Mixed-mode hydrophilic interaction/cation-exchange chromatography (HILIC/CEX) of peptides and proteins

Multidimensional Separations in Top-Down Proteomics

Top-down proteomics (TDP) identifies, quantifies, and characterizes proteins at the intact proteoform level in complex biological samples to understand proteoform function and cellular mechanisms. However, analyzing complex biological samples using TDP is still challenging due to high sample complexity and wide dynamic range. High-resolution separation methods are often applied prior to mass spectrometry (MS) analysis to decrease sample complexity and increase proteomics throughput. These separation methods, however, may not be efficient enough to characterize low abundance intact proteins in complex samples. As such, multidimensional separation techniques (combination of two or more separation methods with high orthogonality) have been developed and applied that demonstrate improved separation resolution and more comprehensive identification in TDP. A suite of multidimensional separation methods that couple various types of liquid chromatography (LC), capillary electrophoresis (CE), and/or gel electrophoresis-based separation approaches have been developed and applied in TDP to analyze complex biological samples. Here, we reviewed multidimensional separation strategies employed for TDP, summarized current applications, and discussed the gaps that may be addressed in the future.

A story of peptides, lipophilicity and chromatography - back and forth in time

Peptides, as part of the beyond the rule of 5 (bRo5) chemical space, represent a unique class of pharmaceutical compounds. Because of their exceptional position in the chemical space between traditional small molecules (molecular weight (MW) < 500 Da) and large therapeutic proteins (MW > 5000 Da), peptides became promising candidates for targeting challenging binding sites, including even targets traditionally considered as undruggable - e.g. intracellular protein-protein interactions. However, basic knowledge about physicochemical properties that are important for a drug to be membrane permeable is missing but would enhance the drug discovery process of bRo5 molecules. Consequently, there is a demand for quick and simple lipophilicity determination methods for peptides. In comparison to the traditional lipophilicity determination methods via shake flask and in silico prediction, chromatography-based methods could have multiple benefits such as the requirement of low analyte amount, insensitivity to impurities and high throughput. Herein we elucidate the role of peptide lipophilicity and different lipophilicity values. Further, we summarize peptide analysis via common chromatographic techniques, in specific reversed phase liquid chromatography, hydrophilic interaction liquid chromatography and supercritical fluid chromatography and their role in drug discovery and development process.

The isolation of water-soluble natural products - challenges, strategies and perspectives

Covering period: up to 2019Water-soluble natural products constitute a relevant group of secondary metabolites notably known for presenting potent biological activities. Examples are aminoglycosides, β-lactam antibiotics, saponins of both terrestrial and marine origin, and marine toxins. Although extensively investigated in the past, particularly during the golden age of antibiotics, hydrophilic fractions have been less scrutinized during the last few decades. This review addresses the possible reasons on why water-soluble metabolites are now under investigated and describes approaches and strategies for the isolation of these natural compounds. It presents examples of several classes of hydrosoluble natural products and how they have been isolated. Novel stationary phases and chromatography techniques are also reviewed, providing a perspective towards a renaissance in the investigation of water-soluble natural products.

PrSM-Level Side-by-Side Comparison of Online LC-MS Methods with Intact Histone H3 and H4 Proteoforms

The heterogeneity of histone H3 proteoforms makes histone H3 top-down analysis challenging. To enhance the detection coverage of the proteoforms, performing liquid chromatography (LC) front-end to mass spectrometry (MS) detection is recommended. Here, using optimized electron-transfer/high-energy collision dissociation (EThcD) parameters, we have conducted a proteoform-spectrum match (PrSM)-level side-by-side comparison of reversed-phase LC-MS (RPLC-MS), "dual-gradient" weak cation-exchange/hydrophilic interaction LC-MS (dual-gradient WCX/HILIC-MS), and "organic-rich" WCX/HILIC-MS on the top-down analyses of H3.1, H3.2, and H4 proteins extracted from a HeLa cell culture. While both dual-gradient WCX/HILIC and organic-rich WCX/HILIC could resolve intact H3 and H4 proteoforms by the number of acetylations, the organic-rich method could enhance the separations of different trimethyl/acetyl near-isobaric H3 proteoforms. In comparison with RPLC-MS, both of the WCX/HILIC-MS methods enhanced the qualities of the H3 PrSMs and remarkably improved the range, reproducibility, and confidence in the identifications of H3 proteoforms.

pH-dependent selective separation of acidic and basic proteins using quaternary ammoniation functionalized cysteine-zwitterionic stationary phase with RPLC/IEC mixed-mode chromatography

In this paper, a cysteine-functionalized zwitterionic stationary phase (Cys-silica) was prepared based on the "thiol-ene" click chemistry between cysteine and vinyl-functionalized silica, and was further modified with bromoethane, 1-bromooctane and 1-bromooctadecane, respectively, to obtain a series of quaternary ammoniation-functionalized stationary phases (Cys-silica-C_n, n = 2, 8 and 18). These zwitterionic stationary phases were regarded as reversed-phase/ion-exchange (RP/IEC) mixed-mode chromatography (MMC) stationary phases for protein separation. The retention behaviors of proteins on these zwitterionic stationary phases were carefully investigated. The results indicated that the retentions of acidic and basic proteins on these zwitterinonic stationary phases were significantly influenced by the acetonitrile and salt concentrations, pH of mobile phase as well as the hydrophobicity of the ligand. The separation selectivity of proteins on these zwitterionic stationary phases strongly depended on the pH value of mobile phase. The baseline separation of 6 kinds of basic proteins can be achieved at pH 8.0 using Cys-silica-C2 or Cys-silica-C8 column, and 5 kinds of acidic proteins can also be separated completely at pH 4.0 with Cys-silica-C2 column. Moreover, owing to the quaternary ammoniation-functionalization on Cys-silica by using appropriately hydrophobic bromoalkanes, the selectivity and separation efficiency of proteins can be enhanced greatly. As a result, the acidic and basic proteins can be separated completely step by step from the complex sample by adjusting pH of mobile phase using a single Cys-silica-C2 column, which illustrates that the cysteine-functionalized zwitterionic stationary phase has a great potential for protein separation.

Particle packed mixed-mode chromatographic stationary phase for the separation of peptide in liquid chromatography

A particle-based stationary phase has been prepared for the separation of five synthetic peptides and a mixture containing tryptic digest of cytochrome C in liquid chromatography. Particles originating from silica monolith were differentially sedimented to obtain 1-2 μm particles. A stationary phase was achieved by the coating of poly(styrene-methacrylic acid-N-phenylacrylamide) copolymer onto the particles via reversible addition-fragmentation chain transfer polymerization reaction. Stainless steel column (30 cm long and 1 mm internal diameter) was packed with stationary phase. Very high separation efficiency (ca. 351 000 plates/m) was achieved for five commercial peptides with a percent relative standard deviation of less than 1%. Protocol for the synthesis and modification of silica monolith particles has been well optimized with a good reproducibility both in particle and pore size. The column resolved about 21 peptide components from a mixture containing tryptic digest of cytochrome C, under the elution conditions of acetonitrile/15 mM ammonium format (65/35 v/v%) with a flow rate of 28 μL/min.

Strong cation- and zwitterion-exchange-type mixed-mode stationary phases for separation of pharmaceuticals and biogenic amines in different chromatographic modes

A set of new mixed-mode ion-exchange stationary phases is presented. The backbone of organic selectors is formed by a linear hydrocarbon chain, which is divided into two parts of various lengths by a heteroatom (oxygen or nitrogen). In all studied cases, there is a sulfonic acid moiety as the terminal group. Therefore, selectors bearing oxygen gave rise to strong cation ion-exchange stationary phases, while selectors with an embedded nitrogen atom (inducing a weak anion exchange capacity) were used to create zwitterion ion-exchange stationary phases. The new mixed-mode stationary phases were chromatographically evaluated in high performance liquid chromatography (HPLC) and supercritical fluid chromatography (SFC) using isocratic elution conditions to disclose their chromatographic potential. In HPLC mode, aqueous-rich reversed phase chromatography, acetonitrile-rich hydrophilic interaction liquid chromatography and methanolic ion-exchange chromatography mobile phases were employed. In these chromatographic modes, retention factors and selectivity values for a test set of basic and zwitterionic analytes were determined. The results were compared and principal component analysis for each chromatographic mode was performed. For all chromatographic modes, the component 1 in the principal component analysis reflected the elution order. The application of different mobile phases on a particular column resulted not only in variation in retention, but also in modified selectivity, and different elution order of the analytes. The orthogonality of the elution order depending on the employed mobile phase conditions was especially reflected for structurally closely related analytes, such as melatonin and N-acetyl-serotonin, tryptamine and serotonin or noradrenalin and octopamine. However, ion-exchange interactions remain the main driving force for retention. From all investigated stationary phases, the SCX 2 (C5-linker and C4-spacer) seems to be the best choice for the separation of basic analytes using different mobile phase conditions.

Analysis of oligonucleotides by ion-pairing hydrophilic interaction liquid chromatography/electrospray ionization mass spectrometry

RATIONALE

Hydrophilic interaction liquid chromatography/electrospray ionization mass spectrometry (HILIC-LC/ESI-MS) has been proved to be useful for the quality control of oligonucleotides. However, the lack of separation for some oligonucleotides using HILIC-LC/MS has proved problematic. This study aimed to improve the resolving ability of HILIC-LC/MS.

METHODS

The study was performed on a Waters UPLC® system coupled to a Waters LCT premier XE ESI-TOF mass spectrometer using a Zorbax® RRHD HILIC column (2.1 mm × 100 mm, 1.8 μm). Buffer systems contained triethylammonium acetate (TEAA) and acetonitrile. The effects of the concentration of TEAA and the type of organic modifiers on the separation of oligonucleotides were investigated.

RESULTS

The results showed that the optimum concentration of TEAA is 10 mM and acetonitrile is a better organic solvent than methanol. The addition of TEAA in the HILIC mobile phase improved the separation of N from N + A significantly compared to the HILIC method buffered with ammonium acetate. The IP-HILIC chromatography has demonstrated that the separation of oligonucleotides is sequence dependent. In addition, the IP-HILIC method produces a much simpler mass spectrum of an oligonucleotide with very efficient desalting.

CONCLUSIONS

The HILIC-LC/MS method with the addition of TEAA at a MS-compatible concentration has improved the separation of oligonucleotides. The IP-HILIC-LC/MS method also produces very simple mass spectra with high desalting efficiency.

Quantitative analysis of acid-catalyzed levulinic acid product mixture from cellulose by mixed-mode liquid chromatography

A mixed-mode weak anion-exchange/reversed-phase liquid chromatography (LC) column was successfully applied for the analysis of levulinic acid (4-oxopentanoic acid, LA) product mixture derived from cellulose. Due to the existence of ionic and neutral byproducts, the analysis of the product mixture usually requires ion chromatography, LC and gas chromatography simultaneously. The new method enables accomplishment of the analysis in one LC run within 6min. LC mobile phase of 10mM phosphate buffer containing 5% acetonitrile with pH=5.5 was used. The linear regression coefficients for the UV signal of standard compounds with the corresponding mass concentrations were greater than 0.999. The method recoveries were between 98.57-103.48%. The limits of quantification were 5, 10,1000, 1500 and 3000ng/mL for 5-hydroxymethylfurfural, furfural, acetic acid, formic acid and LA respectively. The mixed-mode column exhibits comprehensive separation mechanism of both reversed-phase and ion-exchange interactions. The mobile phase with different pH, organic modifier solvent and buffer concentration provided flexible LC method for the sample with different complexity.

Progress in epigenetic histone modification analysis by mass spectrometry for clinical investigations

Chromatin biology and epigenetics are scientific fields that are rapid expanding due to their fundamental role in understanding cell development, heritable characters and progression of diseases. Histone post-translational modifications (PTMs) are major regulators of the epigenetic machinery due to their ability to modulate gene expression, DNA repair and chromosome condensation. Large-scale strategies based on mass spectrometry have been impressively improved in the last decade, so that global changes of histone PTM abundances are quantifiable with nearly routine proteomics analyses and it is now possible to determine combinatorial patterns of modifications. Presented here is an overview of the most utilized and newly developed proteomics strategies for histone PTM characterization and a number of case studies where epigenetic mechanisms have been comprehensively characterized. Moreover, a number of current epigenetic therapies are illustrated, with an emphasis on cancer.

Silica-based polypeptide-monolithic stationary phase for hydrophilic chromatography and chiral separation

Glutathione (GSH)-, somatostatin acetate (ST)- and ovomucoid (OV)-functionalized silica-monolithic stationary phases were designed and synthesized for HILIC and chiral separation using capillary electrochromatography (CEC). GSH, ST and OV were covalently incorporated into the silica skeleton via the epoxy ring-opening reaction between their amino groups and the glycidyl moiety in γ-glycidoxypropyltrimethoxysilane (GPTMS) together with polycondensation and copolymerization of tetramethyloxysilane and GPTMS. Not only could the direction and electroosmotic flow magnitude on the prepared GSH-, ST- and OV-silica hybrid monolithic stationary phases be controlled by the pH of the mobile phase, but also a typical HILIC behavior was observed so that the nucleotides and HPLC peptide standard mixture could be baseline separated using an aqueous mobile phase without any acetonitrile during CEC. Moreover, the prepared monolithic columns had a chiral separation ability to separate dl-amino acids. The OV-silica hybrid monolithic column was most effective in chiral separation and could separate dl-glutamic acid (Glu) (the resolution R=1.07), dl-tyrosine (Tyr) (1.57) and dl-histidine (His) (1.06). Importantly, the chiral separation ability of the GSH-silica hybrid monolithic column could be remarkably enhanced when using gold nanoparticles (AuNPs) to fabricate an AuNP-mediated GSH-AuNP-GSH-silica hybrid monolithic column. The R of dl-Glu, dl-Tyr and dl-His reached 1.19, 1.60 and 2.03. This monolithic column was thus applied to separate drug enantiomers, and quantitative separation of all four R/S drug enantiomers were achieved with R ranging from 4.36 to 5.64. These peptide- and protein-silica monolithic stationary phases with typical HILIC separation behavior and chiral separation ability implied their promise for the analysis of not only the future metabolic studies, but also drug enantiomers recognition.

Applications of hydrophilic interaction chromatography to amino acids, peptides, and proteins

This review summarizes the recent advances in the analysis of amino acids, peptides, and proteins using hydrophilic interaction chromatography. Various reports demonstrate the successful analysis of amino acids under such conditions. However, a baseline resolution of the 20 natural amino acids has not yet been published and for this reason, there is often a need to use mass spectrometry for detection to further improve selectivity. Hydrophilic interaction chromatography is also recognized as a powerful technique for peptide analysis, and there are a lot of papers showing its applicability for proteomic applications (peptide mapping). It is expected that its use for peptide mapping will continue to grow in the future, particularly because this analytical strategy can be combined with reversed-phase liquid chromatography, in a two-dimensional setup, to reach very high resolving power. Finally, the interest in hydrophilic interaction chromatography for intact proteins analysis is less evident due to possible solubility issues and a lack of suitable hydrophilic interaction chromatography stationary phases. To date, it has been successfully employed only for the characterization of membrane proteins, histones, and the separation of glycosylated isoforms of an intact glycoprotein. From our point of view, the number of hydrophilic interaction chromatography columns compatible with intact proteins (higher upper temperature limit, large pore size, etc.) is still too limited.

Evaluation of separation properties of a modified strong cation exchange material named MEX and its application in 2D-MEX × C18 system to separate peptides from scorpion venom

Peptides from scorpion venom represent one of the most promising sources for drug discovery in some specific disease.

Comparison of peak shape in hydrophilic interaction chromatography using acidic salt buffers and simple acid solutions

The retention and peak shape of neutral, basic and acidic solutes was studied on hydrophilic interaction chromatography (HILIC) stationary phases that showed both strong and weak ionic retention characteristics, using aqueous-acetonitrile mobile phases containing either formic acid (FA), ammonium formate (AF) or phosphoric acid (PA). The effect of organic solvent concentration on the results was also studied. Peak shape was good for neutrals under most mobile phase conditions. However, peak shapes for ionised solutes, particularly for basic compounds, were considerably worse in FA than AF. Even neutral compounds showed deterioration in performance with FA when the mobile phase water concentration was reduced. The poor performance in FA cannot be entirely attributed to the negative impact of ionic retention on ionised silanols on the underlying silica base materials, as results using PA at lower pH (where their ionisation is suppressed) were inferior to those in AF. Besides the moderating influence of the salt cation on ionic retention, it is likely that salt buffers improve peak shape due to the increased ionic strength of the mobile phase and its impact on the formation of the water layer on the column surface.

Hydrophilic interaction electrokinetic chromatography using bio-based nanofillers

Hydrophilic interaction (HI)-based separation like HILIC is effective for analyzing hydrophilic biological samples such as carbohydrates, peptides, and metabolites. To overcome the drawbacks of conventional HILIC such as large consumption of organic solvents and easy deterioration of the separation column, we developed HI electrokinetic chromatography (EKC) by employing bio-based nanomaterials as the hydrophilic pseudostationary phase. By mechanical/chemical treatments, cellulose, chitin, and chitosan were processed to 10-nm wide nanofibers/nanowhiskers (NFs/NWs), which are longer/shorter than 1000/200 nm, respectively. In HI-EKC of oligosaccharides using 0.001% uncharged cellulose NFs, strong interaction was observed for the large-size oligosaccharides with the retention factors (k) of up to 1.56, indicating a HILIC-mode interaction. In HI-EKC with 0.1% positively charged chitosan NFs, benzenedisulfonic acid, benzenesulfonic acid (BS), and p-hydroxy BS (HBS) had k values of 0.036, 0.018, and 0.018, respectively, suggesting that the ion-exchange interaction mainly occurred via sulfonate groups. Finally, HI-EKC was demonstrated using 0.05% chitin or chitosan NWs. In both cases using chitin and chitosan NWs, HBS showed much stronger interaction with k > 0.192 compared with BS with k < 0.070. It indicated structural difference between NFs and NWs affected the HI behavior in terms of both the ion-exchange and HILIC modes.

Challenges and opportunities in the purification of recombinant tagged proteins

The purification of recombinant proteins by affinity chromatography is one of the most efficient strategies due to the high recovery yields and purity achieved. However, this is dependent on the availability of specific affinity adsorbents for each particular target protein. The diversity of proteins to be purified augments the complexity and number of specific affinity adsorbents needed, and therefore generic platforms for the purification of recombinant proteins are appealing strategies. This justifies why genetically encoded affinity tags became so popular for recombinant protein purification, as these systems only require specific ligands for the capture of the fusion protein through a pre-defined affinity tag tail. There is a wide range of available affinity pairs "tag-ligand" combining biological or structural affinity ligands with the respective binding tags. This review gives a general overview of the well-established "tag-ligand" systems available for fusion protein purification and also explores current unconventional strategies under development.

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.

A facile versatile polymeric monolith for multiple separations

A hydrophilic versatile polymeric monolith with multiple retention mechanisms including hydrogen-bonding, π-π and electrostatic interactions, was developed by a simple one-step in situ polymerization. High mechanical stability and excellent separation capabilities of various nonpolar and polar analytes were successfully achieved and employed for multiple separations in mixed-mode chromatography.

Enhanced top-down characterization of histone post-translational modifications

Post-translational modifications (PTMs) of core histones work synergistically to fine tune chromatin structure and function, generating a so-called histone code that can be interpreted by a variety of chromatin interacting proteins. We report a novel online two-dimensional liquid chromatography-tandem mass spectrometry (2D LC-MS/MS) platform for high-throughput and sensitive characterization of histone PTMs at the intact protein level. The platform enables unambiguous identification of 708 histone isoforms from a single 2D LC-MS/MS analysis of 7.5 µg purified core histones. The throughput and sensitivity of comprehensive histone modification characterization is dramatically improved compared with more traditional platforms.

Preparation of a novel dual-function strong cation exchange/hydrophobic interaction chromatography stationary phase for protein separation

We have explored a novel dual-function stationary phase which combines both strong cation exchange (SCX) and hydrophobic interaction chromatography (HIC) characteristics. The novel dual-function stationary phase is based on porous and spherical silica gel functionalized with ligand containing sulfonic and benzyl groups capable of electrostatic and hydrophobic interaction functionalities, which displays HIC character in a high salt concentration, and IEC character in a low salt concentration in mobile phase employed. As a result, it can be employed to separate proteins with SCX and HIC modes, respectively. The resolution and selectivity of the dual-function stationary phase were evaluated under both HIC and SCX modes with standard proteins and can be comparable to that of conventional IEC and HIC columns. More than 96% of mass and bioactivity recoveries of proteins can be achieved in both HIC and SCX modes, respectively. The results indicated that the novel dual-function column could replace two individual SCX and HIC columns for protein separation. Mixed retention mechanism of proteins on this dual-function column based on stoichiometric displacement theory (SDT) in LC was investigated to find the optimal balance of the magnitude of electrostatic and hydrophobic interactions between protein and the ligand on the silica surface in order to obtain high resolution and selectivity for protein separation. In addition, the effects of the hydrophobicity of the ligand of the dual-function packings and pH of the mobile phase used on protein separation were also investigated in detail. The results show that the ligand with suitable hydrophobicity to match the electrostatic interaction is very important to prepare the dual-function stationary phase, and a better resolution and selectivity can be obtained at pH 6.5 in SCX mode. Therefore, the dual-function column can replace two individual SCX and HIC columns for protein separation and be used to set up two-dimensional liquid chromatography with a single column (2DLC-1C), which can also be employed to separate three kinds of active proteins completely, such as lysozyme, ovotransferrin and ovalbumin from egg white. The result is very important not only to the development of new 2DLC technology with a single column for proteomics, but also to recombinant protein drug production for saving column expense and simplifying the process in biotechnology.

Preparation and characterization of hybrid-silica monolithic column with mixed-mode of hydrophilic and strong anion-exchange interactions for pressurized capillary electrochromatography

A novel organic-silica hybrid monolithic stationary phase with a mixed-mode of hydrophilic and strong anion-exchange interactions (HI-SAX) was prepared with a modified "one-pot" process of functional monomers and alkoxysilanes. Using a hydrosoluble initiator 2,2'-azobis(2-methylpropionamidine) dihydrochloride (AIBA), the homogeneous prepolymerization system of this hybrid monolith was successfully obtained by a simple operation. The polycondensation of alkoxysilanes (tetramethoxysilane (TMOS) and vinyl-trimethoxysilane (VTMS)) and the in situ copolymerization of a quaternary ammonium group-containing acrylic monomer ([2-(acryloyloxy)ethyl] trimethyl ammonium methyl sulfate (AETA)) on the precondensed siloxanes were achieved. The morphologies of the hybrid-silica monolithic matrixes were observed by SEM, and the performances of the organic-silica hybrid monolithic columns were investigated by pressurized capillary electrochromatography. The mechanical stability and reproducibility of the obtained hybrid monolithic column preformed acceptable. Both hydrophilic interaction chromatography mechanism and strong anion-exchanged interaction were investigated. A mixed mode of HI-SAX was obtained for the analysis of nucleotides with a good resolution, and the separation of polar and basic nucleic acid bases and nucleosides was also achieved without peak tailing.