Applicability of the critical chromatography concept to proteomics problems: Dependence of retention time on the sequence of amino acids

A peptide separation model based on the technique of liquid chromatography of macromolecules at the critical condition was proposed. In terms of this model, the array of experimental data on the separation of peptides is considered. The main phenomenological parameters of the model—effective adsorption energies of amino acid residues—were determined, thus allowing the influence of character of their alternation in the chain on retention times to be predicted. The model is applicable to investigation into the feasibility of separation in different chromatographic modes of not only peptides with the same amino acid composition and different sequences of units in the chain but also peptides containing amino acid isomers and mirror sequences with different terminal groups.     

Applicability of the critical chromatography concept to proteomics problems: Experimental study of the dependence of peptide retention time on the sequence of amino acids in the chain

Experimental data on the separation of synthetic and natural peptides are presented as treated in terms of the separation model proposed by the authors, which allows for the chain connectivity of amino acid residues and the cooperative character of their interaction with the surface. It was shown that the model accurately predicts the separation of peptides with identical amino acid contents and different sequences of units in the chain. The differences in the sequence may be permutation of amino acid residues and the presence of terminal groups, amino acid isomers, or mirror sequences in the chain. The separation model was used to predict the retention times of peptides prepared via the enzymatic hydrolysis of E. coli proteins and bovine serum albumin with trypsin. It was shown that in general the model accurately explains the array of experimental data on the separation of such peptides, thus being the first successful attempt to relate the chain sequence to the retention volume.     

On the utility of predictive chromatography to complement mass spectrometry based intact protein identification

The amino acid sequence determines the individual protein three-dimensional structure and its functioning in an organism. Therefore, “reading” a protein sequence and determining its changes due to mutations or post-translational modifications is one of the objectives of proteomic experiments. The commonly utilized approach is gradient high-performance liquid chromatography (HPLC) in combination with tandem mass spectrometry. While serving as a way to simplify the protein mixture, the liquid chromatography may be an additional analytical tool providing complementary information about the protein structure. Previous attempts to develop “predictive” HPLC for large biomacromolecules were limited by empirically derived equations based purely on the adsorption mechanisms of the retention and applicable to relatively small polypeptide molecules. A mechanism of the large biomacromolecule retention in reversed-phase gradient HPLC was described recently in thermodynamics terms by the analytical model of liquid chromatography at critical conditions (BioLCCC). In this work, we applied the BioLCCC model to predict retention of the intact proteins as well as their large proteolytic peptides separated under different HPLC conditions. The specific aim of these proof-of-principle studies was to demonstrate the feasibility of using “predictive” HPLC as a complementary tool to support the analysis of identified intact proteins in top-down, middle-down, and/or targeted selected reaction monitoring (SRM)-based proteomic experiments.     

Retention behavior of peptides in hydrophilic-interaction chromatography

Selected hydrophilic interaction chromatography (HILIC) columns packed with bare silica, bridge-ethyl hybrid silica, or an amide sorbent chemistry were utilized for an investigation of chromatographic behavior and separation selectivity of tryptic peptides. Retention model was proposed allowing for retention prediction of peptides with correlation coefficient R(2)~0.92-0.97 for various columns. The values of optimized amino acid retention coefficients were compared to those obtained for reversed-phase liquid chromatography (Gilar et al., Anal. Chem. 2010, 82, 265-275) and used to elucidate the impact of different amino acid on peptide HILIC retention. In contrast to reversed-phase chromatography, where presence of Phe, Trp, Ile, and Leu amino acid residues in sequence strongly promoted, and presence of hydrophilic His, Lys and Arg residues strongly reduced peptide retention, the effects of these amino acid residues in HILIC were opposite (His, Lys and Arg promote, Phe, Trp, Ile and Leu demote peptide retention in HILIC). Retention coefficient optimized for pH experiments illustrated the impact of silanols on HILIC retention.     

Applicability of the critical chromatography concept to proteomic problems. II. Effect of mobile phase on the separation of peptides and proteins taking into account the amino acid sequence

The effect of parameters of a binary mobile phase (chemical properties of components, gradient profile, flow rate, and pH) on the separation of peptides and proteins is theoretically investigated using a model of critical chromatography (model BioLCCC). It is demonstrated that the retention volume of peptides can be inverted by changing separation conditions.     

Comparison of various types of stationary phases in non-aqueous reversed-phase high-performance liquid chromatography–mass spectrometry of glycerolipids in blackcurrant oil and its enzymatic hydrolysis mixture

The selection of column packing during the development of high-performance liquid chromatography method is a crucial step to achieve sufficient chromatographic resolution of analyzed species in complex mixtures. Various stationary phases are tested in this paper for the analysis of complex mixture of triacylglycerols (TGs) in blackcurrant oil using non-aqueous reversed-phase (NARP) system with acetonitrile–2-propanol mobile phase. Conventional C₁₈ column in the total length of 45 cm is used for the separation of TGs according to their equivalent carbon number, the number and positions of double bonds and acyl chain lengths. The separation of TGs and their more polar hydrolysis products after the partial enzymatic hydrolysis of blackcurrant oil in one chromatographic run is achieved using conventional C₁₈ column. Retention times of TGs are reduced almost 10 times without the loss of the chromatographic resolution using ultra high-performance liquid chromatography with 1.7 μm C₁₈ particles. The separation in NARP system on C₃₀ column shows an unusual phenomenon, because the retention order of TGs changes depending on the column temperature, which is reported for the first time. The commercial monolithic column modified with C₁₈ is used for the fast analysis of TGs to increase the sample throughput but at cost of low resolution.     

“Sock-Ball” Chromatographic Separation of Some Polycyclic Aromatic Hydrocarbons with C60-Fullerene Stationary Phase

Polycyclic aromatic hydrocarbons (PAHs) of different molecular shapes were tested and compared with a prepared C₆₀-fullerene-phase, and with the commercial Amino-phase or RP-18-phase in the mobile phase of methanol/dichloromethane (90/10 — 70/30) or n-hexane/dichloromethane (80/20). The chromatographic separation results indicate that C₆₀-fullerene-phase achieves the special selectivities and performances for the separation of PAHs. Based on the retention mechanism of “π-π” complex interaction or “Sock-Ball” shaped combination, PAHs undergo more pronounced interaction with C₆₀ ligand. For example, decacyclene, a sock-shaped PAH, the structure of which was calculated by means of semi-empirical molecular orbital methods, possesses stronger retention to give a “Sock-Ball” chromatographic separation with C₆₀-fullerene-phase. However, PAHs with bend, planar, or co-planar structures eluted on C₆₀-fullerene-phase undergo adsorption chromatography, but possess weaker retentions. The retention power of “Sock-Ball” chromatography can successfully recognize the different molecular shapes of PAHs.     

Comparison of a C30 Bonded Silica Column and Columns with Shorter Bonded Ligands in Reversed-Phase LC

The Carotenoid S is a new C₃₀ bonded silica stationary phase, intended for reversed-phase chromatographic applications, which is more hydrophobic and consequently shows stronger retention in comparison to conventionally used C₁₈ stationary phases. We compared the non-polar selectivities of the columns for homologous alkylbenzenes in acetonitrile—water and methanol–water mobile phases and polar reversed-phase selectivities employing the interaction indices and the Linear Free Energy Relationship models. Further, we investigated possibilities of separations of structurally closely related compounds in the groups of phenolic acids, flavones, phthalic acids and related compounds and of acylglycerols on the new C₃₀ column and with different types of columns for reversed-phase chromatography, including shorter alkyl C₄, C₈, C₁₈ and phenyl bonded stationary phases. The C₃₀ column has in some aspects properties similar to the non-endcapped Nova-Pak column for separation of some acylglycerols with equal equivalent carbon numbers, but enables separations of longer chain triacylglycerols in a single gradient run.

     

Isocratic Separation of Fatty Acid Derivatives by Reversed Phase Liquid Chromatography. Influence of the Solvent on Selectivity and Rules for Elution Order

Abstract

The p-bromophenacyl esters of 16 fatty acids (C₁₂-C₂₂) have been separated by isocratic chromatography on a Radial Pak A cartridge (Reverse phase C₁₈ material). The separation factors α were measured using two solvent mixtures of comparable strength and the superiority of methanol-water to acetonitrile-water becomes evident.

Five precise rules are established, which indicates the retention of every fatty acid. They explain the chromatographic process i.e. elution order, resolution and selectivity.     

Separation optimization of quercetin,hesperetin and chrysin in honey by micellar liquid chromatography and experimental design

The chemometrics approach was applied for the separation optimization of flavonoid markers (quercetin, hesperetin and chrysin) in honey using micellar liquid chromatography (MLC). The investigated method combines SPE of flavonoids from honey using C₁₈ cartridge and their separation and quantification by micellar liquid chromatography. A two level full factorial design was carried out to evaluate the effect of four experimental factors including concentration of SDS, alkyl chain length of the alcohol used as the organic modifier (N), volume percentage of the organic modifier (V_m) and volume percentage of acetic acid (AcOH) in mobile phase on analytes retention times. Experiments for analytes retention times modeling and optimization of separation were performed according to central composite design. Multiple linear regression method was used for the construction of the best model based on experimental retention times. Pareto optimal method was used to find suitable compatibility between resolution and analysis time of analytes in honey. The optimum mobile phase composition for separation and determination of analytes in honey were [SDS]=0.124 mol/L; 7.8% v/v ethanol and 5.0% v/v AcOH. Limits of detection and linear range of flavonoid markers were 0.0079–0.0126, 0.05–50.0 mg/L, respectively.     

Evaluation and comparison of n‐alkyl chain and polar ligand bonded stationary phases for protein separation in reversed‐phase liquid chromatography

Protein retention is very sensitive to the change of solvent composition in reversed‐phase liquid chromatography for so called “on–off” mechanism, leading to difficulty in mobile phase optimization. In this study, a novel 3‐chloropropyl trichlorosilane ligand bonded column was prepared for protein separation. The differences in retention characteristics between the 3‐chloropropyl trichlorosilane ligand bonded column and n‐alkyl chain modified (C₂, C₄, C₈) stationary phases were elucidated by the retention equation . Retention parameters (a and c) of nine standard proteins with different molecular weights were calculated by using homemade software. Results showed that retention times of nine proteins were similar on four columns, but the 3‐chloropropyl trichlorosilane ligand bonded column obtained the lowest retention parameter values of larger proteins. It meant that their retention behavior affected by acetonitrile concentration would be different due to lower |c| values. More specifically, protein elution windows were broader, and retentions were less sensitive to the change of acetonitrile concentration on the 3‐chloropropyl trichlorosilane ligand bonded column than that on other columns. Meanwhile, the 3‐chloropropyl trichlorosilane ligand bonded column displayed distinctive selectivity for some proteins. Our results indicated that stationary phase with polar ligand provided potential solutions to the “on–off” problem and optimization in protein separation.     

The Influence of Reversed-Phase n-Alkyl Chain Length on Protein Retention,Resolution and Recovery: Implications for Preparative HPLC

Abstract

High-performance liquid chromatography (HPLC) of proteins on reversed-phase columns of varying n-alkyl chain length (C₂ to C₂₂ was studied using a trifluoroacetic acid/2-propanol mobile phase system. Protein resolution was influenced by chain length but retention times for proteins, unlike those of small molecules, were relatively constant, independent of chain length or carbon loading. Loading capacities were found to be affected by chain length, and aspects of protein interaction with stationary phase are discussed.     

Retention behavior of a homologous series and positional isomers of aliphatic amino acids in hydrophilic interaction chromatography

The retention behavior of several series of free α‐ and ω‐amino acids and positional isomers of amino pentanoic acid in the hydrophilic interaction chromatography mode (HILIC) was studied. The study was carried out on three stationary phases followed by post‐column derivatization with fluorescence detection in order to describe the retention mechanism of the tested amino acids. The effect of chromatographic conditions including acetonitrile content in the mobile phase, mobile phase pH (ranging from 3.5 to 6.5) and concentration of buffer in the mobile phase was investigated. The effect of the number of carbon atoms (n_C) in aliphatic chains of the individual homologue of α‐ and ω‐amino acids and the logarithm of the partition coefficient (logD) on retention was also a part of the presented study. A good correlation (r > 0.98) between the logk and logD values of amino acids or n_C, respectively, was observed. The described linear relationships were subsequently applied to predict the retention behavior of individual members of the homologous series of amino acids and to optimize the mobile phase composition in HILIC. The obtained results confirmed that the retention mechanism of α‐amino acids, ω‐amino acids and positional isomers of amino acids was based on the logD values and the number of carbon atoms in the aliphatic chains of amino acids. The elution order of ω‐amino acids and positional isomers of amino pentanoic acid was strongly dependent on the mobile phase pH in the investigated range whereas the retention factors of all α‐amino acids remained essentially unchanged on all tested stationary phases.     

A Rapid Isolation of Human Chorionic Gonadotropin and Its Subunits by Reversed-Phase High Performance Liquid Chromatography

Abstract

A rapid isolation of human chorionic gonadotropin and its subunits from a commercially available concentrate of human urine has been achieved using reversed-phase high performance liquid chromatography. With μBondapak C₁₈ columns and a gradient employing aqueous trifluoroacetic acid as one solvent and dilute trifluoroacetic acid in acetonitrile as the other, complete separation can be accomplished in one day whereas standard column chromatographic procedures take about two weeks. Specific radioimmunoassays, polyacrylamide gel electrophoresis, and amino acid analyses were used to identify and characterize chromatographic peaks.     

Analysis of Group Retention Contributions for Peptides Separated by Reversed Phase High Performance Liquid Chromatography

Abstract

Within the framework provided by solvophobic theory, selectivities for unprotected peptides separated on fully porous, microparticulate, chemically bonded alkylsilicas can be ascribed to differences between the effective hydrophobic contact areas of the solutes. Furthermore, this theoretical treatment predicts that retention behaviour differences can be evaluated from topological parameters which accomodate the influence of amino acid side chain and end group contributions in the retention process. With data obtained for 57 peptides, including a variety of peptide hormones, eluted under the same conditions from a μBondapak C₁₈ column, these predictions have been rigorously tested using two methods of numerical analysis. The results provide further evidence that the hydrophobic group retention contributions of the amino acid residues in small peptides have an essentially additive effect on peptide retention with alkylsilicas. Divergences in retention behaviour are interpreted in terms of specific silanophilic and solvation interactions.     

Enantiomeric separation of unusual secondary aromatic amino acids

Summary High-performance liquid chromatographic and gas chromatographic methods were developed for the separation of unusual secondary aromatic amino acids. Amino acids containing 1,2,3,4-tetrahydroisoquinoline, 1,2,3,4-tetrahydronorharmane-1-carboxylic acid and 1,2,3,4-tetrahydro-3-carboxy-2-carboline moieties were synthetized in racemic or chiral forms. The high-performance liquid chromatography was carried out either on a teicoplanin-containing chiral stationary phase or on an achiral C₁₈ column. In the latter case the diastereomers of the amino acids formed by precolumn derivatization with the chiral reagents 2,3,4,6-tetra-O-acetyl-β-D-glucopyranosyl isothiocyanate or 1-fluoro-2,4-dinitrophenyl-5-L-alanine amide were separated. The gas chromatographic analyses were based on separation on a Chirasil-L-Val column. Presented at: Balaton Symposium on High-Performance Separation Methods, Siófok, Hungary, September 3–5, 1997     

Adsorption Study of Immunoglobulin G Subclasses from Different Species by Pseudobioaffinity Separation on Histidyl–Bisoxirane–Sepharose

Adsorption chromatography is increasingly used for protein separations and biomedical applications. Therapeutic molecules such as antibodies, cytokines, therapeutic DNA, and plasma proteins must be purified before characterization and utilization. Use of immunoglobulins as immunodiagnostic and therapeutic tools has initiated many attempts to develop new adsorbents for their separation. Protein A and protein G are the affinity ligands most widely used for separation of immunoglobulins. These proteins are reliable, and have good selectivity and specificity, but are very expensive. Much attention has therefore been devoted to developing alternative methods for separation of immunoglobulins. Pseudobiospecific ligands, for example metal ions and amino acids, can be used for separation of a wide range of biological molecules. In this study, IgG₁, IgG₂, and IgG₃, three subclasses of human IgG, were separated from human serum using the amino acid histidine grafted on to bisoxirane-activated Sepharose, as pseudobiospecific adsorbent. Adsorption of IgG from different animal species on the same chromatographic adsorbent was also tested. The high recovery and purification on histidyl–bisoxirane–Sepharose gel of IgG from all the sources tested compared well with results obtained by use of protein A–Sepharose gel.

     

Preparation of High‐capacity,Monodisperse Polymeric Weak Cation Exchange Packings Using Surface‐initiated Atom Transfer Radical Polymerization and Its Chromatographic Properties

A novel stationary phase for weak cation exchange (WCX) chromatography was prepared by "grafting from" strategy. Surface initiated atom transfer radical polymerization (ATRP) of acrylic acid (AA) was conducted in toluene medium, starting from the macromolecule initiators of poly(4‐vinylbenzyl chloride‐co‐divinylbenzene) (P_CMS/DVB) beads. The amounts of poly(acrylic acid) grafted chains with different ATRP formulations were calculated based on the elemental analyses. The poly(acrylic acid) grafted beads obtained with different ATRP formulations were tried as chromatographic packings in the separation of proteins by ion‐exchange chromatography. The effect of the poly(acrylic acid) grafted chain lengths on P_CMS/DVB beads for the separation of proteins was investigated in details. Simultaneously, characterization of the column was investigated as ion chromatographic stationary phase for the separation of inorganic cations. The results show that poly(acrylic acid) grafted columns had excellent performance for separation of proteins and inorganic cations. The highest of the dynamic capacity of the column was 35.55 mg/mL. The columns were provided with high column efficiency.