Optimization of conditions in on-line comprehensive two-dimensional reversed phase liquid chromatography. Experimental comparison with one-dimensional reversed phase liquid chromatography for the separation of peptides

Instrumental and theoretical advancements in pulsed elution-LC × LC: Investigation of pulse parameters and application to wastewater effluent

Due to the decoupling of the first (1D) and second (2D) dimension in pulsed elution-LC × LC (PE-LC × LC), method development is more flexible and straightforward compared to fast comprehensive LC × LC where the dependencies of key parameters between the two dimensions limits its flexibility. In this study we present a method for pulse generation, which is based on a switching valve alternating between one pump that delivers the gradient and a second pump that delivers low eluotrophic strength for the pause state. Consequently, the dwell volume of the system was circumvented and 7.5, and 3.75 times shorter pulse widths could be generated at flow rates of 0.2, and 0.4 mL/min with satisfactory accuracies between programmed and observed mobile phase composition (relative deviation of 6.0 %). We investigated how key parameters including pulse width and step height, 2D gradient time and flow rate affected the peak capacity in PE-LC × LC. The conditions yielding the highest peak capacity for the PE-LC × LC- high-resolution mass spectrometry (HRMS) system were applied to a wastewater effluent sample. The results were compared to a one dimensional (1D)-LC-HRMS chromatogram. The peak capacity increased with a factor 34 from 112 for the 1D-LC run to 3770 for PE-LC × LC-HRMS after correction for undersampling. The analysis time for PE-LC × LC-HRMS was 12.1 h compared to 67.5 min for the 1D-LC-HRMS run. The purity of the mass spectra improved for PE-LC × LC-HRMS by a factor 2.6 (p-value 3.3 × 10-6) and 2.0 (p-value 2.5 × 10-3) for the low and high collision energy trace compared to the 1D-LC-HRMS analysis. Furthermore, the signal-to-noise ratio (S/N) was 4.2 times higher (range: 0.06-56.7, p-value 3.8 × 10-2) compared to the 1D-LC-HRMS separation based on 42 identified compounds. The improvements in S/N were explained by the lower peak volume obtained in the PE-LC × LC-HRMS.

Impact of conditioning runs on hydrophilic interaction chromatography repeatability and its application as a second dimension in online comprehensive two-dimensional liquid chromatography

A common separation approach for polar compounds involves coupling reversed-phase liquid chromatography (RPLC) with hydrophilic interaction chromatography (HILIC) in two-dimensional chromatography. The higher proportion of acetonitrile used in the HILIC mobile phase, which enhances mass spectrometry detection, encourages its use in the second dimension. Previous studies demonstrated that the HILIC column can be partially equilibrated within very short timeframes without compromising retention time stability, rendering it suitable in online comprehensive two-dimensional liquid chromatography (LC×LC) setups. In addition, a specific number of conditioning cycles seems necessary to establish stable retention times. Here, the repeatability of HILIC when employed as second dimension in LC×LC was investigated, with a focus on determining the required number of conditioning cycles to achieve repeatable retention times. Various parameters influenced by the LC×LC online modulation system were studied, such as steep gradient slopes up to 8%, and very short equilibration times, less than or equal to dead time, as well as injection volume and solvent, which depend on the first dimension. Finally, the use of HILIC as a second dimension with tailored conditioning runs was applied to the analysis of hyaluronic acid hydrogel digests. The application of an RPLC×HILIC method using five conditioning runs yielded exceptional stability in second-dimension retention times.

In-silico method development and optimization of on-line comprehensive two-dimensional liquid chromatography via a shortcut model

Comprehensive two-dimensional liquid chromatography (LCxLC) represents a valuable alternative to conventional single column, or one-dimensional, liquid chromatography (1D-LC) for resolving multiple components in a complex mixture in a short time. However, developing LCxLC methods with trial-and-error experiments is challenging and time-consuming, which is why the technique is not dominant despite its significant potential. This work presents a novel shortcut model to in-silico predicting retention time and peak width within an RPLCxRPLC separation system (i.e., LCxLC systems that use reversed-phase columns (RPLC) in both separation dimensions). Our computationally effective model uses the hydrophobic-subtraction model (HSM) to predict retention and considers limitations due to the sample volume, undersampling and the maximum pressure drop. The shortcut model is used in a two-step strategy for sample-dependent optimization of RPLCxRPLC separation systems. In the first step, the Kendall's correlation coefficient of all possible combinations of available columns is evaluated, and the best column pair is selected accordingly. In the second step, the optimal values of design variables, flow rate, pH and sample loop volume, are obtained via multi-objective stochastic optimization. The strategy is applied to method development for the separation of 8, 12 and 16 component mixtures. It is shown that the proposed strategy provides an easy way to accelerate method development for full-comprehensive 2D-LC systems as it does not require any experimental campaign and an entire optimization run can take less than two minutes.

Improving the Accuracy of Predictive 2D-LC Optimization Strategies: Incorporation of Simulated Elution Profiles to Account for Injection Band Broadening in Online Comprehensive Two-Dimensional Liquid Chromatography

Method development in online comprehensive two-dimensional liquid chromatography (LC × LC) requires the selection of a large number of experimental parameters. The complexity of this process has led to several computer-based LC × LC optimization algorithms being developed to facilitate LC × LC method development. One particularly relevant challenge for predictive optimization software is to accurately model the effect of second dimension (2D) injection band broadening under sample solvent mismatch and/or sample volume overload conditions. We report a novel methodology that combines a chromatographic numerical simulation model capable of predicting elution profiles of analytes under conditions where peak distortion occurs with a predictive multiparameter Pareto optimization approach for online LC × LC. Preliminary method optimization is performed using a theoretical model to predict 2D injection profiles, and optimal experimental configurations obtained from the Pareto fronts are then subjected to further optimization using the simulation model. This approach drastically reduces the number of simulations and therefore the computational demand. We show that the optimal experimental conditions obtained in this manner are similar to those obtained using a complete optimization using only the simulation model. Online HILIC × RP-LC separation of phenolic compounds was used to compare experimental data to simulated two- and three-dimensional contour plots. The main advantage of the proposed approach is the ability to predict the formation of split or deformed peaks in the 2D, a significant benefit in online LC × LC method optimization, especially for separation combinations with mismatched mobile phases. A further benefit is that simulated elution profiles can be used for the visualization of predicted two-dimensional chromatograms for method selection.

Theoretical and practical guidelines for solvent dilution between the two dimensions in online comprehensive two-dimensional liquid chromatography

Online comprehensive two-dimensional liquid chromatography (online LC x LC) has become increasingly popular. Among the different chromatographic modes that can be combined, hydrophilic interaction chromatography (HILIC) and reversed-phase liquid chromatography (RPLC) are particularly interesting because they offer a high degree of orthogonality. However, this combination remains complex due to the incompatibility of the solvents in the two dimensions. To avoid this problem, it is possible to dilute the first dimension (1D) effluent with (zdilution -1) volumes of a weaker solvent added to one volume of 1D-effluent, where zdilution represents the extent to which the fraction volume has been multiplied. This can be done using either active solvent modulation technology or an additional pump, prior to the second dimension analysis. The objective of this study was to develop theoretical models to predict whether or not dilution can be effective, and, if so, what is the minimum zdilution value required. This approach is based on the calculation of the ratio (called xdilution) between the peak standard deviation due to the injection process and the peak standard deviation in the absence of extra-column dispersion. xdilution was calculated from theoretical relationships and plotted as a function of zdilution, to predict the value required to obtain good peak shapes for the compound of interest. The maximum xdilution value was found to be of the order of 1 for chromatographically acceptable peak shapes. The proposed theoretical approach was experimentally validated on a number of representative small molecules and peptides. Agreement between experimental results and theoretical models was very high, especially for small molecules. Finally, it is shown that this approach helps to predict the most appropriate set of conditions in HILIC x RPLC, depending on the compounds to be separated.

Reversed HILIC Gradient: A Powerful Strategy for On-Line Comprehensive 2D-LC

The aim of the present work is to evaluate the possibilities and limitations of reversed hydrophilic interaction chromatography (revHILIC) mode in liquid chromatography (LC). This chromatographic mode consists of combining a highly polar stationary phase (bare silica) with a gradient varying from very low (1-5%) to high (40%) acetonitrile content (reversed gradient compared to HILIC). The retention behavior of revHILIC was first compared with that of reversed-phase LC (RPLC) and HILIC using representative mixtures of peptides and pharmaceutical compounds. It appears that the achievable selectivity can be ranked in the order RPLC > revHILIC > HILIC with the two different samples. Next, two-dimensional liquid chromatography (2D-LC) conditions were evaluated by combining RPLC, revHILIC, or HILIC with RPLC in an on-line comprehensive (LC × LC) mode. evHILIC × RPLC not only showed impressive performance in terms of peak capacity and sensitivity, but also provided complementary selectivity compared to RPLC × RPLC and HILIC × RPLC. Indeed, both the elution order and the retention time range differ significantly between the three techniques. In conclusion, there is no doubt that revHILIC should be considered as a viable option for 2D-LC analysis of small molecules and also peptides.

Off-line two-dimensional separation involving supercritical fluid chromatography for the characterization of the wastewater from algae hydrothermal liquefaction

An off-line multidimensional method involving liquid chromatography combined with supercritical fluid chromatography was developed for the characterization of the wastewater of hydrothermal liquefaction of microalgae Chlorella sorokiniana. The first dimension consisted of a phenyl hexyl column operated in reversed-phase mode, whereas the second dimension was performed on a diol stationary phase. Optimization of the kinetic parameters of the first and second dimensions were performed, taking into account the fraction collection system. The beneficial effect of working at high flow rate in both dimensions, as well as the need to work with short columns (50 mm) in the second dimension was evidenced. Injection volume was also optimized in both dimensions. The first dimension benefited from on-column focusing, while in the second dimension, untreated water-rich fractions could be injected without peak deformation. The performances of offline LCxSFC were compared to LC-HRMS, SFC-HRMS and LCxLC-HRMS for the analysis of the wastewater. Despite a long analysis time of 3.3h, the off-line separation coupled to high-resolution mass spectrometry exhibited a very large orthogonality with 75 % occupation rate of the separation space, reaching an effective peak capacity of 1050. While other evaluated techniques were faster, one-dimensional techniques failed to separate the numerous isomers while LCxLC exhibited lower orthogonality (45% occupation rate).

Theoretical and practical comparison of RPLC and RPLC × RPLC: how to consider dilution effects and sensitivity in addition to separation power?

The objective of this work was to provide an unbiased comparison of one-dimensional reversed-phase liquid chromatography (1D-RPLC) and comprehensive two-dimensional RPLC (RPLC × RPLC), through calculations and experimental verifications. For this purpose, various quality descriptors were evaluated, including peak capacity, analysis time, dilution factor, number of runs in the second dimension, and injection volume. The same strategy was applied to small pharmaceuticals and peptides. Whatever the analysis time between 30 and 200 min, short columns of only 30 × 2.1 mm packed with sub-2-µm particles should be selected in both dimensions of the 2D-LC setup to obtain the best compromise in terms of peak capacity and sensitivity. The peak capacity in RPLC × RPLC vs. RPLC was significantly improved for analysis times beyond 5 min. However, extra-column volume located after the second-dimension column was found to be particularly critical for peptides, and up to 50% lower peak capacity was observed with MS vs. UV detection. Contrary to common belief, higher dilution is not always observed in RPLC × RPLC. With adequate analytical conditions, better sensitivity (in theory fivefold and in practice three- to fivefold) could be achieved in RPLC × RPLC compared to 1D-RPLC, regardless of the analysis time.

Solvent strength of organic phase for two biphasic solvent systems in high speed countercurrent chromatography

In this work, relationships between solvent strength of organic phase (ψ) for two biphasic solvent systems in high speed countercurrent chromatography, hexane-ethyl-acetate-methanol-water (HEMWat) and ethyl acetate-n-butanol-water (EBuWat), and partition coefficient (K) were investigated using four retention models, including Jandera's model (ABM), Neue-Kuss model (NK), linear-solvent-strength model (LSS) and quadratic-solvent-strength model (QSS). Experimental results showed that ABM model had the best fitting results for HEMWat system while NK model and QSS model had good fitting results in EBuWat system. Thus, a mathematical relationship between partition coefficient (K) and solvent strength of organic phase (ψ) could be obtained by measurement of partition coefficients of the target compounds with three different volume ratios of organic phase. At the same time, a functional map was proposed to construct to get a maneuverable region so that an optimal two-phase solvent system for separation of a target compound could be selected easily, which saved a lot of manpower for high speed countercurrent chromatographic separation. The application of this new method was declared by successful separation of two components, apigenin-6-C-β-D-xylopyranosyl-8-C-α-L-arabinopyranoside and vicenin-3, from dried leaves of Dendrobium officinale Kimura et Migo using high speed countercurrent chromatography.

The Future of Method Development for Two-Dimensional Liquid Chromatography – Work Smarter, Not Just Harder?

The potential for wider use of two-dimensional liquid chromatography (2D-LC) is becoming more evident as the complexity of samples that must be handled continues to increase in application areas ranging from biopharmaceuticals to biosourced consumer products. Although the sophistication and ease of use have improved in recent years for commercial 2D-LC instruments, many analysts are still intimidated by the method development process for 2D methods because of the larger number of variables involved compared to conventional liquid chromatography. In this article, I share my perspective on the trends in this area, and the developments we are likely to see in the field in the near future.

A simple mathematical treatment for predicting linear solvent strength behaviour in gradient elution: application to biomolecules

This paper describes an approach to rapidly and easily calculate the linear solvent strength parameters, namely log k₀ and S, under reversed‐phase liquid chromatography conditions. This approach, which requires two preliminary gradient experiments to determine the retention parameters, was applied to various representative compounds including small molecules, peptides, and proteins. The retention time prediction errors were compared to the ones obtained with a commercial HPLC modeling software, and a good correlation was found between the values. However, two important constraints have to be accounted for to maintain good predictions with this new approach: i) the retention factor at the initial composition of the preliminary gradient series have to be large enough (i.e., log k_i above 2.1) and ii) the retention models have to be sufficiently linear. While these two conditions are not always met with small molecules or even peptides, the situation is different with large biomolecules. This is why our simple calculation method should be preferentially applied to calculate the linear solvent strength parameters of protein samples.

Perspectives on the Use of Retention Modeling to Streamline 2D-LC Method Development: Current State and Future Prospects

The history of multidimensional liquid chromatography (MDLC) has been dominated by methods that have been developed using highly empirical, experience-driven, trial-and-error approaches. These approaches have been sufficient in progressing the field forward scientifically, primarily in academic research laboratories. However, more widespread usage of multidimensional separations will require more systematic approaches to method development that rely less on user experience and lower the barriers to development and use of methods by a wider community of users. In this mini-review, we discuss recent research aimed at developing such systematic, model-driven approaches to streamline method development and speculate about likely advances in the same direction in the near future. It seems likely that such model-driven approaches would be particularly helpful for methods developed for analyzing biopharmaceutical molecules, which tend to be very sensitive to slight changes in method conditions (for example, mobile phase composition).

A Comprehensive 2D-LC/MS Online Platform for Screening of Acetylcholinesterase Inhibitors

The continuous interest in discovering new bioactive molecules derived from natural products (NP) has stimulated the development of improved screening assays to help overcome challenges in NP-based drug discovery. Here, we describe a unique platform for the online screening of acetylcholinesterase inhibitors without the need for pre-treating the sample. In the current study, we have demonstrated the ability to combine reversed-phase separation with a capillary immobilized enzyme reactor (cIMER) in two-dimensional liquid chromatography system coupled with mass spectrometry detection. We systematically investigated the effects of method parameters that are of practical significance and are known to affect the enzyme assay and interfere in the analysis such as: bioreactor dimensions, loop sizes, amount of immobilized enzyme, second dimension flow rates, reaction time, substrate concentration, presence of organic modifier, limit of detection and signal suppression. The performance of this new platform was evaluated using a mixture containing three known AChE inhibitors (tacrine, galanthamine and donepezil) and an ethanolic extract obtained from the dry bulbs of Hippeastrum calyptratum (Amaryllidaceae) was investigated to provide a proof of concept of the applicability of the platform for the analysis of complex mixtures such as those derived from NPs.

On-line 2D-RPLC x RPLC - HRMS to assess wastewater treatment in a pharmaceutical plant

Pharmaceutical effluents are complex media containing hundreds of compounds including active ingredients, intermediate products and unknown impurities. Bringing an industrial wastewater treatment plant (WWTP) into compliance with European directives requires a thorough analysis of the effluent. In this study, we demonstrate how online comprehensive two-dimensional liquid chromatography (on-line LC × LC) hyphenated to high resolution mass spectrometry (HRMS) can be a powerful analytical methodology to monitoring the outlet water, by analysing the content of known molecules while characterizing unknown compounds. Reversed phase liquid chromatography (RPLC) was used in both dimensions, with a penta-fluoro-phenyl silica-based column at neutral pH in the first dimension (¹D) and a C18 column at acidic pH in the second one (²D). The conditions were optimized for a total analysis time of 60 min. The variability of both retention times and peak areas was evaluated. The average standard deviation on retention times was found to be less than 0.1 s in ²D. The relative standard deviation on peak area was about 7% for run-to-run analysis. This analytical approach, applied to the pharmaceutical effluents before (inlet) and after (outlet) wastewater treatment permitted to detect 240 compounds. These included 27 priority pharmaceutical products, 8 of which were of very high priority and their concentrations could be compared to target values. The comparison of 2D-LC and 1D-LC approaches clearly highlights the power of on-line RPLC x RPLC technique, which allows both targeted quantitative analysis and non-targeted qualitative analysis of pharmaceutical effluents.

Strategies to circumvent the solvent strength mismatch problem in online comprehensive two-dimensional liquid chromatography

On-line comprehensive two-dimensional liquid chromatography is a powerful technique for the separation of highly complex samples. Due to the addition of the second dimension of separation, impressive peak capacities can be obtained within a reasonable analysis time compared to one-dimensional liquid chromatography. In online comprehensive two-dimensional liquid chromatography, the separation power is maximized by selecting two separation dimensions as orthogonal as possible, which most often requires the combination of different mobile phases and stationary phases. The online transfer of a given solvent from the first dimension to the second dimension may cause severe injection effects in the second dimension, mostly due to solvent strength mismatch. Those injection effects may include peak broadening, peak distortion, peak splitting or breakthrough phenomenon. They are often found to reduce significantly the peak capacity and the peak intensity. To overcome such effects, arising specifically in online comprehensive two-dimensional liquid chromatography, different methods have been developed over the years. In this review, we focused on the most recently reported ones. A critical discussion, supported by a theoretical approach, gives an overview of their advantages and drawbacks.

Characterization of positional isomers of drug intermediates by off-line RPLC x SFC hyphenated to high resolution MS

Many steps are needed in the synthesis of a new active pharmaceutical ingredient (API). In a practical case proposed by a French pharmaceutical company, an intermediate synthesis step, needed to protect 8 hydroxyl groups before oxidation, could produce a mixture of neutral compounds containing up to 652 structures being positional isomers of 18 molecular formulas. Some mixtures allowed obtaining the desired API, others did not. An efficient analytical method was needed to characterize these neutral positional isomers and identify the mixtures to reject. Two samples were provided by the pharmaceutical company: Sample A was conform, Sample B was not. 8 RPLC columns were used with different gradients to screen Sample A. Next, the best RPLC separation was used as the second dimension fast analysis in a comprehensive 2D-RPLC systems. Two columns were used as first dimension: a fluorinated one and a zirconium based one. An order of magnitude was gained in peak capacity, but a better sample characterization was still needed. An off-line RPLC x SFC x Q-TOF/MS analysis was performed collecting 96 RPLC fractions and analyzing them by SFC with Q-TOF/MS detection. A home-made software associated the 96 SFC MS chromatograms to produce either base peak (BPC) or extract ion (EIC) contour plots that allowed for a satisfying characterization of the samples. Subtracting the EIC of expected m/z compounds from the Sample B BPC contour plot produced a unique new contour plot clearly pointing out unexpected compounds explaining the failure of the synthesis and possibly allowing improving the synthesis process.

Detailed numerical study of the peak shapes of neutral analytes injected at high solvent strength in short reversed-phase liquid chromatography columns and comparison with experimental observations

We report on a numerical investigation of the different steps in the development of the spatial concentration profiles developing along the axis of a liquid chromatography column when injecting large relative volumes (>10 to 20% of column volume) of analytes dissolved in a high solvent strength solvent band as can be encountered in the second dimension (²D) column of a two-dimensional liquid chromatography (2D-LC) system. More specifically, we made a detailed study of the different retention and the axial band broadening effects leading to the double-headed peak shapes or strongly fronting peaks that can be experimentally observed under certain conditions in 2D-LC. The establishment of these intricate peak profiles is discussed in all its fine, mechanistic details. The effect of the volume of the column, the volume and the shape of the sample band, the retention properties of the analyte and the band broadening experienced by the analytes and the sample solvent are investigated. A good agreement between the simulations and the experimental observations with caffeine and methylparaben injected in acetonitrile/water (ACN/H₂O) mobile phase with different injection volumes is obtained. Save the difference in dwell volume, key features of experimental and simulated chromatograms agree within a few %. The simulations are also validated against a number of simple mathematical rules of thumb that can be established to predict the occurrence of a breakthrough fraction and estimate the amount of breakthrough.

Comparison of existing strategies for keeping symmetrical peaks in on-line Hydrophilic Interaction Liquid Chromatography x Reversed-Phase Liquid Chromatography despite solvent strength mismatch

In two-dimensional liquid chromatography, the combination of hydrophilic interaction liquid chromatography (HILIC) and reversed-phase liquid chromatography (RPLC) is very attractive due to the complementarity of their separation mechanisms. On-line comprehensive HILIC x RPLC is well-known to give rise to a large retention space coverage when dealing with ionisable compounds. However, method development in on-line HILIC x RPLC is challenging due to the reversed solvent strength between both dimensions, which can greatly affect the peak shapes in the second RPLC dimension, and thus the separation quality and the method sensitivity. In the present contribution, we compared four strategies designed to avoid this problem: (1) flow splitting, which consists in reducing the injection volume in the second dimension (²D), (2) on-line dilution with a make-up flow and (3) on-line dilution with Active Solvent Modulation (ASM), which both consist in reducing the solvent strength of the injected fractions, and (4) Total Breakthrough Strategy, which we recently proposed. Unlike the three preceding strategies, this latter one consists in injecting large volumes of strong solvent in ²D. The performance of each strategy was evaluated for sub-hour separations of a tryptic digest in on-line HILIC x RPLC. In this work, we considered the critical case for which the same column internal diameters (i.e. 2.1 mm here) are used in both dimensions. Peak capacity, peak shapes and peak intensities were considered for this evaluation. The highest peak capacity could be achieved with Total Breakthrough Strategy while the lowest one with on-line dilution using ASM. Peak intensities were usually higher with on-line dilution approaches (make-up flow and ASM). However, despite the presence of breakthrough, peak intensities were approximately 7-fold higher with Total Breakthrough Strategy than with flow splitting.

Rapid two-dimensional Protein-A size exclusion chromatography of monoclonal antibodies for titer and aggregation measurements from harvested cell culture fluid samples

The success of monoclonal antibody (mAb) therapeutics have increased pharmaceutical investment in mAb production, which has led to a greater demand of technologies to efficiently characterize these biotherapeutics. The large size and heterogeneity of mAbs require the measurement of multiple critical quality attributes (CQAs) during production. The current workflow to measure CQAs of antibodies involves multiple one-dimensional liquid chromatography methods, including Protein-A (ProA), ion-exchange (IEX), reversed-phase, size exclusion (SEC), hydrophilic interaction, and hydrophobic interaction (HIC). Recent advances in commercial two-dimensional liquid chromatography (2D-LC) affords an opportunity to perform two separations at once to measure multiple CQAs in a single assay. Here, we describe the development of a 2D ProA–SEC method using entirely commercially available instrumentation. Each individual separation and the transfer of material between dimensions were optimized to develop a method that measures titer and aggregation of a target antibody from harvested cell culture fluid in under 5 min. We determined the effects of each parameter of the method on mAb recovery and stability, as well as speed, robustness, resolution, and accuracy of the aggregate amount detected in the second dimension (²D). While there are still sources of error caused by hardware limitations, our rapid ProA-SEC method is an effective screening tool with a significant throughput advantage over previously described methods. Additionally, this work serves as a basis for developing other 2D-LC methods with ProA as the first dimension (¹D) separation coupled with different ²D separation, such as ProA-IEX and ProA-HIC.

Biological Applications for LC-MS-Based Proteomics

Since its inception, liquid chromatography-mass spectrometry (LC-MS) has been continuously improved upon in many aspects, including instrument capabilities, sensitivity, and resolution. Moreover, the costs to purchase and operate mass spectrometers and liquid chromatography systems have decreased, thus increasing affordability and availability in sectors outside of academic and industrial research. Processing power has also grown immensely, cutting the time required to analyze samples, allowing more data to be feasibly processed, and allowing for standardized processing pipelines. As a result, proteomics via LC-MS has become popular in many areas of biological sciences, forging an important seat for itself in targeted and untargeted assays, pure and applied science, the laboratory, and the clinic. In this chapter, many of these applications of LC-MS-based proteomics and an outline of how they can be executed will be covered. Since the field of personalized medicine has matured alongside proteomics, it has also come to rely on various mass spectrometry methods and will be elaborated upon as well. As time goes on and mass spectrometry evolves, there is no doubt that its presence in these areas, and others, will only continue to grow.

On-line two-dimensional liquid chromatography hyphenated to mass spectrometry and ion mobility-mass spectrometry for the separation of carbohydrates from lignocellulosic biomass

Lignocellulosic biomass is a promising resource of renewable energy. Its transformation to ethanol requires efficient pretreatment leading to complex liquid mixtures made of hundreds of oxygenated analytes. A large part of the released compounds belong to the carbohydrates family. To overcome the complexity of such samples, a comprehensive on-line two-dimensional reversed-phase liquid chromatography hyphenated to high-resolution mass spectrometry (RPLC × RPLC-HRMS) was dedicated to the separation of carbohydrates and more specifically oligomers coming from pretreated lignocellulosic biomass. The first part of this study consisted in the optimization of such hyphenation (i.e. selection of stationary phases, mobile phases, sampling time, etc.). Then, the analytical method was applied to an industrial aqueous biomass product coming from the sulfuric acid-based pretreatment of a wheat straw. Around 70 well-resolved chromatographic peaks corresponding to oligomers were obtained. Occupation of the separation space between each chromatographic dimension was estimated to 75%. In the last part of this study, the interest of ion mobility-mass spectrometry in addition to RPLC × RPLC was discussed. Some examples highlighted the additional separation that can bring ion mobility to RPLC × RPLC-IMS-HRMS method. Using this four-dimensional hyphenation method, each analyte was described by two retention times, the collisional cross section and the molecular formula allowing to reach a level of detail never seen for biomass sample compositions.

Recent applications of retention modelling in liquid chromatography

Recent applications of retention modelling in liquid chromatography (2015–2020) are comprehensively reviewed. The fundamentals of the field, which date back much longer, are summarized. Retention modeling is used in retention‐mechanism studies, for determining physical parameters, such as lipophilicity, and for various more‐practical purposes, including method development and optimization, method transfer, and stationary‐phase characterization and comparison. The review focusses on the effects of mobile‐phase composition on retention, but other variables and novel models to describe their effects are also considered. The five most‐common models are addressed in detail, i.e. the log‐linear (linear‐solvent‐strength) model, the quadratic model, the log–log (adsorption) model, the mixed‐mode model, and the Neue–Kuss model. Isocratic and gradient‐elution methods are considered for determining model parameters and the evaluation and validation of fitted models is discussed. Strategies in which retention models are applied for developing and optimizing one‐ and two‐dimensional liquid chromatographic separations are discussed. The review culminates in some overall conclusions and several concrete recommendations.

Development of an Online 2D Ultrahigh-Pressure Nano-LC System for High-pH and Low-pH Reversed Phase Separation in Top-Down Proteomics

The development of novel high-resolution separation techniques is crucial for advancing the complex sample analysis necessary for high-throughput top-down proteomics. Recently, our group developed an offline 2D high-pH RPLC/low-pH RPLC separation method and demonstrated good orthogonality between these two RPLC formats. Specifically, ultrahigh-pressure long capillary column RPLC separation has been applied as the second dimensional low-pH RPLC separation for the improvement of separation resolution. To further improve the throughput and sensitivity of the offline approach, we developed an online 2D ultrahigh-pressure nano-LC system for high-pH and low-pH RPLC separations in top-down proteomics. An online microtrap column with a dilution setup was used to collect eluted proteins from the first dimension high-pH separation and inject the fractions for ultrahigh-pressure long capillary column low-pH RPLC separation in the second dimension. This automatic platform enables the characterization of 1000+ intact proteoforms from 5 μg of intact E. coli cell lysate in 10 online-collected fractions. Here, we have demonstrated that our online 2D pH RP/RPLC system coupled with top-down proteomics holds the potential for deep proteome characterization of mass-limited samples because it allows the identification of hundreds of intact proteoforms from complex biological samples at low microgram sample amounts.

Pharmaceutical impurity analysis by comprehensive two-dimensional temperature responsive × reversed phase liquid chromatography

In this study, the possibilities of temperature responsive × reversed phase liquid chromatography (TRLC × RPLC) are assessed in terms of pharmaceutical impurity analysis. Due to the increased peak capacity per unit time they offer, two-dimensional LC approaches are gaining relevance for the analysis of complex drug formulations. Because the latter depicts a larger predisposition for the occurrence of an increased number of impurities, current 1D-HPLC approaches often prove insufficient. Since many LC × LC methods are limited by modulation, solvent compatibility, orthogonality, and sensitivity issues, the combination of TRLC × RPLC is explored in this work for pharmaceutical impurity analysis. As this combination of a purely aqueous separation with RPLC allows for systematic and optimization-free refocusing in the second dimension, it opens possibilities for generic LC × LC requiring minimal to no method development, in this way overcoming a major perceived contemporary hurdle of LC × LC. The approach is demonstrated with a representative mixture of 17 solutes comprising 11 corticosteroids and 6 progestogens. Orthogonality and peak capacities were assessed on three RP core-shell column selectivities (Poroshell EC-C18, phenyl-hexyl and PFP). Although the TRLC × EC-C18 combination offered somewhat better orthogonality, the combination with the PFP column proved the best for the separation at hand. Depending on the composition of the mixture, the use of full, shifted, or segmented gradients allowed facile optimization of the separation. The developed platform allowed detection of the impurities at the 0.05% level compared to a selected main compound, while also opening up possibilities for analysis of formulations comprising two active ingredients.

Recent applications of chemometrics in one- and two-dimensional chromatography

The proliferation of increasingly more sophisticated analytical separation systems, often incorporating increasingly more powerful detection techniques, such as high-resolution mass spectrometry, causes an urgent need for highly efficient data-analysis and optimization strategies. This is especially true for comprehensive two-dimensional chromatography applied to the separation of very complex samples. In this contribution, the requirement for chemometric tools is explained and the latest developments in approaches for (pre-)processing and analyzing data arising from one- and two-dimensional chromatography systems are reviewed. The final part of this review focuses on the application of chemometrics for method development and optimization.

Comprehensive two-dimensional liquid chromatography with inductively coupled plasma mass spectrometry detection for the characterization of sulfur, vanadium and nickel compounds in petroleum products

The petroleum industry is increasingly concerned with the conversion of vacuum residues as a consequence of decreased conventional crude oil availability. The compositional analysis of heavy oil products has become a key step in conversion processes, but the complexity of these oil matrices tends to increase with their boiling point. In this study, comprehensive two-dimensional liquid chromatography (LCxLC) coupled to inductively coupled mass spectrometry (ICP-MS/MS) is considered with a view to meet new requirements and to bring additional information regarding the species present in these matrices. In search for a high degree of orthogonality, two separation techniques involving two different retention mechanisms were evaluated: Size Exclusion Chromatography (SEC) and Reverse Phase Liquid Chromatography (RPLC). In SEC, the analytes are separated according to their molecular weight while according to their hydrophobicity in RPLC. The separation power of both individual separation techniques was first evaluated. Off-line and on-line LCxLC were compared on the basis of an optimization approach. It is shown that off-line SECxRPLC can provide, for the same analysis time of 150 min, a higher peak capacity (2600 vs 1700) than on-line RPLCxSEC while a similar dilution factor (close to 30) but also requires far fewer fractions to be analyzed (12 vs 400). Asphaltenes which constitute the heaviest fraction of crude oils (obtained from petroleum industry) were analyzed by the developed off-line SECxRPLC method. The resulting 2D-contour plots show that co-elutions could be removed leading, for the first time, to new information on high molecular weight species containing sulfur and vanadium.

Online Comprehensive High pH Reversed Phase × Low pH Reversed Phase Approach for Two-Dimensional Separations of Intact Proteins in Top-Down Proteomics

A proof-of-concept study is presented on the use of comprehensive two-dimensional liquid chromatography mass spectrometry (LC × LC-MS) for the separation of intact protein mixtures using a different mobile phase pH in each dimension. This system utilizes mass spectrometry (MS) friendly pH modifiers for the online coupling of high pH reversed phase liquid chromatography (HPH-RPLC) in the first dimension (¹D) followed by low pH reversed phase liquid chromatography (LPH-RPLC) in the second dimension (²D). Owing to the ionic nature of proteins, the use of a different mobile phase pH was successful to provide altered selectivity between the two dimensions, even for closely related protein variants, such as bovine cytochrome c and equine cytochrome c, which differ by only three amino acids. Subminute gradient separation of proteins in the second dimension was successful to minimize analysis time, while maintaining high peak capacity. Unlike peptides, the elution order of studied proteins did not follow their isoelectric points, where acidic proteins would be expected to be more retained at low pH (and basic proteins at high pH). The steep elution isotherms (on-off retention mechanism) of proteins and the very steep gradients utilized in the second-dimension column succeeded in overcoming pH and organic solvent content mismatch. The utility of the system was demonstrated with a mixture of protein standards and an Escherichia coli protein mixture.

Likelihood of total resolution in selective comprehensive two-dimensional liquid chromatography with parallel processing: Simulation and theory

The probability Pr(sLC×LC) that all peaks are separated by a resolution of 1.5 or more in selective comprehensive two-dimensional liquid chromatography (sLC × LC) is computed for simple model systems of 5 to 60 peaks and first-dimension (¹D) gradient times of 100 to 2000 s. The computations include mimics of a commercial instrument, whose fixed second-dimension (²D) gradient time and use of one cycle time for initialization reduces Pr(sLC×LC) relative to an earlier report. For serial sLC × LC, in which a single device collects and transfers ¹D multiplets to the second dimension, Pr(sLC×LC) under practical conditions is predicted to be only slightly larger than the probability of total resolution in LC × LC for separations of the same duration in each case. To increase Pr(sLC×LC), two model systems are proposed based on parallel processing, in which one device collects multiplets from the first separation while a second device simultaneously transfers fractions from previously collected multiplets to the second dimension for further separation. A sum of probabilities guideline is proposed by which optimal fixed ²D gradient times, ranging from 9.5 to 12 s, are found for both serial and parallel models. The increases of Pr(sLC×LC) based on parallel processing are modest; the largest is only 0.062 for one system and 0.106 for the other, relative to the serial model. A theory is derived that rationalizes the modesty of the increase, which was unexpected. It shows that Pr(sLC×LC) equals the probability of total resolution in the first dimension, plus the product of the probability that all ¹D multiplets are transferred to the second dimension and the probability that all multiplets are separated in the second dimension. The theory shows that, although parallel processing is better than serial processing for multiplet transfer, the ability to leverage this gain is offset by the limited probability that all multiplets are then actually separated in the second dimension, which is only about 0.55 for conditions where the change from serial to parallel processing is most beneficial. With these findings in hand, two scenarios are examined for future consideration: one in which the ²D peak capacity is doubled, and another in which multiplets are always transferred to the second dimension. The latter shows considerable promise for increasing Pr(sLC×LC) substantially beyond its counterpart in LC × LC. For example, a 50% probability of separating all peaks in a 15-component mixture can be reached in 1150 s using LC × LC. The same probability can be reached in the same time for a sample with nearly twice as many components (27) in the case of sLC × LC, assuming transfer of all multiplets to the second dimension. These findings will be useful to those considering systematic approaches to developing 2D-LC methods for moderately complex mixtures, and to those interested in instrument development for 2D-LC.

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.

Multiple heart-cutting two dimensional liquid chromatography quadrupole time-of-flight mass spectrometry of pyrrolizidine alkaloids

Pyrrolizidine alkaloids (PAs) and their and the corresponding N-oxides (PAs-ox) are genotoxic plant metabolites which can be present as unwanted contaminants in food products of herbal origin like tea and food supplements. PAs and PAs-ox come in a wide variety of molecular structures including many structural isomers. For toxicity assessment it is important to determine the composition of a sample and to resolve all isomeric PAs and PAs-ox, which is currently not possible in one liquid or gas chromatographic (LC or GC) run. In this study an online two dimensional liquid chromatography quadrupole time-of-flight mass spectrometry (2D-LC QToF-MS) method was developed to resolve isomeric PAs and PAs-ox. After comprehensive column and mobile phase selection a polar endcapped C₁₈ column was used at pH 3 in the first dimension, and a cross-linked C₁₈ column at pH 10 in the second dimension. Injection solvents, column IDs, flow rates and temperatures were carefully optimized. The method with column selection valve switching described in this study was able to resolve and visualize 20 individual PAs/PAs-ox (6 sets of isomers) in one 2D-LC QToF-MS run. Moreover, it was shown that all isomeric PAs/PAs-ox could be unambiguously annotated. The method was shown to be applicable for the determination and quantification of isomeric PAs/PAs-ox in plant extracts and could be easily extended to include other PAs and PAs-ox.