Monitoring free silanols on reversed-phase supports with peptide standards

An improved approach to hydrophilic interaction chromatography of peptides: salt gradients in the presence of high isocratic acetonitrile concentrations

Hydrophilic interaction chromatography (HILIC) for separations of peptides has been employed infrequently, particularly considering that this technique was introduced over 20 years ago. The present manuscript describes a radical departure from the traditional HILIC elution approach, where separations are achieved via increasing salt (sodium perchlorate) gradients in the presence of high isocratic concentrations (>80%) of acetonitrile, denoted HILIC/SALT. This initial study compared to reversed-phase chromatography (RPC), HILIC and HILIC/SALT for the separation of mixtures of synthetic peptide standards varying in structure (amphipathic α-helix, random coil), length (10-26 residues), number of positively charged residues (+1 to +11) and hydrophilicity/hydrophobicity. Results showed a marked superiority of the HILIC/SALT approach compared to traditional HILIC and excellent complementarity to RPC for peptide separations. We believe these initial results offer a new dimension to HILIC, enabling it to transform from an occasional HPLC approach for peptide separations to a more generally applicable method.

Design of peptide standards with the same composition and minimal sequence variation to monitor performance/selectivity of reversed-phase matrices

The present manuscript extends our de novo peptide design approach to the synthesis and evaluation of a new generation of reversed-phase HPLC peptide standards with the same composition and minimal sequence variation (SCMSV). Thus, we have designed and synthesized four series of peptide standards with the sequences Gly-X-Leu-Gly-Leu-Ala-Leu-Gly-Gly-Leu-Lys-Lys-amide, where the N-terminal is either N(α)-acetylated (Series 1) or contains a free α-amino group (Series 3); and Gly-Gly-Leu-Gly-Gly-Ala-Leu-Gly-X-Leu-Lys-Lys-amide, where the N-terminal is either N(α)-acetylated (Series 2) or contains a free α-amino group (Series 4). In this initial study, the single substitution position, X, was substituted with alkyl side-chains (Ala Collapse

Key Words Collapse

MESH Headings

• Amino Acid Sequence
• Chromatography, High Pressure Liquid/standards
• Chromatography, Reverse-Phase/standards
• Peptides/chemistry
• Reference Standards

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Grants

• R01 GM061855 NIGMS NIH HHS
• R01 GM061855-10 NIGMS NIH HHS
• R01 GM61855 NIGMS NIH HHS

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Affiliation(s)

Colin T. Mant Department of Biochemistry and Molecular Genetics, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA
Robert S. Hodges Department of Biochemistry and Molecular Genetics, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA

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Loss of Bonded Phase in Reversed-Phase Liquid Chromatography in Acidic Eluents and Practical Ways To Improve Column Stability

Silica-based, reversed-phase liquid chromatographic (RPLC) stationary phases are very widely used to separate basic compounds in acidic eluents due to their high efficiency, good mechanical strength, and the versatile selectivity offered by different functional groups and the chemistry on the silica surface. However, the stability in acid of most silica-based stationary phases is poor, especially at elevated temperatures, due to hydrolysis of the siloxane bonds, which hold silanes on the silica substrate. This hydrolysis is commonly believed to be solely the result of catalysis by protons. However, we show that various metal cations (principally Fe3+/Fe2+, Ni2+, and Cr3+) released from acid corrosion of the stainless steel inlet frit greatly accelerate the hydrolysis of the siloxane bond. Furthermore, these metal cations, and not the high acidity per se, are mainly responsible for column instability. We show that removing the stainless steel inlet frit, or use of a titanium frit, greatly reduces or totally eliminates corrosion of the inlet frit and radically improves retention stability. The effects of various acids and types of organic modifier were also studied. These observations suggest a number of practical approaches that can significantly extend the lifetime of any RPLC stationary phase in acidic media at elevated temperature.

HPLC analysis and purification of peptides

High-performance liquid chromatography (HPLC) has proved extremely versatile over the past 25 yr for the isolation and purification of peptides varying widely in their sources, quantity and complexity. This article covers the major modes of HPLC utilized for peptides (size-exclusion, ion-exchange, and reversed-phase), as well as demonstrating the potential of a novel mixed-mode hydrophilic interaction/cation-exchange approach developed in this laboratory. In addition to the value of these HPLC modes for peptide separations, the value of various HPLC techniques for structural characterization of peptides and proteins will be addressed, e.g., assessment of oligomerization state of peptides/proteins by size-exclusion chromatography and monitoring the hydrophilicity/hydrophobicity of amphipathic alpha-helical peptides, a vital precursor for the development of novel antimicrobial peptides. The value of capillary electrophoresis for peptide separations is also demonstrated. Preparative reversed-phase chromatography purification protocols for sample loads of up to 200 mg on analytical columns and instrumentation are introduced for both peptides and recombinant proteins.

The perchlorate anion is more effective than the trifluoroacetate anion as an ion-pairing reagent for reversed-phase chromatography of peptides

The addition of salts, specifically sodium perchlorate (NaClO4), to mobile phases at acidic pH as ion-pairing reagents for reversed-phase high-performance liquid chromatography (RP-HPLC) has been generally overlooked. To demonstrate the potential of NaClO4 as an effective anionic ion-pairing reagent, we applied RP-HPLC in the presence of 0-100 mM sodium chloride (NaCl), sodium trifluoroacetate (NaTFA) or NaClO4 to two mixtures of synthetic 18-residue peptides: a mixture of peptides with the same net positive charge (+4) and a mixture of four peptides of +1, +2, +3 and +4 net charge. Interestingly, the effect of increasing NaClO4 concentration on increasing peptide retention times and selectivity changes was more dramatic than that of either NaCl or NaTFA, with the order of increasing anion effectiveness being Cl- << TFA- < C104-. Such effects were more marked when salt addition was applied to eluents containing 10 mM phosphoric acid (H3PO4) compared to 10 mM trifluoroacetic acid (TFA) due to the lesser starting anion hydrophobicity of the former mobile phase (containing the phosphate ion) compared to the latter (containing the TFA- ion).

Effect of anionic ion-pairing reagent concentration (1-60 mM) on reversed-phase liquid chromatography elution behaviour of peptides

The homologous series of volatile perfluorinated acids-trifluoroacetic acid (TFA), pentafluoropropionic acid (PFPA) and heptafluorobutyric acid (HFBA)--continue to be excellent anionic ion-pairing reagents for reversed-phase high-performance liquid chromatography (RP-HPLC) after more than two decades since their introduction to this field. It was felt that a thorough, step-by-step re-examination of the effects of anionic ion-pairing reagents over a wide concentration range on RP-HPLC peptide elution behaviour is now due, particularly considering the continuing dominance of such reagents for peptide applications. Thus, RP-HPLC was applied over a range of 1-60 mM phosphoric acid, TFA, PFPA and HFBA to two mixtures of 18-residue synthetic peptides containing either the same net positive charge (+4) or varying positive charge (+1, +2, +3, +4). Peptides with the same charge are resolved very similarly independent of the ion-pairing reagent used, although the overall retention times of the peptides increase with increasing hydrophobicity of the anion: phosphate < TFA- < PFPA- < HFBA-. Peptides of differing charge move at differing rates relative to each other depending on concentration of ion-pairing reagents. All four ion-pairing reagents increased peptide retention time with increasing concentration, albeit to different extents, again based on hydrophobicity of the anion, i.e., the more hydrophobic the anion, the greater the increase in peptide retention time at the same reagent concentration. Interestingly, phosphoric acid produced the best separation of the four-peptide mixture (+1 to +4 net charge). In addition, concentrations above 10 mM HFBA produced a reversal of the elution order of the four peptides (+1 < + 2 < + 3 < + 4) compared to the elution order produced by the other three reagents over the entire concentration range (+4 < + 3 < + 2 < + 1).

Study of overloading of basic drugs and peptides in reversed-phase high-performance liquid chromatography using pH adjustment of weak acid mobile phases suitable for mass spectrometry

Serious losses in column efficiency for ionised basic drugs and peptides occur due to overloading of C18 phases when weak acid mobile phases of low ionic strength suitable for mass spectrometric detection are used. Measurable changes in retention time and efficiency can be observed even for levels around 0.01 microg of basic drugs on 0.46 cm I.D. columns; the overloading process is a continuum, rather than an event which takes place only once a certain threshold value has been reached. Overloading can be reduced by increasing the mobile phase pH, e.g to the pKa of the weak acid, which increases the ionic strength, allowing a greater degree of ion pairing and perhaps also physical screening of the adsorbed solute ions by buffer ions. Buffer capacity is also optimum at its pKa. Silanol ionisation and kinetic tailing effects were mostly absent at aqueous pH up to 4.75 on the hybrid inorganic-organic C18 phase employed in this study, except when analysing the most highly charged peptides. The exact cause of overloading of these ionic species is unclear.

Optimum concentration of trifluoroacetic acid for reversed-phase liquid chromatography of peptides revisited

Trifluoroacetic acid (TFA) remains the dominant mobile phase additive for reversed-phase high-performance liquid chromatography (RP-HPLC) of peptides after more than two decades since its introduction to this field. Generally, TFA has been employed in a concentration range of 0.05-0.1% (6.5-13 mM) for the majority of peptide separations. In order to revisit the question as to whether such a concentration range is optimum for separations of peptide mixtures containing peptides of varying net positive charge, the present study examined the effect of varying TFA concentration on RP-HPLC at 25 and 70 degrees C of three groups of synthetic 10-residue synthetic peptides containing either one (+1) or multiple (+3, +5) positively charged groups. The results show that the traditional range of TFA concentrations employed for peptide studies is not optimum for many, perhaps the majority, of peptide applications. For efficient resolution of peptide mixtures, particularly those containing peptides with multiple positive charges, our results show that 0.2-0.25% TFA in the mobile phase will achieve optimum resolution. In addition, the use of high temperature as a complement to such TFA concentration levels is also effective in maximizing peptide resolution.

Selectivity differences in the separation of amphipathic α-helical peptides during reversed-phase liquid chromatography at pHs 2.0 and 7.0

In an ongoing effort to understand the effect of varying reversed-phase high-performance liquid chromatography (RP-HPLC) parameters on the retention behaviour of peptides, necessary for the rational development of separation/optimization protocols, we believe it is important to delineate the contribution of alpha-helical structure to the selectivity of peptide separations. The present study reports the effects of varying column packing, mobile phase conditions and temperature on RP-HPLC retention behaviour at pHs 2.0 and 7.0 of peptides based on the amphipathic peptide sequence Ac-EAEKAAKEXEKAAKEAEK-amide (with position X in the centre of the hydrophobic face of the alpha-helix), where position X is substituted by L- or D-amino acids. At pH 2.0, an increase in trifluoroacetic acid concentration or the addition of sodium perchlorate to a phosphoric acid-based mobile phase had the similar effect of improving peak shape as well as increasing peptide retention time due to ion-pairing effects with the positively-charged peptides; in contrast, at pH 7.0, the addition of salt had little effect save an improvement in peak shape. Temperature was shown to have a complex influence on peptide selectivity due to varying effects on peptide conformation. In addition, subtle effects on peptide selectivity were also noted based on the column packings employed at pHs 2.0 and 7.0.

Effect of buffer on peak shape of peptides in reversed-phase high performance liquid chromatography

The effect of changing the buffer at constant low pH in the mobile phase is investigated with respect to the separation of a mixture of basic peptides. Considerably worse peak shapes, leading to poorer resolution of complex peptide mixtures, were obtained when using formic acid favoured in LC-MS applications compared with non volatile phosphate buffers or with trifluoroacetic acid (TFA). Poorer peak shapes were largely attributable to reduced column capacity for the peptides when using mobile phases of low ionic strength, due to the increased mutual repulsion of ions held on the hydrophobic column surface which is facilitated in these buffers. However, ion-pairing between the peptides and additives such as TFA or even phosphate may also lessen mutual repulsion effects, leading to greater column capacity. Overloading effects could be observed when sample masses around only 0.1 microg were injected on to standard size analytical columns in formic acid containing mobile phases; sample masses around only 1.5 microg may cause loss of half the system peak capacity in such mobile phases. Results were broadly comparable (after scaling sample size according to column diameter) on columns of both conventional (4.6 mm i.d.) and capillary (0.075 mm i.d.) dimensions. Ammonium formate may be a useful alternative buffer for some applications due to its higher ionic strength.

Repeatability and reproducibility of retention data and band profiles on reversed-phase liquid chromatography columns

The general goal of this work is to investigate the precision of chromatographic data and to determine which properties of chromatographic columns influence this factor. Chromatographic data were acquired under five different sets of experimental conditions for 30 neutral, acidic and basic test compounds on columns packed with Vydac 218TP C18, a polymeric, wide-pore silica-based stationary phase. Five columns packed with samples from the same batch of this packing material were used to measure the column-to-column reproducibility and six columns packed with material from six different batches to measure the batch-to-batch reproducibility. The parameters studied were the retention time, the retention and separation factors, the hydrophobic and the steric selectivities, the column efficiency, and the tailing factor.

Chromatographic silanol activity test procedures: the quest for a universal test

Reversed-phase chromatography is the most used and the most studied method of modern liquid chromatography. There is yet no ideal support available for preparing reversed-phase stationary phases, but the vast majority have historically been and are still prepared on microparticulate silica. The silica surface has a number of properties which make it attractive for derivatization, including easily controlled particle size and porosity and mechanical stability. There are several types of surface silanols which have their own unique properties that affect both chemical derivatization reactions and adsorptive interactions with solutes. The relative distribution of these different types of silanols may affect the characteristics of silica-based stationary phases more than the absolute number of surface silanol groups. The relative importance of each of these different types of silanols has not yet been unambiguously established. Free or isolated silanols, internally hydrogen-bonded vicinal silanols, and geminal silanols all have been implicated as the primary reaction and adsorption sites. There are many different synthetic schemes that have been used to block the remaining silanols, and "deactivated" phases are very popular. Unfortunately, there is still no universally agreed upon method to measure the accessibility or interaction of these silanols with solute molecules. Many tests have been proposed, focusing mainly on chromatographic probe molecules, but different tests run on the same column will often show different interactions. We will briefly review the surface chemistry of silica and focus on the multitude of tests that have been proposed. Our focal point will be silanol activity test; other aspects of column performance will not be included. Where possible, comparisons among the methods will be made.

De novo design of a model peptide sequence to examine the effects of single amino acid substitutions in the hydrophobic core on both stability and oligomerization state of coiled-coils

A model peptide sequence was de novo designed to investigate the hydrophobicity, stability and oligomerization state resulting from single amino acid substitutions in the hydrophobic core a position of the central heptad of a five heptad coiled-coil. This involved selecting a hydrophobic core consisting of Val and Leu at a and d positions, respectively, known to form both two- and three-stranded coiled-coils. In addition, the sequence provided the correct overall coiled-coil stability and maximized the hydrophobicity surrounding the substitution site by having Leu in the hydrophobic core above and below the site of substitution. To control oligomerization state we exploited differential placement of an interhelical disulfide-bridge, which was placed in the coiled-coil hydrophobic core at the C-terminal d position, or alternatively outside of the core at the N-terminal via a Cys-Gly-Gly linker. We found that the Cys-Gly-Gly linker allowed assessment of both relative stability and oligomerization state after extensive biophysical characterization of the models by circular dichroism, sedimentation equilibrium, sedimentation velocity and finally high-performance size-exclusion chromatography (HPSEC) under both benign and denaturing conditions. The Cys-Gly-Gly linker was found to be unique in allowing the inherent two- or three-stranded oligomerization state to be observed in benign medium, while also allowing the stability to be determined by concentration independent chemical denaturation of a two-stranded coiled-coil. This entails a two-state transition from a folded disulfide-bridged two-stranded coiled-coil (monomeric state) to the unfolded monomer, even for analogs where the coiled-coil is a trimer of disulfide-bridged peptides in benign medium. We also developed novel HPSEC methodology for monitoring the chemical denaturation of a folded monomeric protein in fast exchange with the corresponding unfolded protein, which elutes as a single peak throughout the denaturation process.

Use of sodium perchlorate at low pH for peptide separations by reversed-phase liquid chromatography. Influence of perchlorate ion on apparent hydrophilicity of positively charged amino acid side-chains

The reversed-phase liquid chromatography (RPLC) behavior of synthetic model peptides containing positively charged amino acid residues was studied in the presence or absence of 100 mM sodium perchlorate in order to determine the effect on apparent side-chain hydrophilicity of a charged residue at low pH. The peptides used in this study were either non-helical peptides or amphipathic alpha-helical peptides, where the effect of the negatively charged perchlorate ion on a charged residue in either the hydrophobic face or hydrophilic face of the helix was monitored. We have shown that the addition of 100 mM perchlorate to RPLC separations of positively charged peptides performed in a 20 mM aqueous phosphoric acid-acetonitrile system resulted in an increase in retention time of a peptide relative to the same peptide in the absence of perchlorate. This effect occurred independent of conformation, i.e., whether comparing the effect of positively charged residue substitutions in the hydrophobic or hydrophilic face of an amphipathic alpha-helix or in a peptide with negligible secondary structure. From these results, suggesting that positively charged side-chain hydrophilicity is decreased by ion-pairing with the perchlorate ion, we have shown practical examples where mixtures of non-helical and amphipathic alpha-helical peptides showed enhanced resolution in the presence of perchlorate at pH 2, compared to in its absence. In addition, it was shown that an aqueous phosphoric acid-perchlorate-acetonitrile mobile phase may show markedly different selectivity for peptide separations at low pH compared to the more traditional aqueous trifluoroacetic acid-acetonitrile system.

Determination of two neuropeptide growth factor antagonists, [D-Arg1,D-Phe5,D-Trp7,9,Leu11]-substance P and [Arg6,D-Trp7,9,N-MePhe8]- substance P(6-11), by high-performance liquid chromatography with electrochemical detection

The neuropeptide growth factor antagonists [D-Arg1,D-Phe5,D-Trp7,9,Leu11]-substance P (D) and [Arg6,D-Trp7,9, [corrected] N-MePhe8]-substance P(6-11) (G) are currently undergoing preclinical evaluation as potential anticancer agents and clinical trials are planned for G in the near future. A reversed-phase high-performance liquid chromatographic separation has been developed which is both sensitive (limit of detection 250 pg/263 fmol for G; 500 pg/330 fmol for D) and selective, based on electrochemical detection of the two tryptophan residues present in each peptide. Two ion-pairing agents were included in the isocratic mobile phase to eliminate adsorption of the peptides onto the analytical column. Extensive sample clean-up procedures have been developed for plasma, tissue and tumour based on solid-phase extraction. Precision and accuracy of each assay was 91.3 +/- 16.9% (between-day) for G and 99.3 +/- 16.9% (between-day) for D. The assays were able to detect the intact peptides and a number of their metabolites in plasma, liver and the WX 322 SCLC human xenograft in nude mice for at least 6 hr after administration of therapeutic and pharmacological doses.

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.

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.

Unexpected elution behaviour of peptides with various reversed-phase columns

Gastrin and cholecystokinin peptides were separated by reversed-phase chromatography on conventional bristle-type and polymer-coated stationary phases. The retention of the sulphated and non-sulphated isomeric forms of both peptides is governed by the structure of the peptide, the net charge and additional polar interactions with the stationary phases. Polymer-coated phases are optimum for separations according to chain length, whereas polar interactions are required for the separation of sulphated and non-sulphated peptides of identical chain length.

Food analysis on silica-bound HPLC phases

HPLC analysis of food on various silica bonded phases has been described. Technical and theoretical aspects of the materials such as normal-, reverse-, ion-exchange-, affinity-, chiral-, size-exclusion-, and ion-phases have been discussed. Special problems such as mobile phase or solvent-selection, selectivity and mechanisms of resolution on these bonded phases have been mentioned. Application of various bonded materials such as amino, cyano, diol, amino-cyano, C-18, C-8, anion-exchangers, strong and weak-cation exchangers, chiral and enzyme bound affinity phases to analyze and determine food components such as carbohydrates, food colors and pigments, flavors, proteins, vitamins and toxins has been described.

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.

Computer simulation of high-performance liquid chromatographic separations of peptide and protein digests for development of size-exclusion, ion-exchange and reversed-phase chromatographic methods

A computer program, called Pro Digest-LC, has been developed which 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. Pro Digest-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, Pro Digest-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, mobile-phase selection, and has the ability to examine the effects of flow-rate, gradient-rate, and sample size on the separation. We have designed a set of peptide standards for each mode of chromatography to aid the researcher in eliminating non-specific interactions, to standardize retention behaviour on the user's columns, to monitor column performance and to compare packing materials. In the development of each prediction mode, experimental peak heights, peak widths, and retention times from model synthetic peptide standards were incorporated directly into the program and can be used as default values. Pro Digest-LC is an interactive program, in that researchers can run peptide standards on their particular columns and enter the peak width at half-height, peak height, retention time and quantity injected to adjust the simulation to their particular column. The simulated experiments eliminate the time-consuming trial-and-error methods used to suitable separation or purification procedures. The researcher would perform the actual experiment only after predicting the optimized conditions, thereby saving valuable sample and research time. The general concepts of the program along with representative separations of protein digests are displayed.