Study on behaviors and performances of universal N-glycopeptide enrichment methods

Glycosylation is a crucial process in protein biosynthesis. However, the analysis of glycopeptides through MS remains challenging due to the microheterogeneity and macroheterogeneity of the glycoprotein. Selective enrichment of glycopeptides from complex samples prior to MS analysis is essential for successful glycoproteome research. In this work, we systematically investigated the behaviors and performances of boronic acid chemistry, ZIC-HILIC, and PGC of glycopeptide enrichment to promote understanding of these methods. We also optimized boronic acid chemistry and ZIC-HILIC enrichment methods and applied them to enrich glycopeptides from mouse liver. The intact N-glycopeptides were interpreted using the in-house analysis software pGlyco 2.0. We found that boronic acid chemistry in this study preferred to capture glycopeptides with high mannose glycans, ZIC-HILIC enriched most N-glycopeptides and did not show significant preference during enrichment and PGC was not suitable for separating glycopeptides with a long amino acid sequence. We performed a detailed study on the behaviors and performances of boronic acid chemistry, ZIC-HILIC, and PGC enrichment methods and provide a better understanding of enrichment methods for further glycoproteomics research.

Improving deep proteome and PTMome coverage using tandem HILIC-HPRP peptide fractionation strategy

Despite being orthogonal to reverse-phase separation and valuable for posttranslational modification (PTM) pre-enrichment, hydrophilic interaction liquid chromatography (HILIC) has not been widely adopted for large-scale proteomic applications. Here, we first evaluated the performance of HILIC in comparison with the popular high-pH reverse-phase (HPRP) separation, as the first dimension for tryptic peptide fractionation in a shotgun workflow to characterize the complex 293T cell proteome. The data indicated that the complementary nature of HILIC and HPRP for peptide separation was mainly due to different hydrophobicity preferences. Realizing that uncaptured components from one mode can be resolved in the other mode, we then designed and compared two multidimensional separation schemes using HILIC and HPRP in tandem for peptide prefractionation, in terms of identification efficiency and coverage at peptide, protein, and PTM levels. A total of 22,604 and 23,566 peptides corresponding to 4481 and 4436 proteins from 293T cell lysate were detected using HILIC-HPRP- and HPRP-HILIC-based shotgun proteomics workflow, respectively. In addition, without assistance of enrichment techniques, the tandem fractionation methods aided to identify 46 different PTMs from over 10,000 of spectra using blind modification search algorithm. We concluded that HILIC is a valuable alternative option for peptide prefractionation in a large-scale proteomic study, but can be further augmented with the use of a secondary HPRP separation.

HPLC Enantioseparations with Polysaccharide-Based Chiral Stationary Phases in HILIC Conditions

In contrast to achiral hydrophilic interaction liquid chromatography (HILIC), which is a popular and largely applied technique to analyze polar compounds such as pharmaceuticals, metabolites, proteins, peptides, amino acids, oligonucleotides, and carbohydrates, the introduction of the HILIC concept in enantioselective chromatography has been relatively recent and scarcely debated. In this chapter, the HILIC enantioseparations carried out on polysaccharide-based chiral stationary phases are grouped and discussed. Another objective of this chapter is to provide a comprehensive overview and insight into the experimental conditions needed to operate under HILIC mode. Finally, to stimulate and facilitate the application of this chromatographic technique, a detailed experimental protocol of a chiral resolution on a chlorinated cellulose-based chiral stationary phase under HILIC conditions is described.

Exploring the Effect of Buffer Strength on the Retention Time of Weak Acids, Neutral and Weak Bases in Hydrophilic Interaction Liquid Chromatography (HILIC) Mode

Background:

Hydrophilic Interaction Liquid Chromatography (HILIC) orthogonal to conventional reversed phase High-Performance Liquid Chromatography (HPLC) mode allowing separation of polar compounds. HILIC has been reported to be an alternative to normal phase liquid chromatography, yet the separation mechanism reported in HILIC is much more complicated than that in normal phase liquid chromatography.

Objective:

To investigate the effect of water layer thickness on silica gel and the amount of ammonium ions present within the buffer on retention mechanism in hydrophilic interaction chromatography.

Methodology:

A test system was designed which used weak acids, neutrals and weak bases as probes with three different strengths (5, 10 and 20 mM) of ammonium acetate, ammonium formate and ammonium propionate as the counter-ions to compete with the test probes with ionised silanol groups and water present in the stationary phase. A Kromasil 60-5SIL column (150 mm×4.6 mm×4 μm, pore size 60Å) was used as the stationary phase to perform the study.

Results:

Retention times were examined for the test probes at 90% acetonitrile (ACN) with 10% of 5, 10 and 20 mM of ammonium acetate, ammonium formate and ammonium propionate. As the buffer strength increases, the thickness of the water layer on the surface of the silica gel increases and also the repulsion between ionized silanol groups and acidic test probes will decrease. On the other hand, such increase in buffer strength will increase the competition between the ammonium ions and basic test probes. In addition, the hydration energy of buffer’s counter ions and hydrophilicity may be important in retention mechanism in HILIC mode.

Conclusion:

At 20 mM buffer strength acidic probes with low log P values retain more due to reduced repulsion by silanol groups, while basic probes retention time will decrease due to increased competition from ammonium counter ions. However, in 5 mM buffer strength basic probes with low logP value will be retained longer, while acidic probes will be eluted earlier due to the repulsion between ionized acids and ionized silanol groups.

Surface-bonded amide-functionalized imidazolium ionic liquid as stationary phase for hydrophilic interaction liquid chromatography

The amide group modified silica materials are popular stationary phases for hydrophilic interaction liquid chromatography (HILIC). Meanwhile, surface-confined imidazolium ionic liquids (ILs) have been proved to be useful HILIC stationary phases and possess many unique properties. In this study, the synthesis of an amide-functionalized imidazolium IL was conducted which was then bonded onto silica surface to obtain a novel imidazolium-embedded amide stationary phase for HILIC. The combination of the amide group and imidazolium IL moiety might bring some advantages in selectivity or retention and therefore extended its applications. After characterizing the prepared IL and the resulting modified silica materials, the chromatographic performance and separation selectivity of the packed column were evaluated and compared with a commercial amide column. Then, the retention behavior was investigated through observing the retention factors at different chromatographic conditions using a wide range of compounds. Exceptionally, the prepared amide IL column exhibited superior separation performance towards complex samples such as flavonoids mixture, soybean flavonoids and human urine. All the results indicated that the novel amide IL column possessed an anion-exchange/HILIC mixed-mode retention mechanism and could be useful in the sample analysis as a promising candidate for HILIC stationary phase.

Method optimization of hydrophilic interaction chromatography separation of nucleotides using design of experiment approaches I: Comparison of several zwitterionic columns

A systematic method in hydrophilic interaction chromatography (HILIC) was developed for the separation of four monophosphate nucleotides using design of experiment (DOE) approaches. Three HPLC parameters, the buffer concentration (ammonium acetate concentration), gradient time, and temperature, were evaluated within the quality design framework, and the effects on chromatographic parameters were investigated. Four zwitterionic columns (ZIC-HILIC, ZIC-cHILIC, NUCLEODUR HILIC, and PC HILIC) were used to separate four nucleotides, and the HPLC conditions for each column were successfully optimized, although PC HILIC did not give peaks that were suitable for optimization. In addition, it was proved that optimized HPLC conditions differed from column to column even when the same types of zwitterionic sulfobetaine-functionalized columns were applied. This tendency was explained by differences in the separation characteristics of each column, the thickness of the water-enriched layer on the surface of the silica supports, and the pH. DOE for development of the HPLC method provides an effective explanation of the interactions among the variable parameters, especially in HILIC mode. Finally, a robust analytical method could be established by setting the optimum parameters. Among the employed columns, ZIC-cHILIC provided the widest range of suitable analytical conditions. NUCLEODUR HILIC was difficult to build a robust analytical method since the elution order of cytidine monophosphate and guanosine monophosphate was reversed.

Optimizing separations in online comprehensive two-dimensional liquid chromatography

Online comprehensive two-dimensional liquid chromatography has become an attractive option for the analysis of complex nonvolatile samples found in various fields (e.g. environmental studies, food, life, and polymer sciences). Two-dimensional liquid chromatography complements the highly popular hyphenated systems that combine liquid chromatography with mass spectrometry. Two-dimensional liquid chromatography is also applied to the analysis of samples that are not compatible with mass spectrometry (e.g. high-molecular-weight polymers), providing important information on the distribution of the sample components along chemical dimensions (molecular weight, charge, lipophilicity, stereochemistry, etc.). Also, in comparison with conventional one-dimensional liquid chromatography, two-dimensional liquid chromatography provides a greater separation power (peak capacity). Because of the additional selectivity and higher peak capacity, the combination of two-dimensional liquid chromatography with mass spectrometry allows for simpler mixtures of compounds to be introduced in the ion source at any given time, improving quantitative analysis by reducing matrix effects. In this review, we summarize the rationale and principles of two-dimensional liquid chromatography experiments, describe advantages and disadvantages of combining different selectivities and discuss strategies to improve the quality of two-dimensional liquid chromatography separations.

One-step preparation of zirconia coated silica microspheres and modification with d-fructose 1, 6-bisphosphate as stationary phase for hydrophilic interaction chromatography

In this study, ZrO₂ layer coated silica microspheres (ZrO₂/SiO₂) were successfully prepared by a facile one-step surfactant-free hydrothermal route under low pH condition. The synthesized ZrO₂/SiO₂ material was then modified with d-fructose 1, 6-bisphosphate (FDP) to improve the chromatographic separation property of the material. Fused-silica capillary columns were prepared with the modified material for evaluation. Phenolic, nucleobases and alkaloids compounds in hydrophilic interaction chromatographic (HILIC) mode showed symmetrical peaks. The FDP-ZrO₂/SiO₂ stationary phase showed better performance than ZrO₂/SiO₂ packing material and demonstrated great potential for application in HILIC mode.

Modelling of Hydrophilic Interaction Liquid Chromatography Stationary Phases Using Chemometric Approaches

Metabolomics is a powerful and widely used approach that aims to screen endogenous small molecules (metabolites) of different families present in biological samples. The large variety of compounds to be determined and their wide diversity of physical and chemical properties have promoted the development of different types of hydrophilic interaction liquid chromatography (HILIC) stationary phases. However, the selection of the most suitable HILIC stationary phase is not straightforward. In this work, four different HILIC stationary phases have been compared to evaluate their potential application for the analysis of a complex mixture of metabolites, a situation similar to that found in non-targeted metabolomics studies. The obtained chromatographic data were analyzed by different chemometric methods to explore the behavior of the considered stationary phases. ANOVA-simultaneous component analysis (ASCA), principal component analysis (PCA) and partial least squares regression (PLS) were used to explore the experimental factors affecting the stationary phase performance, the main similarities and differences among chromatographic conditions used (stationary phase and pH) and the molecular descriptors most useful to understand the behavior of each stationary phase.

Chemometric-assisted method development in hydrophilic interaction liquid chromatography: A review

With an enormous growth in the application of hydrophilic interaction liquid chromatography (HILIC), there has also been significant progress in HILIC method development. HILIC is a chromatographic method that utilises hydro-organic mobile phases with a high organic content, and a hydrophilic stationary phase. It has been applied predominantly in the determination of small polar compounds. Theoretical studies in computer-aided modelling tools, most importantly the predictive, quantitative structure retention relationship (QSRR) modelling methods, have attracted the attention of researchers and these approaches greatly assist the method development process. This review focuses on the application of computer-aided modelling tools in understanding the retention mechanism, the classification of HILIC stationary phases, prediction of retention times in HILIC systems, optimisation of chromatographic conditions, and description of the interaction effects of the chromatographic factors in HILIC separations. Additionally, what has been achieved in the potential application of QSRR methodology in combination with experimental design philosophy in the optimisation of chromatographic separation conditions in the HILIC method development process is communicated. Developing robust predictive QSRR models will undoubtedly facilitate more application of this chromatographic mode in a broader variety of research areas, significantly minimising cost and time of the experimental work.

Recent Liquid Chromatographic Approaches and Developments for the Separation and Purification of Carbohydrates

Carbohydate purification remains a bottleneck in securing analytical standards from natural sources or by chemical or enzymatic synthesis. This review highlights the scope and remaining limitations of recent approaches and methods development in liquid chromatography for robust and higher-throughput carbohydrate separation and isolation.

Polar silica-based stationary phases. Part II- Neutral silica stationary phases with surface bound maltose and sorbitol for hydrophilic interaction liquid chromatography

Two neutral polyhydroxylated silica bonded stationary phases, namely maltose-silica (MALT-silica) and sorbitol-silica (SOR-silica), have been introduced and chromatographically characterized in hydrophilic interaction liquid chromatography (HILIC) for a wide range of polar compounds. The bonding of the maltose and sorbitol to the silica surface was brought about by first converting bare silica to an epoxy-activated silica surface via reaction with γ-glycidoxypropyltrimethoxysilane (GPTMS) followed by attaching maltose and sorbitol to the epoxy surface in the presence of the Lewis acid catalyst BF₃.ethereate. Both silica based columns offered the expected retention characteristics usually encountered for neutral polar surface. The retention mechanism is majorly based on solute' differential partitioning between an organic rich hydro-organic mobile phase (e.g., ACN rich mobile phase) and an adsorbed water layer on the surface of the stationary phase although additional hydrogen bonding was also responsible in some cases for solute retention. The MALT-silica column proved to be more hydrophilic and offered higher retention, separation efficiency and resolution than the SOR-silica column among the tested polar solutes such as derivatized mono- and oligosaccharides, weak phenolic acids, cyclic nucleotide monophosphate and nucleotide-5'-monophosphates, and weak bases, e.g., nucleobases and nucleosides.

Application of Hydrophilic Interaction Liquid Chromatography for the Quantification of Flavonoids in Genista tinctoria Extract

Hydrophilic interaction chromatography (HILIC) was employed to investigate chromatographic behavior of selected flavonoids from their different subgroups differing in polarity. Chromatographic measurements were performed on two different HILIC columns: unmodified silica (Atlantis-HILIC) and zwitterionic sulfoalkylbetaine (SeQuant ZIC-HILIC). Separation parameters such as content and type of organic modifier were studied. On ZIC column retention factors were observed to be inversely proportional to the buffer content in the mobile phase, which is the typical partitioning mechanism. In the case of bare silica column more or less apparent dual retention mechanism was observed, depending on the water component content in the mobile phase. ZIC-HILIC showed better selectivity (in comparison to silica column) with the detection limit of 0.01 mg/L (only for rutin was 0.05 mg/L). Finally, this chromatographic procedure was validated and applied for the determination of some flavonoids in Genista tinctoria L. extract.