Reversed-phase HPLC of peptides: Assessing column and solvent selectivity on standard, polar-embedded and polar endcapped columns

Chromatographic separation of glycated peptide isomers derived from glucose and fructose

Amino groups in proteins can react with aldehyde groups in aldoses or keto groups in ketoses, e.g., D-glucose and D-fructose, yielding Schiff bases that rearrange to more stable Amadori and Heyns products, respectively. Analytical strategies to identify and quantify each glycation product in the presence of the corresponding isomer are challenged by similar physicochemical properties, impeding chromatographic separations, and by identical masses including very similar fragmentation patterns in tandem mass spectrometry. Thus, we studied the separation of seven peptide families, each consisting of unmodified, glucated, and fructated 15mer to 22mer peptides using reversed-phase (RP) and hydrophilic interaction chromatography (HILIC). In RP-HPLC using acidic acetonitrile gradients, unglycated peptides eluted ~ 0.1 to 0.8 min after the corresponding glycated peptides with four of seven peptides being baseline separated. Isomeric glucated and fructated peptides typically coeluted, although two late-eluting peptides were partially separated. Neutral eluents (pH 7.2) improved the chromatographic resolution (R_s), especially in the presence of phosphate, providing good and often even baseline separations for six of the seven isomeric glycated peptide pairs with fructated peptides eluting earlier (R_s = 0.7 to 1.5). Some glucated and unmodified peptides coeluted, but they can be distinguished by mass spectrometry. HILIC separated glycated and unmodified peptides well, whereas glucated and fructated peptides typically coeluted. In conclusion, HILIC efficiently separated unmodified and the corresponding glycated peptides, while isomeric Amadori and Heyns peptides were best separated by RP-HPLC using phosphate buffered eluents.

Synthetic pharmaceutical peptides characterization by chromatography principles and method development

As per United States Food and Drug Administration, any polymer/chain composed of 40 or fewer amino acids is called as a peptide, where more than 40 amino acids are considered as proteins. In many occasions there is a change in the source of manufacturing of the peptide active pharmaceutical ingredient, where one has to prove the sameness of that product with the existing formulation by considering several aspects like presence of impurities/degradation products, extent of aggregations etc. For the same, several chromatographic characterization techniques such as; Reverse phase high performance liquid chromatography-ultraviolet/high resolution mass spectrometry, supercritical fluid chromatography, size exclusion chromatography, Ion exchange chromatography etc are widely used in pharmaceutical industry. It is well known that the method development of peptide molecules is often challenging as many variables are to be kept in mind which can affect the separation, recovery and stability of molecule. The present review focuses on the basics of peptide degradation and method development by using various chromatographic techniques for characterization. It also covers a deep insight of method development parameters and variables to be considered which might directly or indirectly affect the chromatographic separation and recovery, and also provides a guide on selection of chromatographic parameters. This article is protected by copyright. All rights reserved.

Investigation into reversed-phase chromatography peptide separation systems Part IV: Characterisation of mobile phase selectivity differences

The differentiation of mobile phase compositions between sub-classes which exhibit distinct chromatographic selectivity (i.e. termed characterisation) towards a range of peptide probes with diverse functionality and hence the possibility for multi-modal retention mechanisms has been undertaken. Due to the complexity of peptide retention mechanisms in given mobile phase conditions, no attempt has been made to explain these, instead mobile phases have simply been classified into distinct groups with an aim of identifying those yielding differing selectivities for use in strategic method development roadmaps for the analysis of peptide mixtures. The selectivity differences between nine synthetic peptides (fragments of [Ile27]-Bovine GLP-2) were used to assess how fifty-one RPC mobile phase compositions of differing pH (range 1.8 - 7.8), salt types, ionic strengths, ion-pair reagents and chaotropic / kosmotropic additives affected chromatographic selectivity on a new generation C18 stationary phase (Ascentis Express C18). The mobile phase compositions consisted of commonly used and novel UV or MS compatible additives. The chemometric tool of Principal Component Analysis (PCA) was used to visualise the differences in selectivity generated between the various mobile phases evaluated. The results highlight the importance of screening numerous mobile phases of differing pH, ion-pair reagents and ionic strength in order to maximise the probability of achieving separation of all the peptides of interest within a complex mixture. PCA permitted a ranking of the relative importance of the various mobile phase parameters evaluated. The concept of using this approach was proven in the analysis of a sample of Bovine GLP-2 (1-15) containing synthesis related impurities. Mobile phases with high ionic strength were demonstrated to be crucial for the generation of symmetrical peaks. The observations made on the C18 phase were compared on three additional stationary phases (i.e. alkyl amide, fluorophenyl and biphenyl), which had previously been shown to possess large selectivity differences towards these peptides, on a limited sub-set of mobile phases. With the exception of the ion-pair reagent, similar trends were obtained for the C18, fluorophenyl and biphenyl phases intimating the applicability of these findings to the vast majority of RPC columns (i.e. neutral or weakly polar in character) which are suitable for the analysis of peptides. The conclusions were not relevant for columns with a more disparate nature (i.e. containing a high degree of positive charge).

Surface properties of stationary phases with embedded polar group based on secondary interaction, zeta potential measurement and linear solvatation energy relationship studies

The chromatographic properties of six non-commercially available stationary phases with ester or phosphodiester functional groups embedded into alkyl chain were studied. Zeta potential values of stationary phases suspended in water, organic solvent and their mixtures were measured. Moreover, the selectivity coefficients were calculated on the basis of the retention factor for the test solutes. Separations were performed under hydrophilic interaction liquid chromatographic conditions. Hydrophobic and polar properties of the investigated columns were compared. Based on the chromatographic properties, polar embedded packing materials were classified. Also two phases with different spacer but the same embedded polar group and alkyl chain (Amino-P-C18 and Diol-P-C18) were used for comparison with homemade materials. Amino-P-C18 stationary phase exhibits positive values of zeta potential which is in accordance with the observed anion exchange properties. The highest negative values of zeta potential were observed for Diol-P-C18, together with cation exchange properties. The highest methylene selectivity, polar selectivity and configurational selectivity were observed for the stationary phase with an ester bond and a phenyl group.

Peptide separation selectivity in proteomics LC-MS experiments: Comparison of formic and mixed formic/heptafluorobutyric acids ion-pairing modifiers

Separation selectivity and detection sensitivity of reversed-phase high-performance liquid chromatography with tandem mass spectrometry analyses were compared for formic (0.1%) and formic/heptafluorobutyric (0.1%/0.005%) acid based eluents using a proteomic data set of ∼12 000 paired peptides. The addition of a small amount of hydrophobic heptafluorobutyric acid ion-pairing modifier increased peptide retention by up to 10% acetonitrile depending on peptide charge, size, and hydrophobicity. Retention increase was greatest for peptides that were short, highly charged, and hydrophilic. There was an ∼3.75-fold reduction in MS signal observed across the whole population of peptides following the addition of heptafluorobutyric acid. This resulted in ∼36% and ∼21% reduction of detected proteins and unique peptides for the whole cell lysate digests, respectively. We also confirmed that the separation selectivity of the formic/heptafluorobutyric acid system was very similar to the commonly used conditions of 0.1% trifluoroacetic acid, and developed a new version of the Sequence-Specific Retention calculator model for the formic/heptafluorobutyric acid system showing the same ∼0.98 R² -value accuracy as the Sequence-Specific Retention calculator formic acid model. In silico simulation of peptide distribution in separation space showed that the addition of 0.005% heptafluorobutyric acid to the 0.1% formic acid system increased potential proteome coverage by ∼11% of detectable species (tryptic peptides ≥ four amino acids).

A comparative study on properties of fish meat hydrolysates produced by an enzymatic process at high pressure

Fish meat hydrolysates (FMHs) were produced from nine fishes at a high pressure of 300 MPa using Flavourzyme 500MG and a protease mixture including Flavourzyme 500MG, Alcalase 2.4L, Protamex, and Marugoto E. The electropherograms of the FMHs showed major far-migrating peptide bands in the vicinity of 5 kDa. The total soluble solids (TSS) and soluble nitrogen content in the FMHs were species-specific and were mostly higher in the case of four-enzyme hydrolysis. Most of the HPLC peptide peaks of the rockfish meat hydrolysates appeared within 10 min of elution, and total free amino acids in the hydrolysate increased abruptly as a result of four-enzyme hydrolysis. The FMHs, which were high in TSS and soluble nitrogen, may be applicable for use in food as seasoning, and could be produced efficiently via the enzymatic process used in this study.

Investigation into reversed phase chromatography peptide separation systems part I: Development of a protocol for column characterisation

A protocol was defined which utilised peptides as probes for the characterisation of reversed phase chromatography peptide separation systems. These peptide probes successfully distinguished between differing stationary phases through the probe's hydrophobic, electrostatic, hydrogen bonding and aromatic interactions with the stationary phase, in addition, to more subtle interactions such as the phase's ability to separate racemic or isomeric probes. The dominating forces responsible for the chromatographic selectivity of peptides appear to be hydrophobic as well as electrostatic and polar in nature. This highlights the need for other types of stationary phase ligands with possibly mixed mode functionalities / electrostatic / polar interactions for peptide separations rather than the hydrophobic ligands which dominate small molecule separations. Selectivity differences are observed between phases, but it appears that it is the accessibility differences between these phases which play a crucial role in peptide separations i.e. accessibility to silanols, the hydrophobic acetonitrile / ligand layer or a thin adsorbed water layer on the silica surface.

The versatility of N,O-dialkylphosphoramidate stationary phase-separations in HILIC, highly aqueous RP LC conditions and purely aqueous mobile phase

The chromatographic properties of N,O-dialkylphosphoramidate stationary phase with an octadecyl chain (Amino-P-C18) were studied.

Identification of a p53-based portable degron based on the MDM2-p53 binding region

In recent years the ubiquitin proteasome system (UPS) has garnered increasing interest as a target for chemotherapeutics. Due to the success of the proteasome inhibitors Bortezomib and Carfilzomib in the treatment of multiple myeloma, several new compounds have been developed to target E3 ubiquitin ligases and the proteasome in numerous human cancers. This has increased the need for new analytical methods to precisely measure intracellular enzyme activity in cells. A key component of a desired analytical method is a substrate that is capable of rapid intracellular ubiquitination yet easily incorporated into the next generation of more sophisticated UPS reporters. Portable degradation sequences, or degrons, have the ability to bind to E3 ligases and promote substrate ubiquitination when the sequence is presented in isolation or appended to other entities such as fluorescent peptide-based reporters. Previous work identified an E3 ligase (MDM2)-binding element at p53 amino acids 92-112, which was later demonstrated to be rapidly ubiquitinated in cytosolic lysates effectively functioning as a transportable degron. In this work, a shortened p53 sequence within amino acids 92-112 that displayed rapid ubiquitination kinetics was identified. A nine-member peptide library was synthesized using sequence elements of various sizes and lengths, all based on the initial 22 amino acid long sequence, containing a single ubiquitination site lysine. The ubiquitination kinetics were determined using a combination of gel electrophoresis and analytical high performance liquid chromatography (HPLC) to rank the members of the library and identify the optimal ubiquitination sequence. This analysis identified the five amino acid sequence, KGSYG, corresponding to residues 105-108 with an added N-terminal lysine, as a portable degron since this sequence demonstrated the most rapid ubiquitination kinetics.

Development of quantitative method for determination of γ-glutamyl peptides by capillary electrophoresis tandem mass spectrometry: an efficient approach avoiding matrix effect

Serum γ-glutamyl di- and tripeptides have proven to be useful biomarkers to accurately predict nine different forms of liver disease. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS) with multiple reaction monitoring (MRM), serum and liver samples spiked with γ-glutamyl peptide standards were analyzed to estimate accuracy. Unexpectedly, the recovery rates for several γ-glutamyl peptides in the serum samples were quite low, whereas values for some γ-glutamyl peptides in the liver samples were highly elevated. Most of these peptides were barely retained on the reverse-phase column, resulting in significant ion suppression or enhancement. In contrast, a capillary electrophoresis tandem mass spectrometry (CE-MS/MS) method with MRM was minimally affected by matrix effects. Of the 39 tested compounds, most of γ-glutamyl peptides that did not contain a thiol substituent in its structure gave acceptable recoveries (70-120%), and limits of detection for the analytes were between 3.6 and 800 nmol/l with pressure injection at 5 kPa for 10 s (ca. 10 nl). The CE-MS/MS method provided high resolution and proved to be highly selective and sensitive, its utility being demonstrated by the determination of γ-glutamyl di- and tripeptides in serum and liver samples.

Liquid chromatography/mass spectrometry methods for measuring dipeptide abundance in non-small-cell lung cancer

RATIONALE

Metabolomic profiling is a promising methodology of identifying candidate biomarkers for disease detection and monitoring. Although lung cancer is among the leading causes of cancer-related mortality worldwide, the lung tumor metabolome has not been fully characterized.

METHODS

We utilized a targeted metabolomic approach to analyze discrete groups of related metabolites. We adopted a dansyl [5-(dimethylamino)-1-naphthalene sulfonamide] derivatization with liquid chromatography/mass spectrometry (LC/MS) to analyze changes of metabolites from paired tumor and normal lung tissues. Identification of dansylated dipeptides was confirmed with synthetic standards. A systematic analysis of retention times was required to reliably identify isobaric dipeptides. We validated our findings in a separate sample cohort.

RESULTS

We produced a database of the LC retention times and MS/MS spectra of 361 dansyl dipeptides. Interpretation of the spectra is presented. Using this standard data, we identified a total of 279 dipeptides in lung tumor tissue. The abundance of 90 dipeptides was selectively increased in lung tumor tissue compared to normal tissue. In a second set of validation tissues, 12 dipeptides were selectively increased.

CONCLUSIONS

A systematic evaluation of certain metabolite classes in lung tumors may identify promising disease-specific metabolites. Our database of all possible dipeptides will facilitate ongoing translational applications of metabolomic profiling as it relates to lung cancer.

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.

The use of methyl-β-cyclodextrin to solubilize cholesterol prior to coating onto a C18 stationary phase

The use of methyl-β-cyclodextrin (MBCD) as a mobile phase additive in reversed-phase liquid chromatography is explored, with the primary goal of using MBCD to solubilize cholesterol in reversed-phase mobile phases for cholesterol-coating of C18 stationary phases. MBCD is shown to increase the solubility of cholesterol in typical reversed-phase mobile phases, especially when the stoichiometric ratio of MBCD to cholesterol exceeds 2:1. Additional equivalents of MBCD further increase solubility, or allow for weaker solvents to be used. The use of weaker solvents allows for larger coating levels of cholesterol onto a C18 stationary phase than are possible without the use of MBCD. Stationary phases coated with cholesterol using MBCD as a co-additive have different selectivity than uncoated phases, especially with regards to phenyl and shape selectivity. Further, the use of MBCD as a mobile phase additive for the elution of cholesterol is examined. It is seen via van't Hoff analysis that the reduction in retention of cholesterol when MBCD is added to the mobile phase is enthalpically driven.

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

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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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