-LEC) are described. Procedures for multimodal column switching are also included, as are guidelines for a systematic approach to method development. Example separations help illustrate the procedures. The standard operating conditions for the eight basic modes of HPLC are presented in this unit.

Simultaneous variation of temperature and gradient steepness for reversed-phase high-performance liquid chromatography method development. II. The use of further changes in conditions

The preceding paper (Part I) suggests that simply optimizing temperature and gradient steepness will often provide an adequate reversed-phase HPLC separation. In some cases, however, this procedure will prove unsuccessful, and then further method-development experiments (involving change in other separation conditions) will be required. One strategy is to change a variable other than temperature or gradient steepness, followed by re-optimization of the latter two variables. The present paper examines the application of this approach with the aid of computer simulation to several samples.

Maintaining fixed band spacing when changing column dimensions in gradient elution

In gradient elution separations, it may be required to change either column length (to increase resolution or shorten run time) or column diameter (for an increase in sensitivity or for preparative separations). In either of these changes of column dimensions, it is usually desired to maintain the same relative band spacing (selectivity), so as to increase resolution in proportion to (column plate number)1/2 when increasing column length, or to maintain constant resolution when changing column diameter. A general rule for avoiding changes in band spacing in these situations is to maintain the quantity [(gradient time) x (flow-rate)/(column volume)] constant, while holding the initial and final gradient mobile phase compositions (%B) fixed. This rule is only valid as long as the equipment hold-up volume (dwell volume) is negligible, or if all sample components are strongly retained at the start of the gradient. When neither of the latter conditions apply, then significant changes in band spacing may result when changing column size. Rules are presented for recognizing this potential problem for a given sample/HPLC-equipment combination, and adjustments in separation conditions that can avoid this problem are discussed. Changes in band spacing as a result of change in column size are of special concern when developing procedures for preparative chromatography under gradient conditions.

Selectivity due to conformational differences between helical and non-helical peptides in reversed-phase chromatography

The reversed-phase retention behaviour of two series of peptides, one non-helical and the other alpha-helical, was studied under various linear AB gradients in order to determine the effect of peptide conformation on selectivity of the separation. The non-helical series, designated X1, with the sequence Ac-XLGAKGAGVG-amide, exhibited negligible alpha-helical content in a hydrophobic medium; whereas, the amphipathic alpha-helical series, designated AX9, with the sequence Ac-EAEKAAKEXEKAAKEAEK-amide, exhibited high alpha-helical content in a hydrophobic medium. We have shown that plots of log k vs. phi (where k is the median capacity factor and phi is the median volume fraction of organic solvent) are very similar for any one peptide conformation, i.e., peptides from either the non-helical or amphipathic alpha-helical series exhibit similar S (solute parameter) values and the b (gradient steepness parameter) values are also similar for 17 different amino acid substitutions within each series of peptides. If mixtures of peptides from the two different series are separated using either increasing or decreasing gradient rates, large increases in resolution occur due to selectivity, which may be attributed to the difference in the log k vs. phi plots for each series of peptides. In addition, by using a polymer of an X1 peptide, which is 20 residues in length, it has been shown that the molecular mass difference between the X1 and the AX9 series of peptides is not sufficient to account for the selectivity difference. The S value of a non-amphipathic alpha-helical peptide further suggested that the difference in selectivity between the two series of peptides was due to differences in conformation. We believe that the peptide mixtures presented here provide a good model for studying selectivity effects due to conformational differences between peptides, an important concern when attempting to develop rational approaches to the prediction and optimization of peptide separation protocols from primary sequence information alone.

Temperature as a variable in reversed-phase high-performance liquid chromatographic separations of peptide and protein samples. I. Optimizing the separation of a growth hormone tryptic digest

Peptide and protein samples are often complex mixtures that contain a number of individual compounds. The initial HPLC separation of such samples typically results in the poor resolution of one or more band pairs. Various means have been suggested for varying separation selectivity so as to minimize this problem. In this study of a tryptic digest of recombinant human growth hormone, the simultaneous variation of temperature and gradient steepness was found to be a convenient and effective means of varying selectivity and optimizing the separation. The use of computer simulation greatly facilitated this investigation.

Implementation and use of gradient predictions for optimization of reversed-phase liquid chromatography of peptides. Practical considerations

The options in the implementation of gradient theory for optimization work are critically reviewed and evaluated for the case of the reversed-phase liquid chromatography of peptides. Various models are covered together with methods for the determination of model parameters. Approaches for calculating retention times and band widths from experimental data are discussed. Different kinds of extrapolation are compared with interpolation. This study was aimed at finding the best compromise between number of experiments, accuracy of predictions and simplicity of calculations. Implementation and the use of gradient predictions can be simple, and practical recommendations are given.

Computer simulation as a tool for the rapid optimization of the high-performance liquid chromatographic separation of a tryptic digest of human growth hormone

Computer simulation was used to optimize the separation of a tryptic digest of recombinant human growth hormone using reversed-phase high-performance liquid chromatography in a gradient mode. DryLab G/plus software modelled the retention behavior of the complex tryptic digest mixture as a function of gradient conditions, based on data from two experimental gradient runs. The theoretical optimum separation conditions were rapidly obtained and reproduced experimentally. Resolution did not simply increase as gradient steepness was decreased, rather, an intermediate gradient time provided maximum sample resolution. The simulation results also indicate that the method is reasonably rugged, with little change in the separation expected for different high-performance liquid chromatography systems, and changes in the separation can be compensated by a change in the gradient steepness. Computer simulation can also be useful to quickly reoptimize conditions for a new column, if it fails to provide the same separation.

Factors influencing the performance of peptide mapping by reversed-phase high-performance liquid chromatography

Factors controlling the performance of peptide mapping on reversed-phase columns were systematically evaluated. Performance criteria included resolution (peak capacity and selectivity), system reproducibility, sensitivity and analysis speed. Column configuration, characteristics of packing materials, mobile phase composition, operating variables and instrumental designs were found to influence the performance of peptide mapping. Considerations for peptide identification techniques are discussed.

DryLab computer simulation for high-performance liquid chromatographic method development. II. Gradient elution

Computer simulation (DryLab software) as an aid for the development of gradient high-performance liquid chromatographic methods is reviewed. Several examples of its application are presented and the accuracy of such predictions is discussed.

Reversed-phase chromatographic method development for peptide separations using the computer simulation program ProDigest-LC

A computer program, ProDigest-LC, has been developed that assists scientists in devising methods of size-exclusion, cation-exchange and reversed-phase high-performance liquid chromatography for the analytical separation and purification of biologically active peptides and peptide fragments from enzymatic and chemical digests of proteins. ProDigest-LC accurately predicts the retention behaviour of peptides of known composition, containing 2-50 amino acid residues, and simulates the elution profiles in all three modes of chromatography. In addition, ProDigest-LC is a user-friendly program, designed as a teaching aid for both students and researchers in selecting the correct conditions for chromatography, that is, the mode of chromatography, column selection and mobile-phase selection, and has the ability to examine the effects of gradient-rate, flow-rate and sample size on the separation. The simulation capabilities of ProDigest-LC as they apply to the reversed-phase chromatography of peptides were examined. The development of the reversed-phase simulation features of the program is described, stressing the importance of peptide standards in the development, testing and practical use of ProDigest-LC. The ease of use of the program is clearly demonstrated by presenting a step-by-step procedure to produce several of the simulations illustrated in the paper. The predictive accuracy of the program was rigorously tested by its application to retention time prediction, at different gradient-rates and flow-rates, for a sample mixture containing peptides exhibiting a wide range of size (11-50 residues), charge (+1 to +8 net charge), hydrophobicity and conformation (random coil to considerable alpha-helical structure). The excellent accuracy of these peptide retention time predictions complemented the successful simulation (in terms of peptide retention times, peptide resolution, peak heights and peak widths) of the effects of gradient-rate and flow-rate on the elution profile of a mixture of closely related peptide analogues.

Hydrophobic interaction chromatography of proteins on Separon hema. I. The effect of an initial salt concentration on the separation of proteins

The influence of an initial salt concentration, phi(0), on the gradient separation of proteins using hydrophobic interaction chromatography on Separon HEMA 1000 was investigated. The results obtained were compared with the retention times and peak widths calculated according to a mathematical model.