High-throughput glycosaminoglycan extraction and UHPLC-MS/MS quantification in human biofluids

Glycosaminoglycans (GAGs) are linear, unbranched heteropolysaccharides whose structural complexity determines their function. Accurate quantification of GAGs in biofluids at high throughput is relevant for numerous biomedical applications. However, because of the structural variability of GAGs in biofluids, existing protocols require complex pre-analytical procedures, have limited throughput and lack accuracy. Here, we describe the extraction and quantification of GAGs by using ultra-high-performance liquid chromatography coupled with triple-quadrupole mass spectrometry (UHPLC-MS/MS). Designed for 96-well plates, this method enables the processing of up to 82 study samples per plate, with the remaining 14 wells used for calibrators and controls. Key steps include the enzymatic depolymerization of GAGs, their derivatization with 2-aminoacridone and their quantification via UHPLC-MS/MS. Each plate can be analyzed in a single UHPLC-MS/MS run, offering the quantitative and scalable analysis of 17 disaccharides from chondroitin sulfate, heparan sulfate and hyaluronic acid, with a level of precision and reproducibility sufficient for their use as biomarkers. The procedure from sample thawing to initiating the UHPLC-MS/MS run can be completed in ~1.5 d plus 15 min of MS runtime per sample, and it is structured to fit within ordinary working shifts, thus making it a valuable tool for clinical laboratories seeking high-throughput analysis of GAGs. The protocol requires expertise in UHPLC-MS/MS.

Hydrophilic interaction liquid chromatography: An efficient tool for assessing thorium interaction with phosphorylated biomimetic peptides

In the field of nuclear toxicology, the knowledge of the interaction of actinides (An) with biomolecules is of prime concern in order to elucidate their toxicity mechanism and to further develop selective decorporating agents. In this work, we demonstrated the great potential of hydrophilic interaction liquid chromatography (HILIC) to separate polar thorium (Th) biomimetic peptide complexes, as a key starting point to tackle these challenges. Th4+ was used as plutonium (Pu4+) analogue and pS16 and pS1368 as synthetic di- and tetra-phosphorylated peptides capable of mimicking the interaction sites of these An in osteopontin (OPN), a hyperphosphorylated protein. The objective was to determine the relative affinity of pS16 and pS1368 towards Th4+, and to evaluate the pS1368 selectivity when Th4+ was in competition complexation reaction with UO22+ at physiological pH. To meet these aims, HILIC was simultaneously coupled to electrospray ionization mass spectrometry (ESI-MS) and inductively coupled plasma mass spectrometry (ICP-MS), which allowed to identify online the molecular structure of the separated complexes and quantify them, in a single step. Dedicated HILIC conditions were firstly set up to separate the new dimeric Th2(peptide)2 complexes with good separation resolution (peptide = pS16 or pS1368). By adding pS16 and pS1368 in different proportions relatively to Th4+, we found that lower or equal proportions of pS16 with respect to pS1368 were not sufficient to displace pS1368 from Th2pS13682 and pS16 proportion higher than pS1368 led to the formation of a predominant ternary complex Th2(pS16)(pS1368), demonstrating preferential Th4+ binding to the tetra-phosphorylated peptide. Finally, online identification and quantification of the formed complexes when Th4+ and UO22+ were mixed in equimolar ratio relatively to pS1368 showed that in spite of pS1368 has been specifically designed to coordinate UO22+, pS1368 is also Th4+-selective and exhibits stronger affinity for this latter than for UO22+. Hence, the results gathered through this approach highlight the impact of Th4+ coordination chemistry on its interaction with pS1368 and more widely to its affinity for biomolecules.

Liquid chromatographic methods in the determination of inosine monophosphate dehydrogenase enzyme activity: a review

Inosine monophosphate dehydrogenase (IMPDH) is a crucial enzyme involved in the de novo synthesis of purine nucleotides. IMPDH activity is used to evaluate the pharmacodynamics/pharmacokinetics of immunosuppressant drugs such as mycophenolic acid and thiopurines. These drugs are often used to prevent organ transplant rejection and as steroid-sparing agents in autoinflammatory diseases such as inflammatory bowel disease and rheumatoid arthritis. Numerous analytical techniques have been employed to evaluate IMPDH activity in biological matrices. However, hyphenated LC techniques were most widely used in the literature. This review focuses on hyphenated LC methods used to measure IMPDH activity and provides detailed insight into the sample preparation techniques, chromatographic conditions, enzymatic assay conditions, detectors and normalization factors employed in those methods.

Determination of levodopa by chromatography-based methods in biological samples: a review

Levodopa (L-DOPA) is the most effective drug for Parkinson's disease; however, various side effects occur during therapy. L-DOPA metabolites and the high cumulative dose of L-DOPA were responsible for its side effects. It is necessary to monitor the concentration of L-DOPA and its metabolites for individualized therapy. This review focuses on L-DOPA analysis by chromatography-based methods in biological matrices. Literature published up to September 2021 was collected in the PubMed, Web of Science, and Embase by using search strategy ("levodopa" OR "L-DOPA") AND ("chromatography"). A total of 1249 articles were identified and 32 articles were included. The contents for method development and validation were summarized and analyzed. Due to the instability of catecholamines (L-DOPA, dopamine, and 3-O-methyldopa) and carbidopa, antioxidation (0.5 mg sodium metabisulfite for 100 μL sample) and environment temperature control were used alone or in combination to enhance stability. Sample was mainly pretreated by protein precipitation (0.4-0.7 M perchloric acid). Separation was usually achieved using methanol or acetonitrile:water (with formic acid) on C18 columns. Mass spectrometry, electrochemical detector, ultraviolet-visible detector and fluorescence detector were used for detection. For L-DOPA, the calibration range was 2.5-10,000 ng/mL, the matrix effect and its coefficient of variation was 85-115 and -9.0-8.5%, and the recovery was 66.8-127.0%. Without stabilization strategy, L-DOPA was stable in plasma at room temperature for 1-7 h (4-6 h for most studies), at - 70 °C to - 80 °C for 10-20 days and after 3-5 freeze-thaw cycles. With stabilization strategies, the stability of L-DOPA in plasma was significantly improved. Metabolites of L-DOPA and enzyme inhibitors (carbidopa, entacapone, tolcapone and benserazide) were all stable in biological matrix. This study might be useful for researchers to develop their methods for individualized therapy of patients with Parkinson.

New multimodal stationary phases prepared by Ugi multicomponent approach

Eight different stationary phases based on two aminopropyl silicas of different brands suitable for multimodal chromatography applications have been prepared by a four-component Ugi reaction. The intention was to synthesize stationary phases significantly differing in their properties hereby demonstrating flexibility of the Ugi synthetic protocol. Diverse functional groups including a nonpolar long aliphatic chain, phenyl moiety, cholic acid scaffold, phenylboronic and monosaccharide units, charged betaine, and arginine moieties were immobilized on a silica surface. The novel sorbents were extensively characterized by elemental analysis, Raman spectroscopy, and chromatography. Considering the anchored chemical structures covalently bonded to the silica surface, reversed-phase, hydrophilic, and ion-exchange separation modes were expected. The chromatographic evaluation was performed directed to map the potential of the individual columns specifically in the mentioned chromatographic modes. The Ugi synthetic protocol has proven to be a simple, feasible, and versatile tool for the synthesis of sorbents of variable properties. The newly prepared stationary phases differed considerably in hydrophobicity and ion-exchange ability. A significant influence of the supporting aminopropyl silica on the final chromatographic behavior was observed. Finally, one practical example confirming applicability of the newly prepared sorbents was demonstrated in separation of cytarabine.

Trends in sample preparation and separation methods for the analysis of very polar and ionic compounds in environmental water and biota samples

Recent years showed a boost in knowledge about the presence and fate of micropollutants in the environment. Instrumental and methodological developments mainly in liquid chromatography coupled to mass spectrometry hold a large share in this success story. These techniques soon complemented gas chromatography and enabled the analysis of more polar compounds including pesticides but also household chemicals, food additives, and pharmaceuticals often present as traces in surface waters. In parallel, sample preparation techniques evolved to extract and enrich these compounds from biota and water samples. This review article looks at very polar and ionic compounds using the criterion log P ≤ 1. Considering about 240 compounds, we show that (simulated) log D values are often even lower than the corresponding log P values due to ionization of the compounds at our reference pH of 7.4. High polarity and charge are still challenging characteristics in the analysis of micropollutants and these compounds are hardly covered in current monitoring strategies of water samples. The situation is even more challenging in biota analysis given the large number of matrix constituents with similar properties. Currently, a large number of sample preparation and separation approaches are developed to meet the challenges of the analysis of very polar and ionic compounds. In addition to reviewing them, we discuss some trends: for sample preparation, preconcentration and purification efforts by SPE will continue, possibly using upcoming mixed-mode stationary phases and mixed beds in order to increase comprehensiveness in monitoring applications. For biota analysis, miniaturization and parallelization are aspects of future research. For ionic or ionizable compounds, we see electromembrane extraction as a method of choice with a high potential to increase throughput by automation. For separation, predominantly coupled to mass spectrometry, hydrophilic interaction liquid chromatography applications will increase as the polarity range ideally complements reversed phase liquid chromatography, and instrumentation and expertise are available in most laboratories. Two-dimensional applications have not yet reached maturity in liquid-phase separations to be applied in higher throughput. Possibly, the development and commercial availability of mixed-mode stationary phases make 2D applications obsolete in semi-targeted applications. An interesting alternative will enter routine analysis soon: supercritical fluid chromatography demonstrated an impressive analyte coverage but also the possibility to tailor selectivity for targeted approaches. For ionic and ionizable micropollutants, ion chromatography and capillary electrophoresis are amenable but may be used only for specialized applications such as the analysis of halogenated acids when aspects like desalting and preconcentration are solved and the key advantages are fully elaborated by further research. Graphical abstract.

Development and validation of a quantitative ultra performance LC® hydrophilic interaction liquid chromatography MS/MS method to measure fructose and sorbitol in human plasma

AIM

Fructose and sorbitol are utilized as biomarkers for nonalcoholic steatohepatitis. Measurement of fructose and sorbitol levels helps understanding disease progression, drug response and underlying mechanism.

MATERIALS & METHODS

Stable isotope-labeled fructose and sorbitol were used as surrogate standards and internal standards. Human plasma samples were processed and analyzed by ultra performance LC^®-MS/MS via chromatographic separation on a hydrophilic interaction liquid chromatography analytical column without derivatization. Assay was validated with biomarker fit-for-purpose concept.

RESULTS

A 12-min ultra performance LC^®-MS/MS method was developed and validated to directly measure fructose and sorbitol in human plasma with acceptable intra- and inter-assay precision and accuracy.

CONCLUSION

This sensitive, selective, and high-throughput assay with suitable dynamic ranges was successfully applied to clinical studies to provide reliable fructose and sorbitol biomarker data.

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

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

Modelling of Hydrophilic Interaction Liquid Chromatography Stationary Phases Using Chemometric Approaches

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

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

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

Quantitative mass spectrometry methods for pharmaceutical analysis

Quantitative pharmaceutical analysis is nowadays frequently executed using mass spectrometry. Electrospray ionization coupled to a (hybrid) triple quadrupole mass spectrometer is generally used in combination with solid-phase extraction and liquid chromatography. Furthermore, isotopically labelled standards are often used to correct for ion suppression. The challenges in producing sensitive but reliable quantitative data depend on the instrumentation, sample preparation and hyphenated techniques. In this contribution, different approaches to enhance the ionization efficiencies using modified source geometries and improved ion guidance are provided. Furthermore, possibilities to minimize, assess and correct for matrix interferences caused by co-eluting substances are described. With the focus on pharmaceuticals in the environment and bioanalysis, different separation techniques, trends in liquid chromatography and sample preparation methods to minimize matrix effects and increase sensitivity are discussed. Although highly sensitive methods are generally aimed for to provide automated multi-residue analysis, (less sensitive) miniaturized set-ups have a great potential due to their ability for in-field usage.This article is part of the themed issue 'Quantitative mass spectrometry'.

Liquid phase separation methods for N-glycosylation analysis of glycoproteins of biomedical and biopharmaceutical interest. A critical review

Comprehensive carbohydrate analysis of glycoproteins from human biological samples and biotherapeutics are important from diagnostic and therapeutic points of view. This review summarizes the current state-of-the-art liquid phase separation techniques used in N-glycosylation analysis. The different liquid chromatographic techniques and capillary electrophoresis methods are critically discussed in detail. Miniaturization of these methods is also important to increase throughput and decrease analysis time. The sample preparation and labeling methods for asparagine linked oligosaccharides are also addressed.

Challenges for the in vivo quantification of brain neuropeptides using microdialysis sampling and LC-MS

In recent years, neuropeptides and their receptors have received an increased interest in neuropharmacological research. Although these molecules are considered relatively small compared with proteins, their in vivo quantification using microdialysis is more challenging than for small molecules. Low microdialysis recoveries, aspecific adsorption and the presence of various multiply charged precursor ions during ESI-MS/MS detection hampers the in vivo quantification of these low abundant biomolecules. Every step in the workflow, from sampling until analysis, has to be optimized to enable the sensitive analysis of these compounds in microdialysates.

Bacterial Electron Transfer Chains Primed by Proteomics

Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.