Comprehensive liquid chromatography: Fundamental aspects and practical considerations—A review

Maximizing sensitivity and selectivity in LC × LC-HRMS for pesticide analysis via exploitation of per-aqueous liquid chromatography

Accurate monitoring of pesticide residues at minimal concentrations is imperative for adherence to stringent regulatory standards in numerous countries. This study presents an innovative methodology employing comprehensive two-dimensional liquid chromatography coupled with high-resolution mass spectrometry (LC × LC-HRMS). The approach ensures high sensitivity and selectivity in detecting targeted compounds. A pivotal component of this methodology is the utilization of per-aqueous liquid chromatography (PALC) as the first dimension, facilitating the use of water-based mobile phases and addressing solvent mismatch issues. The second dimension employs reversed-phase liquid chromatography (RPLC), enhancing the separation of compounds. PALC proves instrumental in refocusing and enables the practical application of narrow-diameter columns (1.5 mm I.D.). This column design permits a direct split-free connection of the LC × LC to an electrospray-based mass spectrometer (ESI-MS), contributing to heightened sensitivity. The MS acquisition is performed in a targeted single-ion monitoring mode, ensuring reliable quantification and identification of the pesticide compounds. A comprehensive evaluation of key performance metrics, including signal-to-noise ratio, limit of detection, and response linearity, is conducted. The methodology achieves a limit of detection below the ng mL-1 and exhibits response linearity within the concentration range of 1-100 ng mL-1. The robustness of the approach is further demonstrated through intra-day and inter-day repeatability validations. Furthermore, the platform is finally tested on a surface water sample. This study not only introduces an advanced analytical methodology for pesticide multi-residue analysis but also underscores the significance of PALC in enhancing sensitivity by facilitating the use of smaller-diameter columns and water-based mobile phases, along with the role of RPLC in enhancing separation. The proposed approach showcases promising results in achieving detection limits that match the stringent regulatory standards and reliable quantification for effective pesticide residue monitoring.

Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry

Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.

Development of a rapid screening method utilizing 2D LC for effect-directed analysis in the identification of environmental toxicants

Effect-directed analysis (EDA) is a crucial tool in environmental toxicology, effectively integrating toxicity testing with chemical analysis. The conventional EDA approach, however, presents challenges such as significant solvent consumption, extended analysis time, labor intensity, and potential contamination risks. In response, we introduce an innovative alternative to the conventional EDA. This method utilizes the MTT bioassay and online two-dimensional liquid chromatography (2D LC) coupled with high-resolution mass spectrometry (HR-MS), significantly reducing the fractionation steps and leveraging the enhanced sensitivity of the bioassay and automated chemical analysis. In the chemical analysis phase, a switching valve interface is employed for comprehensive analysis. We tested the performance of both the conventional and our online 2D LC-based methods using a household product. Both methods identified the same number of toxicants in the sample. Our alternative EDA is 22.5 times faster than the conventional method, fully automated, and substantially reduces solvent consumption. This novel approach offers ease, cost-effectiveness, and represents a paradigm shift in EDA methodologies. By integrating a sensitive bioassay with online 2D LC, it not only enhances efficiency but also addresses the challenges associated with traditional methods, marking a significant advancement in environmental toxicology research.

Two-dimensional liquid chromatography with reversed phase in both dimensions: A review

Two-dimensional liquid chromatography (2D-LC), and in particular comprehensive two-dimensional liquid chromatography (LC×LC), offers increased peak capacity, resolution and selectivity compared to one-dimensional liquid chromatography. It is commonly accepted that the technique produces the best results when the separation mechanisms in the two dimensions are completely orthogonal; however, the use of similar separation mechanisms in both dimensions has been gaining popularity as it helps avoid difficulties related to mobile phase incompatibility and poor column efficiency. The remarkable advantages of using reversed phase in both dimensions (RPLC×RPLC) over other separation mechanisms made it a promising technique in the separation of complex samples. This review discusses some physical and practical considerations in method development for 2D-LC involving the use of RP in both dimensions. In addition, an extensive overview is presented of different applications that relied on RPLC×RPLC and 2D-LC with reversed phase column combinations to separate components of complex samples in different fields including food analysis, natural product analysis, environmental analysis, proteomics, lipidomics and metabolomics.

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.

Beyond the Bottle: Exploring Health-Promoting Compounds in Wine and Wine-Related Products-Extraction, Detection, Quantification, Aroma Properties, and Terroir Effects

Health-promoting compounds in wine and wine-related products are important due to their potential benefits to human health. Through an extensive literature review, this study explores the presence of these compounds in wine and wine-related products, examining their relationship with terroir and their impact on the aromatic and flavor properties that are perceived orally: sunlight exposure, rainfall patterns, and soil composition impact grapevines' synthesis and accumulation of health-promoting compounds. Enzymes, pH, and the oral microbiome are crucial in sensory evaluation and perception of health promotion. Moreover, their analysis of health-promoting compounds in wine and wine-related products relies on considerations such as the specific target compound, selectivity, sensitivity, and the complexity of the matrix.

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.

Two-Dimensional High-Performance Liquid Chromatography as a Powerful Tool for Bioanalysis: The Paradigm of Antibiotics

The technique of two-dimensional high-performance liquid chromatography has managed to gain the recognition it deserves thanks to the advantages of satisfactory separations it can offer compared to simple one-dimensional. This review presents in detail key features of the technique, modes of operation, and concepts that ensure its optimal application and consequently the best possible separation of even the most complex samples. Publications focusing on the separation of antibiotics and their respective impurities are also presented, providing information concerning the analytical characteristics of the technique related to the arrangement of the instrument and the chromatographic conditions.

Toward the analysis of functional proteoforms using mass spectrometry-based stability proteomics

Functional proteomics aims to elucidate biological functions, mechanisms, and pathways of proteins and proteoforms at the molecular level to examine complex cellular systems and disease states. A series of stability proteomics methods have been developed to examine protein functionality by measuring the resistance of a protein to chemical or thermal denaturation or proteolysis. These methods can be applied to measure the thermal stability of thousands of proteins in complex biological samples such as cell lysate, intact cells, tissues, and other biological fluids to measure proteome stability. Stability proteomics methods have been popularly applied to observe stability shifts upon ligand binding for drug target identification. More recently, these methods have been applied to characterize the effect of structural changes in proteins such as those caused by post-translational modifications (PTMs) and mutations, which can affect protein structures or interactions and diversify protein functions. Here, we discussed the current application of a suite of stability proteomics methods, including thermal proteome profiling (TPP), stability of proteomics from rates of oxidation (SPROX), and limited proteolysis (LiP) methods, to observe PTM-induced structural changes on protein stability. We also discuss future perspectives highlighting the integration of top-down mass spectrometry and stability proteomics methods to characterize intact proteoform stability and understand the function of variable protein modifications.

Development and validation of a multi-class analysis of pesticides in corn products by comprehensive two-dimensional liquid chromatography-tandem mass spectrometry

Due to the growing trend of organic food, there is still concern over the use of chemicals and pesticides in agriculture. In recent years, several procedures have been validated for the control of pesticides in food. In the present research, a comprehensive two-dimensional liquid chromatography coupled with tandem mass spectrometry is proposed for the first time for a multi-class analysis of 112 pesticides in corn-based products. Notably, a "reduced" QuEChERS-based method as extraction and clean-up procedure prior to the analysis, was successfully employed. Limits of quantification values were lower than the ones fixed by the European legislation; intra-day and inter-day precision were lower than 12.9% and 15.1%, respectively (at the 500 μg/kg concentration levels). Over 70% of the analytes provided recoveries between 70% and 120% range (at 50, 500 and 1000 µg/kg concentration levels) with standard deviation values below 20%. In addition, matrix effect values were in the range between 13% to 161%. The method was applied to the analysis of real samples, and three pesticides were detected at trace levels in both samples. The findings of this work pave the way for the treatment of complex matrices such as corn products.

Quantitative Structure Retention-Relationship Modeling: Towards an Innovative General-Purpose Strategy

Reversed-Phase Liquid Chromatography (RPLC) is a common liquid chromatographic mode used for the control of pharmaceutical compounds during their drug life cycle. Nevertheless, determining the optimal chromatographic conditions that enable this separation is time consuming and requires a lot of lab work. Quantitative Structure Retention Relationship models (QSRR) are helpful for doing this job with minimal time and cost expenditures by predicting retention times of known compounds without performing experiments. In the current work, several QSRR models were built and compared for their adequacy in predicting the retention times. The regression models were based on a combination of linear and non-linear algorithms such as Multiple Linear Regression, Support Vector Regression, Least Absolute Shrinkage and Selection Operator, Random Forest, and Gradient Boosted Regression. Models were built for five pH conditions, i.e., at pH 2.7, 3.5, 6.5, and 8.0. In the end, the model predictions were combined using stacking and the performances of all models were compared. The k-nearest neighbor-based application domain filter was established to assess the reliability of the prediction for further compound prioritization. Altogether, this study can be insightful for analytical chemists working with RPLC to begin with the computational prediction modeling such as QSRR to predict the separation of small molecules.

Miniaturized Two-Dimensional Heart Cutting for LC-MS-Based Metabolomics

Liquid chromatography-mass spectrometry (LC-MS)-based metabolomics usually combines hydrophilic interaction liquid chromatography (HILIC) and reversed-phase (RP) chromatography to cover a wide range of metabolomes, requiring both significant sample consumption and analysis time for separate workflows. We developed an integrated workflow enabling the coverage of both polar and nonpolar metabolites with only one injection of the sample for each ionization mode using heart-cutting trapping to combine HILIC and RP separations. This approach enables the trapping of some compounds eluted from the first chromatographic dimension for separation later in the second dimension. In our case, we applied heart-cutting to non-retained metabolites in the first dimension. For that purpose, two independent miniaturized one-dimensional HILIC and RP methods were developed by optimizing the chromatographic and ionization conditions using columns with an inner diameter of 1 mm. They were then merged into one two-dimensional micro LC-MS method by optimization of the trapping conditions. Equilibration of the HILIC column during elution on the RP column and vice versa reduced the overall analysis time, and the multidimensionality allows us to avoid signal measurements during the solvent front. To demonstrate the benefits of this approach to metabolomics, it was applied to the analysis of the human plasma standard reference material SRM 1950, enabling the detection of hundreds of metabolites without the significant loss of some of them while requiring an injection volume of only 0.5 μL.

Random swapping, an effective and efficient way to boost the intensities of cross peaks in a 2D asynchronous spectrum

Analysis of mixture via chromatographic-spectroscopic and analogous experiments is a common task in analytical chemistry. A 2D/nD asynchronous spectrum is effective in retrieving spectra of pure substances even if different components cannot be separated. However, noise in the 2D/nD asynchronous spectrum becomes a bottleneck in the analysis. Finding a suitable sequence of the 1D spectra used in constructing the 2D/nD asynchronous spectrum is helpful to improve the signal-to-noise level. A 2D/nD asynchronous spectrum is often produced via a large number of 1D spectra. The resultant colossal number of the possible sequences makes stochastic search the only possible way to find a suitable sequence. Random changing (RC) and random swapping (RS) are two ways to obtain a new sequence. We found that the possibility of finding a better sequence via an RS is significantly higher than that via an RC in the advanced stage of stochastic searching. This is the reason why the performance of RS is superior to that of RC in two model systems where 2D asynchronous spectra are used. We applied the RS approach on the analysis of water/isopropanol mixtures, and satisfactory sequences are acquired with affordable computational cost. Thus, the RS approach brings about an opportunity increase the signal-to-noise level of a 2D asynchronous spectrum in the analysis of the bilinear data from complex mixed samples.

Comprehensive two-dimensional temperature-responsive × reversed phase liquid chromatography for the analysis of wine phenolics

Phenolic compounds are an interesting class of natural products because of their proposed contribution to health benefits of foods and beverages and as a bio-source of organic (aromatic) building blocks. Phenolic extracts from natural products are often highly complex and contain compounds covering a broad range in molecular properties. While many 1D-LC and mass spectrometric approaches have been proposed for the analysis of phenolics, this complexity inevitably leads to challenging identification and purification. New insights into the composition of phenolic extracts can be obtained through online comprehensive two-dimensional liquid chromatography (LC × LC) coupled to photodiode array and mass spectrometric detection. However, several practical hurdles must be overcome to achieve high peak capacities and to obtain robust methods with this technique. In many LC × LC configurations, refocusing of analytes at the head of the ²D column is hindered by the high eluotropic strength of the solvent transferred from the ¹D to the ²D, leading to peak breakthrough or broadening. LC × LC combinations whereby a purely aqueous mobile phase is used in the ¹D and RPLC is used in the ²D are unaffected by these phenomena, leading to more robust methods. In this contribution, the combination of temperature-responsive liquid chromatography (TRLC) with RPLC is used for the first time for the analysis of phenolic extracts of natural origin to illustrate the potential of this alternative combination for natural product analyses. The possibilities of the combination are investigated through analysis of wine extracts by TRLC × RPLC-DAD and TRLC × RPLC-ESI-MS.

A systematic investigation of the effect of sample solvent on peak shape in nano- and microflow hydrophilic interaction liquid chromatography columns

A frequently encountered problem in the practical application of nano- and microflow hydrophilic interaction chromatography (HILIC) columns is the distortion of peak shapes arising from a mismatch between the sample solvent and the mobile phase. An unmatched or improperly matched sample solvent can distort the peak shape of analytes and influence their retention times, thereby affecting the quality of the resulting chromatogram. In this work, the effect of sample solvent composition (mixtures of acetonitrile, water, methanol and isopropanol in different ratios) and injection volume (20-100 nL) was systematically investigated using a selection of neutral and charged compounds on a series of zwitterionic and charged small I.D. (0.1-0.3 mm) HILIC columns. For retained compounds, pure ACN was demonstrated to be the best sample solvent to obtain narrow peaks, while for compounds that eluted very close to the solvent peak, the peak shape was distorted when the sample solvent consisted of pure ACN. A highly aqueous sample solvent, which interferes with the partitioning of polar analytes into the stationary phase, was demonstrated to be detrimental for the peak shape of retained neutral compounds, while for unretained compounds that do not or hardly interact with the stationary phase, a high amount of water in the sample solvent was not problematic. For charged compounds, water in the sample solvent favored the electrostatic attraction with the stationary phase. Therefore, the retention time of charged analytes was shown to increase with increasing water content in the sample solvent. Even when a large amount of water was present in the sample solvent, the peak shapes of these compounds were still acceptable. For highly polar compounds with a limited solubility in aqueous sample solvents, it was found that a mixture of ACN and MeOH or IPA is a good alternative.

Chronic Kidney Disease Cohort Studies: A Guide to Metabolome Analyses

Kidney diseases still pose one of the biggest challenges for global health, and their heterogeneity and often high comorbidity load seriously hinders the unraveling of their underlying pathomechanisms and the delivery of optimal patient care. Metabolomics, the quantitative study of small organic compounds, called metabolites, in a biological specimen, is gaining more and more importance in nephrology research. Conducting a metabolomics study in human kidney disease cohorts, however, requires thorough knowledge about the key workflow steps: study planning, sample collection, metabolomics data acquisition and preprocessing, statistical/bioinformatics data analysis, and results interpretation within a biomedical context. This review provides a guide for future metabolomics studies in human kidney disease cohorts. We will offer an overview of important a priori considerations for metabolomics cohort studies, available analytical as well as statistical/bioinformatics data analysis techniques, and subsequent interpretation of metabolic findings. We will further point out potential research questions for metabolomics studies in the context of kidney diseases and summarize the main results and data availability of important studies already conducted in this field.

Development, validation, and application of a multi-method for the determination of mycotoxins, plant growth regulators, tropane alkaloids, and pesticides in cereals by two-dimensional liquid chromatography tandem mass spectrometry

Mycotoxins and pesticides regularly co-occur in agricultural products worldwide. Thus, humans can be exposed to both toxic contaminants and pesticides simultaneously, and multi-methods assessing the occurrence of various food contaminants and residues in a single method are necessary. A two-dimensional high performance liquid chromatography tandem mass spectrometry method for the analysis of 40 (modified) mycotoxins, two plant growth regulators, two tropane alkaloids, and 334 pesticides in cereals was developed. After an acetonitrile/water/formic acid (79:20:1, v/v/v) multi-analyte extraction procedure, extracts were injected into the two-dimensional setup, and an online clean-up was performed. The method was validated according to Commission Decision (EC) no. 657/2002 and document N° SANTE/12682/2019. Good linearity (R2 > 0.96), recovery data between 70-120%, repeatability and reproducibility values < 20%, and expanded measurement uncertainties < 50% were obtained for a wide range of analytes, including very polar substances like deoxynivalenol-3-glucoside and methamidophos. However, results for fumonisins, zearalenone-14,16-disulfate, acid-labile pesticides, and carbamates were unsatisfying. Limits of quantification meeting maximum (residue) limits were achieved for most analytes. Matrix effects varied highly (-85 to +1574%) and were mainly observed for analytes eluting in the first dimension and early-eluting analytes in the second dimension. The application of the method demonstrated the co-occurrence of different types of cereals with 28 toxins and pesticides. Overall, 86% of the samples showed positive findings with at least one mycotoxin, plant growth regulator, or pesticide.

Brownian Sieving Effect for Boosting the Performance of Microcapillary Hydrodynamic Chromatography. Proof of Concept

Microcapillary hydrodynamic chromatography (MHDC) is a well-established technique for the size-based separation of suspensions and colloids, where the characteristic size of the dispersed phase ranges from tens of nanometers to micrometers. It is based on hindrance effects which prevent relatively large particles from experiencing the low velocity region near the walls of a pressure-driven laminar flow through an empty microchannel. An improved device design is here proposed, where the relative extent of the low velocity region is made tunable by exploiting a two-channel annular geometry. The geometry is designed so that the core and the annular channel are characterized by different average flow velocities when subject to one and the same pressure drop. The channels communicate through openings of assigned cut-off length, say A. As they move downstream the channel, particles of size bigger than A are confined to the core region, whereas smaller particles can diffuse through the openings and spread throughout the entire cross section, therein attaining a spatially uniform distribution. By using a classical excluded-volume approach for modeling particle transport, we perform Lagrangian-stochastic simulations of particle dynamics and compare the separation performance of the two-channel and the standard (single-channel) MHDC. Results suggest that a quantitative (up to thirtyfold) performance enhancement can be obtained at operating conditions and values of the transport parameters commonly encountered in practical implementations of MHDC. The separation principle can readily be extended to a multistage geometry when the efficient fractionation of an arbitrary size distribution of the suspension is sought.

Development of a Single-Step Antibody-Drug Conjugate Purification Process with Membrane Chromatography

Membrane chromatography is routinely used to remove host cell proteins, viral particles, and aggregates during antibody downstream processing. The application of membrane chromatography to the field of antibody-drug conjugates (ADCs) has been applied in a limited capacity and in only specialized scenarios. Here, we utilized the characteristics of the membrane adsorbers, Sartobind^® S and Phenyl, for aggregate and payload clearance while polishing the ADC in a single chromatographic run. The Sartobind^® S membrane was used in the removal of excess payload, while the Sartobind^® Phenyl was used to polish the ADC by clearance of unwanted drug-to-antibody ratio (DAR) species and aggregates. The Sartobind^® S membrane reproducibly achieved log-fold clearance of free payload with a 10 membrane-volume wash. Application of the Sartobind^® Phenyl decreased aggregates and higher DAR species while increasing DAR homogeneity. The Sartobind^® S and Phenyl membranes were placed in tandem to simplify the process in a single chromatographic run. With the optimized binding, washing, and elution conditions, the tandem membrane approach was performed in a shorter timescale with minimum solvent consumption and high yield. The application of the tandem membrane chromatography system presents a novel and efficient purification scheme that can be realized during ADC manufacturing.

[Size exclusion-reverse liquid column chromatography-mass spectrometry and its application in the identification of post-translationally modified proteins in rat kidney]

Proteomics is an emerging field that has been shown to play a crucial role in unveiling the mechanisms underlying physiological and pathological processes, and liquid chromatography-mass spectrometry (LC-MS) is one of the most important methods employed in this field. However, in complex biological systems, such as eukaryotes, it is challenging to perform a comprehensive and unbiased proteome analysis due to the high complexity of biological samples and enormous differences in sample contents. For example, post-translational modifications (PTMs) in proteins are imperative for cell signaling, but post-translationally modified proteins account for about 1% of the total proteins in a single cell, making their identification extremely difficult. Therefore, chromatographic separation methods based on different principles are generally applied to reduce the complexity of biological samples and enrich trace proteins for their identification through mass spectrometry (MS). In this study, we developed a new proteomics method by combining size exclusion chromatography (SEC) and reversed-phase chromatography (RPLC), to separate and identify trace proteins in complex systems. SEC was used to separate and enrich kidney-specific proteins. After optimization of the method, it was found that 30 mmol/L of ammonium acetate could efficiently separate rat kidney proteins from the total protein fraction so that they could be eluted based on their relative molecular mass. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis and LC-MS results showed that our SEC separation method not only refined the protein composition of the biological sample but also enhanced the relative contents of trace proteins through multiple injections. The collected protein fractions were further concentrated through ultrafiltration centrifugation followed by freeze-drying, which further improved the recovery of trace proteins by approximately 90% and largely decreased the time required with the use of freeze-drying alone. Thereafter, five protein fractions were separately digested using trypsin, and the resultant peptides were further analyzed by reverse phase chromatography-MS analysis. In the RPLC column, the peptides were isolated mainly based on their hydrophobicity. As a result, by combining SEC and RPLC, 23621 peptides and 1345 proteins were identified from the kidney, with an increase in numbers by 69% and 27%, respectively, when compared to those obtained using the common 2D strong cation exchange (SCX)-RPLC-MS method. However, no significant difference was observed in the pI and grand average of hydropathicity (GRAVY) values. Gene ontology (GO) analysis revealed an increase in the number of proteins in each cell component, especially the membrane. Furthermore, identification of a higher rate of identified peptides than proteins suggested that the protein coverage was also improved, thereby facilitating the detection of PTM proteins. Consequently, five common PTMs in biological processes, including methylation, acetylation, carbamylation, oxidation, and phosphorylation, were examined and compared between the two methods. As expected, the number of post-translationally modified peptides identified using SEC-RPLC-MS were 1.7-1.9 times more than those determined using the SCX-RPLC-MS method. Especially for the identification of phosphorylated peptides, we could achieve the level of the targeted enrichment strategy; however no significant difference was observed in the extents of phosphorylation among serine, threonine, and tyrosine. These results further indicate that upon combining SEC and RPLC, high efficiency could be achieved by decreasing the complexity of the protein sample, and the identification was unbiased. Finally, the phosphorylation of some kidney proteins, such as spectrin, L-lactate dehydrogenase, and ATPases, was found, which is critical for their functions. In summary, the SEC-RPLC-MS approach was developed for the identification of rat kidney proteins and is especially applicable for the identification of PTM proteins. Using this method, the identification efficiency for PTM peptides increased significantly. Therefore, this method has potential for better understanding the impact of PTM on kidney proteins and further elucidating the potential mechanisms underlying its physiological and pathological functions.

Measuring atropisomers of BMS-986142 using 2DLC as an enabling technology

BMS-986142 has been developed as an innovative Bruton's tyrosine kinase inhibitor for treatment of several autoimmune diseases. The drug substance of BMS-986142 may contain three potential atropisomeric impurities due to its unique structural characteristics. Developing a single liquid chromatography (LC) method to separate all four highly structurally related atropisomers and other process impurities from each other turned out to be a daunting task. Two-dimensional LC (2DLC) was found to be an extremely powerful enabling technology for extracting purity information out of the complex sample impurity profile and facilitated process development before a final single dimension method was discovered. The off-the-shelf 2DLC instrument could be configured to allow injection of the targeted first dimension peak through either no-loss multiple heart-cutting fractions or as a large, single volume fraction with on-line dilution. Excellent precision (relative standard deviation of 0.3 %) and recovery (101.2 ± 0.2 %) was achieved for an atropisomer impurity at a 10 % monitoring level in the first configuration with sensitivity down to 0.2 % w/w. With the second instrument configuration, which eliminated the need for fraction recombination, similar figures of merit were maintained for the second dimension at the cost of losing the ability to collect and park multiple fractions.

Analytical Chemistry in the 21st Century: Challenges, Solutions, and Future Perspectives of Complex Matrices Quantitative Analyses in Biological/Clinical Field

Nowadays, the challenges in analytical chemistry, and mostly in quantitative analysis, include the development and validation of new materials, strategies and procedures to meet the growing need for rapid, sensitive, selective and green methods. In this context, considering the constantly updated International Guidelines, constant innovation is mandatory both in the pre-treatment procedures and in the instrumental configurations to obtain reliable, true, and reproducible information. In this context, additionally to the classic plasma (or serum) matrices, biopsies, whole blood, and urine have seen an increase in the works that also consider non-conventional matrices. Obviously, all these studies have shown that there is a correlation between the blood levels and those found in the new matrix, in order to be able to correlate and compare the results in a robust way and reduce any bias problems. This review provides an update of the most recent developments currently in use in the sample pre-treatment and instrument configurations in the biological/clinical fields. Furthermore, the review concludes with a series of considerations regarding the role and future developments of Analytical Chemistry in light of the forthcoming challenges and new goals to be achieved.

Strategies for effective development of ultra-sensitive LC–MS/MS assays: application to a novel STING agonist

Background: The continual need for the development and validation of ultra-sensitive (low pg/ml) LC–MS/MS assays in the pharmaceutical industry is largely driven by the ultra-low analyte exposure or very low sample volume. Methodology: Strategies and systematic approaches for sensitivity enhancement are provided which cover all aspects of a LC–MS/MS bioanalysis. A case study where such strategies were applied for the validation of a 5.0 pg/ml assay for a STING agonist is discussed. Conclusion: Analytical protocols were developed to extract analytes from large volume of plasma samples (600 and 400 μl) with high throughput. The guidance provided in this publication can serve as a resource to influence LC–MS/MS method development activities.

Application of the new at-column dilution (ACD) modulator for the two-dimensional RP×HILIC analysis of Buddleja davidii

The focus of this study was the analysis of the complex chemical composition from different parts of Buddleja davidii, whose species are commonly known as ornamental plants and herbal medicines in many countries. As an herbal medicine, it has been utilized for stroke treatments, headache, wound healing, neurological disorder, etc. However, the understanding of its chemical matrices is still insufficient. Therefore, an online two-dimensional reversed phase liquid chromatography x hydrophilic interaction liquid chromatography (RPLCxHILIC) system coupled with mass spectrometry was applied for further detailed investigation of the chemical constituents in Buddleja dividii. In this two-dimensional liquid chromatography (2D-LC) method, a new at-column dilution (ACD) modulator was introduced in the 2D-LC system to solve the incompatibility problem of the mobile phase between two dimensions, which resulted in a 2D-LC analysis with high orthogonality. For the root extract, as one of the analyzed samples, the optimization of the ¹D and ²D gradients was carried out carefully. With this new modulator, much better peak separation and better peak shape were achieved compared to two-dimensional liquid chromatography system using a traditional standard (TS) modulator. With a similar approach, the other four parts of Buddleja davidii were well separated. Comparing the different analyzed parts, flowers and leaves showed the most complex profiles. MS and MS/MS data were obtained successfully, which demonstrated the potential of the proposed RPLCxHILIC-MS system in the constituents’ analysis of herbal medicine. However, due to the lack of reported reference information, 24 compounds could be tentatively identified.

A novel systematic absence of cross peaks-based 2D-COS approach for bilinear data

A novel approach to use two-dimensional correlation spectroscopy (2D-COS) to analyze bilinear data is proposed. A phenomenon called Systematic Absence of Cross Peaks (SACPs) is observed in a 2D asynchronous spectrum. Two theorems relevant to SACPs have been derived. The SACP-based 2D-COS method has been successfully applied on analyzing bilinear data from mixed samples (including one model system and two real systems). Implicit isolated peaks can be identified and assigned to different components based on characteristic pattern of SACPs even if the time-related profiles of different components are severely overlapped. Based on the results of SACPs, spectra of pure components can be retrieved. Identification of SACPs can still be achieved in the presence of artifacts. Thus, neither noise nor baseline drift can produce significant influence on the results obtained from the approach described in this paper. We have used several well-established chemometric methods, including N-Findr, VCA, and MCR with various initial settings, on two systems that can be successfully solved using the 2D-COS method. The chemometric methods mentioned above cannot provide correct spectra of pure components because of severe problem of rotational ambiguity derived from severe overlapping of the time-related profiles. Only when the information from SACPs in 2D-COS is used as additional constraints in MCR calculation, correct spectra can be obtained. That is to say, the SACP-based 2D-COS method provides intrinsic information which is crucial in the analysis of chromatographic-spectroscopic and analogous data even if the time-related profiles of different components overlap severely.

Improving enantiomeric resolutions by avoiding peak distortion effects in on-line coupled liquid chromatography to gas chromatography

In this work, we study the effect of different variables affecting elution profile distortion on the enantiomeric resolution eventually achievable when working with on-line coupled liquid chromatography to gas chromatography (LC-GC). Specifically, the proposed configuration combines achiral reversed-phase liquid chromatography (RPLC) and chiral gas chromatography (enantio-GC), with heptakis-(2,3,6-tri-O-methyl)-β-cyclodextrin as enantioselective stationary phase to analyse target fractions transferred (from LC to GC) via the through oven transfer adsorption desorption (TOTAD) interface. The high degree of orthogonality resulting from the combination of two chromatographic columns having very different separation mechanisms (and also requiring mobile phases in distinct physical states), as well as integration of the sample preparation step in the first dimension of the system, significantly contributed to exploit the performance of the proposed two-dimensional approach. Occasional adverse effects, which may result in severe peak distortions during LC-GC analysis and could be explained by flow instabilities due to viscous fingering, are circumvented by using the outstanding capacity of the TOTAD interface for achieving effective elimination of the eluent arriving from the LC preseparation.

A preliminary study on constructing a high-dimensional asynchronous spectrum to analyze bilinear data

A novel approach to constructing high-dimensional asynchronous spectra (nD-Asyn) is proposed. Three theorems relevant to 1D slices of nD-Asyn are revealed. nD-Asyn is used to analyze bilinear data from mixtures containing multiple components obtained via hyphenated techniques. The spectral contribution of different components can be removed in a stepwise manner by increasing the dimensions of asynchronous spectra. As a result, the spectra of different components can be faithfully recovered even if the time-related profiles of different components severely overlap. Moreover, correct results can still be obtained via the nD-Asyn even if a considerable level of noise and baseline drift are present. The nD-Asyn approach is compared with MCR-ALS using different constraints in analyzing the data for a simulated and also for a real system. The nD-Asyn produced correct spectrum of every component. Only when complete constraints obtained from nD-Asyn method is utilized in the MCR-ALS calculation, correct spectra of all the components can be obtained. Thus, nD-Asyn can be used alone or in conjunction with MCR-ALS to analyze bilinear data containing contributions of multiple components.

Simultaneous determination of pesticides, mycotoxins, tropane alkaloids, growth regulators, and pyrrolizidine alkaloids in oats and whole wheat grains after online clean-up via two-dimensional liquid chromatography tandem mass spectrometry

In this study, a two-dimensional liquid chromatography tandem mass spectrometry method was developed and validated for the determination of pesticide residues and contaminants in whole wheat grains and oats. The samples were extracted with a mixture of acetonitrile and water and were injected into the two-dimensional LC-MS/MS system without any further clean-up or sample preparation. Samples were analyzed with four different matrix matched calibrations. Matrix effects were evaluated by comparing analyte signals in the respective matrix matched standard with the neat solvent standards. The final method was validated according to the current Eurachem validation guide and SANTE document. The number of successfully validated analytes throughout all three validation levels in oats and wheat, respectively, were as follows: 330 and 316 out of 370 pesticides, 6 and 13 out of 18 pyrrolizidine alkaloids and 7 out of 9 regulated mycotoxins. Moreover, both plant growth regulators mepiquat and chlormequat as well as the tropane alkaloids atropine and scopolamine met the validation criteria. The majority of pesticides showed limits of detection below 1 µg kg^-1, pyrrolizidine alkaloids below 0.7 µg kg^-1, tropane alkaloids below 0.2 µg kg^-1, growth regulators below 0.7 µg kg^-1 and mycotoxins below 8 µg kg^-1 in both matrices.

Determination of Ochratoxin A traces in foodstuffs: Comparison of an automated on-line two-dimensional high-performance liquid chromatography and off-line immunoaffinity-high-performance liquid chromatography system

Automated on-line two-dimensional high-performance liquid chromatography method (2D-HPLC) is proposed to determine Ochratoxin A (OTA) in food samples as an alternative to OTA immunoaffinity column (IAC). An on-line 2D-HPLC system is designed for the analysis of OTA using an affinity-based monolithic column in the first dimension and reversed-phase C18 column in the second dimension. Initially, optimal OTA separation efficiency is determined through traditional HPLC system consisting of a P(HEMAPA) monolithic column coupled with HPLC system. Secondly, after providing optimum conditions, OTA determination was investigated through the 2D-HPLC system. According to results, 2D-HPLC system showed good linearity in the range 0.5 to 20 ng/mL with limit of detection (LOD) and limit of quantification (LOQ) values of 21.2 pg/mL and 64.3 pg/mL, respectively. The P(HEMAPA)-4 monolithic column displayed good recovery of OTA ranging from 104.34% to 107.33%. Relative standard deviations (RSD) varied in the range 0.21% to 1.31% thus indicating the efficiency of P(HEMAPA)-4 monolithic column developed for OTA.

Enhancing the Possibilities of Comprehensive Two-Dimensional Liquid Chromatography through Hyphenation of Purely Aqueous Temperature-Responsive and Reversed-Phase Liquid Chromatography

Comprehensive two-dimensional liquid chromatography (LC × LC) allows for substantial gains in theoretical peak capacity in the field of liquid chromatography. However, in practice, theoretical performance is rarely achieved due to a combination of undersampling, orthogonality, and refocusing issues prevalent in many LC × LC applications. This is intricately linked to the column dimensions, flow rates, and mobile-phase compositions used, where, in many cases, incompatible or strong solvents are introduced in the second-dimension (²D) column, leading to peak broadening and the need for more complex interfacing approaches. In this contribution, the combination of temperature-responsive (TR) and reversed-phase (RP) LC is demonstrated, which, due to the purely aqueous mobile phase used in TRLC, allows for complete and more generic refocusing of organic solutes prior to the second-dimension RP separation using a conventional 10-port valve interface. Thus far, this was only possible when combining other purely aqueous modes such as ion exchange or gel filtration chromatography with RPLC, techniques which are limited to the analysis of charged or high MW solutes, respectively. This novel TRLC × RPLC combination relaxes undersampling constraints and complete refocusing and therefore offers novel possibilities in the field of LC × LC including temperature modulation. The concept is illustrated through the TRLC × RPLC analysis of mixtures of neutral organic solutes.