Separation of cytochromes c by reversed-phase high-performance liquid chromatography

Reversed-Phase Liquid Chromatography of Peptides for Bottom-Up Proteomics: A Tutorial

The performance of the current bottom-up liquid chromatography hyphenated with mass spectrometry (LC-MS) analyses has undoubtedly been fueled by spectacular progress in mass spectrometry. It is thus not surprising that the MS instrument attracts the most attention during LC-MS method development, whereas optimizing conditions for peptide separation using reversed-phase liquid chromatography (RPLC) remains somewhat in its shadow. Consequently, the wisdom of the fundaments of chromatography is slowly vanishing from some laboratories. However, the full potential of advanced MS instruments cannot be achieved without highly efficient RPLC. This is impossible to attain without understanding fundamental processes in the chromatographic system and the properties of peptides important for their chromatographic behavior. We wrote this tutorial intending to give practitioners an overview of critical aspects of peptide separation using RPLC to facilitate setting the LC parameters so that they can leverage the full capabilities of their MS instruments. After briefly introducing the gradient separation of peptides, we discuss their properties that affect the quality of LC-MS chromatograms the most. Next, we address the in-column and extra-column broadening. The last section is devoted to key parameters of LC-MS methods. We also extracted trends in practice from recent bottom-up proteomics studies and correlated them with the current knowledge on peptide RPLC separation.

Automated Programmable Generation of Broad pH Range Volatile Ionic Eluents for Liquid Chromatography

Many of the universal detectors in liquid chromatography, including mass spectrometry, must completely volatilize the chromatographic eluent first before further processing and detection of the analytes. A basic requirement is that the eluent does not contain a nonvolatile dissolved component. However, separation of biomolecules must be conducted in mostly aqueous media of compatible pH and ionic strength if their biological activity must survive the separation process. Combinations of ammonia with acetic and formic acids are commonly used as eluent for this purpose but generally maximum concentrations that can be tolerated are relatively low. Further, buffering is good only over a limited pH range. We describe a system where the eluent is generated in an automated pressure-programmed manner from high-purity gaseous NH₃ and CO₂ through gas-permeable membrane devices. This can be aided by the prior presence of formic/acetic acids in the mobile phase to extend the attainable low pH limit. We outline the fundamental pH, ionic strength, and buffer intensity considerations and demonstrate the application of such eluents in the separation of amino acids, proteins, and monoclonal antibodies. We also demonstrate the use of dissolved CO₂ as an ion-pairing agent in the separation of chiral amines.

Method development in interaction polymer chromatography

Interaction polymer chromatography (IPC) is an umbrella term covering a large variety of primarily enthalpically-dominated macromolecular separation methods. These include temperature-gradient interaction chromatography, interactive gradient polymer elution chromatography (GPEC), barrier methods, etc. Also included are methods such as liquid chromatography at the critical conditions and GPEC in traditional precipitation-redissolution mode. IPC techniques are employed to determine the chemical composition distribution of copolymers, to separate multicomponent polymeric samples according to their chemical constituents, to determine the tacticity and end-group distribution of polymers, and to determine the chemical composition and molar mass distributions of select blocks in block copolymers. These are all properties which greatly affect the processing and end-use behavior of macromolecules. While extremely powerful, IPC methods are rarely employed outside academic and select industrial laboratories. This is generally because most published methods are "bespoke" ones, applicable only to the particular polymer being examined; as such, potential practitioners are faced with a lack of inductive information regarding how to develop IPC separations in non-empirical fashion. The aim of the present review is to distill from the literature and the author's experience the necessary fundamental macromolecular and chromatographic information so that those interested in doing so may develop IPC methods for their particular analytes of interest, regardless of what these analytes may be, with as little trial-and-error as possible. While much remains to be determined in this area, especially, for most techniques, as regards the role of temperature and how to fine-tune this critical parameter, and while a need for IPC columns designed specifically for large-molecule separations remains apparent, it is hoped that the present review will help place IPC methods in the hands of a more general, yet simultaneously more applied audience.

Generic approach to the method development of intact protein separations using hydrophobic interaction chromatography

We describe a liquid chromatography method development approach for the separation of intact proteins using hydrophobic interaction chromatography. First, protein retention was determined as function of the salt concentration by isocratic measurements and modeled using linear regression. The error between measured and predicted retention factors was studied while varying gradient time (between 15 and 120 min) and gradient starting conditions, and ranged between 2 and 15%. To reduce the time needed to develop optimized gradient methods for hydrophobic interaction chromatography separations, retention-time estimations were also assessed based on two gradient scouting runs, resulting in significantly improved retention-time predictions (average error < 2.5%) when varying gradient time. When starting the scouting gradient at lower salt concentrations (stronger eluent), retention time prediction became inaccurate in contrast to predictions based on isocratic runs. Application of three scouting runs and a nonlinear model, incorporating the effects of gradient duration and mobile-phase composition at the start of the gradient, provides accurate results (improved fitting compared to the linear solvent-strength model) with an average error of 1.0% and maximum deviation of -8.3%. Finally, gradient scouting runs and retention-time modeling have been applied for the optimization of a critical-pair protein isoform separation encountered in a biotechnological sample.

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.

Peak capacity in gradient reversed-phase liquid chromatography of biopolymers. Theoretical and practical implications for the separation of oligonucleotides

Reversed-phase ultra-performance liquid chromatography was used for biopolymer separations in isocratic and gradient mode. The gradient elution mode was employed to estimate the optimal mobile phase flow rate to obtain the best column efficiency and the peak capacity for three classes of analytes: peptides, oligonucleotides and proteins. The results indicate that the flow rate of the Van Deemter optimum for 2.1 mm I.D. columns packed with a porous 1.7 microm C18 sorbent is below 0.2 mL/min for our analytes. However, the maximum peak capacity is achieved at flow rates between 0.15 and 1.0 mL/min, depending on the molecular weight of the analyte. The isocratic separation mode was utilized to measure the dependence of the retention factor on the mobile phase composition. Constants derived from isocratic experiments were utilized in a mathematical model based on gradient theory. Column peak capacity was predicted as a function of flow rate, gradient slope and column length. Predicted peak capacity trends were compared to experimental results.

Implications of column peak capacity on the separation of complex peptide mixtures in single- and two-dimensional high-performance liquid chromatography

Column peak capacity was utilized as a measure of column efficiency for gradient elution conditions. Peak capacity was evaluated experimentally for reversed-phase (RP) and cation-exchange high-performance liquid chromatography (HPLC) columns, and compared to the values predicted from RP-HPLC gradient theory. The model was found to be useful for the prediction of peak capacity and productivity in single- and two-dimensional (2D) chromatography. Both theoretical prediction and experimental data suggest that the number of peaks separated in HPLC reaches an upper limit, despite using highly efficient columns or very shallow gradients. The practical peak capacity value is about several hundred for state-of-the-art RP-HPLC columns. Doubling the column length (efficiency) improves the peak capacity by only 40%, and proportionally increases both the separation time and the backpressure. Similarly, extremely shallow gradients have a positive effect on the peak capacity, but analysis becomes unacceptably long. The model predicts that a 2D-HPLC peak capacity of 15,000 can be achieved in 8 h using multiple fraction collection in the first dimension followed by fast RP-HPLC gradients employing short, but efficient columns in the second dimension.

Protein selectivity in immobilized metal affinity chromatography based on the surface accessibility of aspartic and glutamic acid residues

The interaction of different species variants of cytochrome c and myoglobin, as well as hen egg white lysozyme, with the hard Lewis metal ions Al3+, Ca2+, Fe3+, and Yb3+ and the borderline metal ion Cu2+, immobilized to iminodiacetic acid (IDA)-Sepharose CL-4B, has been investigated over the range pH 5.5-8.0. With appropriately chosen buffer and metal ion conditions, these proteins can be bound to the immobilized Mn+-IDA adsorbents via negatively charged amino acid residues accessible on the protein surface. For example, tuna heart cytochrome c, which lacks surface-accessible histidine residues, readily bound to the Fe3+-IDA adsorbent, while the other proteins also showed affinity toward immobilized Fe3+-IDA adsorbents when buffers containing 30 mM of imidazole were used. These studies document that protein selectivity can be achieved with hard-metal-ion immobilized metal ion affinity chromatography (IMAC) systems through the interaction of surface-exposed aspartic and glutamic acid residues on the protein with the immobilized Mn+-IDA complex. These investigations have also documented that the so-called soft or borderline immobilized metal ions such as the Cu2+-IDA adsorbent can also interact with surface-accessible aspartic and glutamic acid residues in a protein-dependent manner. A relationship is evident between the number of clustering of the surface-accessible aspartic and glutamic residues and protein selectivity with these IMAC systems. The use of elution buffers which contain organic compound modifiers which replicate the carboxyl group moieties of these amino acids on the surface of proteins is also described.

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.

Dependence of retention on the organic modifier concentration and multicomponent adsorption behavior in reversed-phase chromatography

A three-parameter equation is derived to express the dependence of the logarithmic retention factor, kappa, on the volume fraction of the retention modulator, phi, in a binary eluent (such as the organic modifier in the hydro-organic eluents used in reversed-phase chromatography). It is based on the competitive binary adsorption isotherm of the eluite and the modulator generated by employing the ideal adsorbed solution (IAS) method. The equation is found to describe adequately the trends in the kappa-phi relationship experimentally observed in reversed-phase systems. Furthermore, the expression affords an estimation of the single-component adsorption isotherm of the eluite from the corresponding kappa versus phi plot and thus provides a simple means to gather data of importance in the design of separations by non-linear chromatography. For instance, the method can be used to determine whether a pair of eluite isotherms cross one another, a situation that could lead to difficulties in preparative separations. The inherent limitations of the IAS approach may restrict the usefulness of the expression in specific cases. Nevertheless, the approach presented here establishes an explicit, thermodynamically consistent link between the eluite-modulator multicomponent isotherm and corresponding plots and allows a rational description of the generally observed retention behavior in reversed-phase chromatography. The results of this work also illustrate the limitations of the competitive Langmuir isotherm, which is most frequently used to treat competitive adsorption, in the study of the kappa-phi relationship specifically and in investigating and modeling non-linear chromatography at large.

Separation of proteins by reversed-phase high-performance liquid chromatography. II. Optimizing sample pretreatment and mobile phase conditions

The effects of separation variables such as temperature, pH and composition of the mobile phase (including additives such as chaotropes, ion-pairing agents and surfactants), sample size and sample pretreatment for reversed-phase high-performance liquid chromatography (RP-HPLC) of proteins is examined. Experimental optimization of these parameters using the preferred instrumental and column conditions described previously lead to well behaved chromatographic performance for most proteins. This allowed us to achieve the required level of performance for the first dimension (RP-HPLC) separation of most protein samples by the chromatophoresis process.

Prediction of peptide retention times

A new approach for predicting the retention times of peptides, either with isocratic or gradient elution is described. The isocratic capacity factors of peptides are correlated with their molecular weights and with their hydrophobicities. Given the experimental conditions, and the amino acid composition, it is possible to calculate the retention time of a peptide eluted by a gradient, for any slope of gradient, flow-rate and column length.

High-performance liquid chromatography column length designed for submicrogram scale protein isolation

High-performance liquid chromatography of small amounts of protein was readdressed with respect to current gas-phase sequencing technology. Useful primary sequence information can be obtained from as little as 5-100 pmol of material. This corresponds on a mass level to the nanogram to microgram range where, unfortunately, HPLC columns often give low recoveries depending on the size and surface hydrophobicity of the peptide or protein. It was rationalized in this study that reduced column length could have a beneficial effect on recovery without significant loss of resolution. To demonstrate this, six HPLC columns ranging from 0.2 to 25 cm in length were made and evaluated in terms of protein loading and resolution. Column lengths of less than 1 cm were found to increase recovery of surface hydrophobic proteins without loss of resolution, as shown for a standard protein profile. These columns resolve proteins best when loaded with less than 10 micrograms, with recoveries greater than 90%. All column internal diameters were at least 4.1 mm so that standard HPLC pumps could be used to generate gradients.

Reversed-phase high-performance liquid chromatography of human haemoglobin chains

A reversed-phase high-performance liquid chromatographic method for the separation of human haemoglobin chains has been devised. Using a LiChrospher 100 CH-8/2 column and a ternary eluent (acetonitrile-methanol-0.155 M NaCl, pH 2.7) improved resolution was achieved between (delta beta) Lepore, beta A, beta S, alpha, G gamma and A gamma chains within a 60-min linear gradient. The A gamma T chain can also be separated by increasing the gradient time and decreasing the flow-rate. Silanophilic interactions play an important role in the retention mechanism, and NaCl addition was necessary in order to suppress adsorption on free silanols. Increasing the methanol concentration to 10% caused a slight increase in chain retention, probably owing to solvation of the stationary phase. The recovery was 82% and the reproducibility of retention times was as good as +/- 1.5%. Quantitation of chains is likely to be possible by peak area measurement. Owing to its sensitivity, the proposed method may be useful in the diagnosis of haemoglobinopathies and in the study of haemoglobin variants.

Protein separations on reversed-phase high-performance liquid chromatography minicolumns

The resolution of cytochrome c, bovine serum albumin and ovalbumin on reversed-phase columns under gradient elution conditions was found to be constant or to improve as column length was decreased from 45 to 6.3 mm. The resolution remained constant even when the column length decreased to 1.6 mm. Recovery of protein in the first gradient cycle was improved by the use of short columns.

Ca2+-binding proteins: a comparative study of their behavior during high-performance liquid chromatography using gradient elution on reverse-phase supports

Reverse-phase high-performance liquid chromatography has been shown to be applicable to the isolation of Ca2+-binding proteins, specifically parvalbumins, from tissue extracts or from preparations first purified by "conventional" chromatography. Through an investigation of the behavior of a series of Ca2+-binding proteins as a function of buffer composition, pH, and organic eluant it has been possible to define mild conditions allowing for chromatography of the proteins in their native states. The elution positions of parvalbumins were not observed to correlate with the "overall" protein hydrophobicity, calculated using hydrophobicity values for the individual amino acids, thus indicating that factors such as hydrophobic/hydrophilic surface areas are important in determining the degree of association with the support. The usefulness of reverse-phase chromatography as an analytical tool for determining protein homogeneity is illustrated. Samples which had been isolated via "conventional" chromatography methods, and thought to be homogeneous, were observed to contain multiple species of the same protein.

Reversed-phase high-performance liquid chromatography of virus proteins and other large hydrophobic proteins in formic acid containing solvents

The excellent dissolving capacity of formic acid together with a propanol-2 gradient is utilized in a new system for reversed-phase high-performance liquid chromatographic separation of poliovirus polypeptides and a variety of large proteins. Differences in elution characteristics were detected between reduced and non-reduced proteins containing disulphide bridges as well as proteins modified at cysteinyl residues. The retention coefficients of single amino acids were used to calculate those of proteins. The correlation of calculated coefficients with actual retention times indicates that some proteins are bound via their full, unfolded length to the reversed-phase support, whereas others partly preserved their secondary structure. Treatment of proteins with sodium dodecyl sulphate prior to injection dissociates these structural elements and leads to an increase in retention times. The high resolution of the system described should be applicable to the isolation and characterization of components of mixtures of proteins, particularly those of water-insoluble proteins of membranes or viruses, on the analytical and semi-preparative scales.