Porous graphitic carbon: A versatile stationary phase for liquid chromatography

Linear solvent strength model on porous graphitic carbon stationary phase using high temperature liquid chromatographic method for allopurinol related substances analysis

A high-performance liquid chromatography (HPLC) method was developed for the analysis of Allopurinol and its Ph.Eur. impurities using a porous graphitic carbon (PGC) stationary phase. Retention behavior of solutes was studied across a wide temperature range (30-90 °C) and various gradient times (5-20 min). Analysis of the data revealed distinct retention mechanisms between reversed-phase and PGC phases. However, it was proved that the retention of Allopurinol and its Ph.Eur. impurities on PGC stationary phase can be effectively modeled using the linear solvent strength (LSS) theory. This allows for the utilization of LSS-based method development software to optimize methods under these conditions. By using commercial chromatographic modeling software, separation of Allopurinol and Ph.Eur. impurities was optimized within a large design space. At the optimized operating conditions (pH = 2.0, tG = 6 min, T = 60 °C), all solutes were separated within 6 min with baseline resolution. Comparison between predicted and experimentally measured chromatograms further confirmed the applicability of LSS theory in developing analytical methods for PGC-based HPLC systems. The presented approach offers a general framework for method development on PGC phases.

Principles and applications of porous graphitic carbon stationary phase in liquid chromatography: An update

The introduction of carbon black particles as packaging material for liquid chromatography columns dates back to the late 70's, in an attempt to overcome common drawbacks associated with silica-based packings. The latter consisted of the difficulty in eliminating or shielding the polar residual silanol groups, responsible for secondary interactions with non-polar ligands, but also the fragility and instability of the bonded ligands. Since then, numerous advances have been made in the synthesis of carbon-based stationary phases, achieving excellent objectives in terms of chromatographic performance and versatility, mainly related to the possibility of working under a wide range of pH (1-14) and temperature (higher than 200 °C). The purpose of this review is to summarize the most significant advances in the synthesis and application of the porous graphitic carbon phase (PGC), in the last decade. Literature reports based on the use of PGC columns are focused on the analysis of a wide range of chemicals, spanning from polar compounds to apolar polymers. More in detail, polar analytes have included both small molecules and larger biomolecules (such as oligo- and polysaccharides, peptides, and glycopeptides), with special emphasis on additional selectivity for isomer separation. On the other hand, applications devoted to the analysis of non-polar analytes could benefit from the use of high temperatures, allowing for the achievement of satisfactory separations within reduced analysis time.

Advanced nanofibrous sorbents for the extraction of pollutants from river water and protein-containing matrices

The extraction efficiencies of thirty types of fibers produced by meltblown, alternating current electrospinning, and meltblown-co-electrospinning technologies were tested as advanced sorbents for on-line solid-phase extraction in a high-performance liquid chromatography system have been tested and compared with a commercial C18 sorbent. The properties of each fiber, which were often depended on the production process, and their applicability were demonstrated with the extraction of the model analytes nitrophenols and chlorophenols from various matrices including river water and to purify complex matrix human serum and bovine serum albumin from macromolecular ballast. Polycaprolactone fibers outperformed other polymers and were selected for subsequent modifications including (i) incorporation of hybrid carbon nanoparticles, i.e., graphene, activated carbon, and carbon black into the polymer prior to fiber fabrication, and (ii) surface modification by dip coating with polyhydroxy modifiers including graphene oxide, tannin, dopamine, hesperidin, and heparin. These novel fibrous sorbents were comparable to commercial C18 sorbent and provided excellent analyte recoveries of 70-112% even from the protein-containing matrices.

Inclusion of Porous Graphitic Carbon Chromatography Yields Greater Protein Identification and Compartment and Process Coverage and Enables More Reflective Protein-Level Label-Free Quantitation

The ubiquity of mass spectrometry-based bottom-up proteomic analyses as a component of biological investigation mandates the validation of methodologies that increase acquisition efficiency, improve sample coverage, and enhance profiling depth. Chromatographic separation is often ignored as an area of potential improvement, with most analyses relying on traditional reversed-phase liquid chromatography (RPLC); this consistent reliance on a single chromatographic paradigm fundamentally limits our view of the observable proteome. Herein, we build upon early reports and validate porous graphitic carbon chromatography (PGC) as a facile means to substantially enhance proteomic coverage without changes to sample preparation, instrument configuration, or acquisition methods. Analysis of offline fractionated cell line digests using both separations revealed an increase in peptide and protein identifications by 43% and 24%, respectively. Increased identifications provided more comprehensive coverage of cellular components and biological processes independent of protein abundance, highlighting the substantial quantity of proteomic information that may go undetected in standard analyses. We further utilize these data to reveal that label-free quantitative analyses using RPLC separations alone may not be reflective of actual protein constituency. Together, these data highlight the value and comprehension offered through PGC-MS proteomic analyses. RAW proteomic data have been uploaded to the MassIVE repository with the primary accession code MSV000091495.

Application of a porous graphitic carbon column to carbon and nitrogen isotope analysis of underivatized individual amino acids using high-performance liquid chromatography coupled with elemental analyzer/isotope ratio mass spectrometry

RATIONALE

Isolation of underivatized amino acids (AAs) using high-performance liquid chromatography (HPLC) is becoming a popular method for carbon (δ13 C) and nitrogen isotope (δ15 N) analyses of AAs because of the high analytical precision and for performing dual-isotope analysis. However, some AAs in natural samples, especially small, hydrophilic AAs, are not suitably separated using reversed-phase columns (e.g., C18) and ion-exchange columns (e.g., Primesep A).

METHODS

We developed a new method for HPLC using a porous graphitic carbon column for the separation of nine hydrophilic AAs. After purification, δ13 C and δ15 N values of AAs were determined using elemental analyzer/isotope ratio mass spectrometry (EA/IRMS). We demonstrated the application of this method by determining δ13 C and δ15 N values of individual hydrophilic AAs in a biological sample, the muscle of blue mackerel (Scomber australasicus).

RESULTS

Chromatographically, the baseline separation of hydrophilic AAs was achieved in both the standard mixture and the biological sample. We confirmed that δ13 C and δ15 N values of AA standards remained unchanged during the whole experimental procedure. The δ13 C values of AAs in mackerel muscle are also in good agreement with the values obtained using another verified method for δ13 C analysis.

CONCLUSIONS

The good separation performance of hydrophilic AAs and the reliability of δ13 C and δ15 N analyses of individual AAs using the porous graphite column offer a significant advantage over conventional settings. We suggest that, in the future, the HPLC × EA/IRMS method can be used for reliable δ13 C and δ15 N analyses of AAs in natural samples.

Application of chromatography in purification and structural analysis of natural polysaccharides: A review

Polysaccharides are widely distributed in natural sources from monocytic microorganisms to higher animals, and are found in a variety of biological activities in recent decades. Natural polysaccharides have the characteristics of large molecular weight, diverse composition, and complex structure, so their purification and structural analysis are difficult issues in research. Chromatography as a powerful separation technique, plays an irreplaceable role in the separation and structural analysis of natural polysaccharides, especially in the purification of polysaccharides, the separation of hydrolysates, and the analysis of monosaccharide composition. The separation mechanisms and application of different chromatographic methods in the studies of polysaccharides were summarized in this review. Moreover, the advantages and drawbacks of various chromatography methods were discussed as well.

Right in two: capabilities of ion mobility spectrometry for untargeted metabolomics

This mini review focuses on the opportunities provided by current and emerging separation techniques for mass spectrometry metabolomics. The purpose of separation technologies in metabolomics is primarily to reduce complexity of the heterogeneous systems studied, and to provide concentration enrichment by increasing sensitivity towards the quantification of low abundance metabolites. For this reason, a wide variety of separation systems, from column chemistries to solvent compositions and multidimensional separations, have been applied in the field. Multidimensional separations are a common method in both proteomics applications and gas chromatography mass spectrometry, allowing orthogonal separations to further reduce analytical complexity and expand peak capacity. These applications contribute to exponential increases in run times concomitant with first dimension fractionation followed by second dimension separations. Multidimensional liquid chromatography to increase peak capacity in metabolomics, when compared to the potential of running additional samples or replicates and increasing statistical confidence, mean that uptake of these methods has been minimal. In contrast, in the last 15 years there have been significant advances in the resolution and sensitivity of ion mobility spectrometry, to the point where high-resolution separation of analytes based on their collision cross section approaches chromatographic separation, with minimal loss in sensitivity. Additionally, ion mobility separations can be performed on a chromatographic timescale with little reduction in instrument duty cycle. In this review, we compare ion mobility separation to liquid chromatographic separation, highlight the history of the use of ion mobility separations in metabolomics, outline the current state-of-the-art in the field, and discuss the future outlook of the technology. "Where there is one, you're bound to divide it. Right in two", James Maynard Keenan.

Recent progress in quantitative phosphoproteomics

INTRODUCTION

Protein phosphorylation is a critical post-translational modification involved in the regulation of numerous cellular processes from signal transduction to modulation of enzyme activities. Knowledge of dynamic changes of phosphorylation levels during biological processes, under various treatments or between healthy and disease models is fundamental for understanding the role of each phosphorylation event. Thereby, LC-MS/MS based technologies in combination with quantitative proteomics strategies evolved as a powerful strategy to investigate the function of individual protein phosphorylation events.

AREAS COVERED

State-of-the-art labeling techniques including stable isotope and isobaric labeling provide precise and accurate quantification of phosphorylation events. Here, we review the strengths and limitations of recent quantification methods and provide examples based on current studies, how quantitative phosphoproteomics can be further optimized for enhanced analytic depth, dynamic range, site localization, and data integrity. Specifically, reducing the input material demands is key to a broader implementation of quantitative phosphoproteomics, not least for clinical samples.

EXPERT OPINION

Despite quantitative phosphoproteomics is one of the most thriving fields in the proteomics world, many challenges still have to be overcome to facilitate even deeper and more comprehensive analyses as required in the current research, especially at single cell levels and in clinical diagnostics.

Determination of Pentacyclic Triterpenoids in Plant Biomass by Porous Graphitic Carbon Liquid Chromatography-Tandem Mass Spectrometry

Pentacyclic triterpenoids (PCTs), which possess a number of bioactive properties, are considered one of the most important classes of secondary plant metabolites. Their chromatographic determination in plant biomass is complicated by the need to separate a large number of structurally similar compounds belonging to several classes that differ greatly in polarity (monools, diols, and triterpenic acids). This study proposes a rapid, sensitive, and low-cost method for the simultaneous quantification of ten PCTs (3β-taraxerol, lupeol, β-amyrin, α-amyrin, betulin, erythrodiol, uvaol, betulinic, oleanolic, and ursolic acids) by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) using porous graphitic carbon (Hypercarb) as a stationary phase capable of hydrophobic retention and specific interactions with analytes. Revealing the effects of the mobile phase composition, pH, ionic strength, and column temperature on retention and selection of chromatographic conditions on this basis allowed for the effective separation of all target analytes within 8 min in gradient elution mode and attaining limits of detection in the range of 4-10⁴ µg L^-1. The developed method was fully validated and successfully tested in the determination of PCTs in common haircap (Polytrichum commune) and prairie sphagnum (Sphagnum palustre) mosses, and fireweed (Chamaenerion angustifolium) stems and leaves.

Expanding the Epitranscriptomic RNA Sequencing and Modification Mapping Mass Spectrometry Toolbox with Field Asymmetric Waveform Ion Mobility and Electrochemical Elution Liquid Chromatography

Post-transcriptional modifications of RNA strongly influence the RNA structure and function. Recent advances in RNA sequencing and mass spectrometry (MS) methods have identified over 140 of these modifications on a wide variety of RNA species. Most next-generation sequencing approaches can only map one RNA modification at a time, and while MS can assign multiple modifications simultaneously in an unbiased manner, MS cannot accurately catalog and assign RNA modifications in complex biological samples due to limitations in the fragment length and coverage depth. Thus, a facile method to identify novel RNA modifications while simultaneously locating them in the context of their RNA sequences is still lacking. We combined two orthogonal modes of RNA ion separation before MS identification: high-field asymmetric ion mobility separation (FAIMS) and electrochemically modulated liquid chromatography (EMLC). FAIMS RNA MS increases both coverage and throughput, while EMLC LC-MS orthogonally separates RNA molecules of different lengths and charges. The combination of the two methods offers a broadly applicable platform to improve the length and depth of MS-based RNA sequencing while providing contextual access to the analysis of RNA modifications.

Selective determination of formaldehyde by high-performance liquid chromatography with porous graphitic carbon column using N,N'-bis(9-anthrylmethyl)propane-1,3-diamine as derivatizing reagent

Aromatic compounds containing two secondary amino groups were designed and prepared as new derivatizing reagents for aldehydes. One of them, N,N'-bis(9-anthrylmethyl)propane-1,3-diamine (APD), could achieve selective determination of formaldehyde (FA) on a porous graphitic carbon (PGC) column using xylenes, chlorobenzene, and 1-chloronaphthalene as mobile phases by high-performance liquid chromatography (HPLC). The APD-FA derivative was eluted from the PGC column, while the other APD-aldehyde derivatives remained on the column during the HPLC measurements. This specific elution was not observed using mobile phases such as acetonitrile, 1,4-dioxane, tetrahydrofuran, N,N-dimethylformamide, N,N-dimethylacetamide, N-methyl-2-pyrrolidone, chloroform, benzene, toluene, benzyl alcohol, 2-ethyl-1-hexanol, and pyridine. The APD-FA derivative had a six-membered ring of two tertiary amines identified using ¹H NMR spectroscopy. When the π-π interaction of the solvent molecule of the mobile phase with PGC overcame that between the APD-FA derivative and PGC, the APD-FA derivative could be eluted from the column. The best resolution between the peak of the APD-FA derivative and that of free APD was observed when using o-xylene. The optimum derivatization and the HPLC conditions for selective HPLC determination of FA were to conduct the derivatization of FA by heating in an aqueous phase with APD in o-xylene at 100 °C. In this method, FA could be derivatized with APD at a mildly neutral pH of 6.7, unlike the low pH required for the derivatization of aldehydes with 2,4-dinitrophenylhydrazine (DNPH), which is commonly used for the derivatization of aldehydes. The detection and quantification limits of FA were 0.8 and 3.5 ng mL^-1 in this HPLC method with fluorescent detection, respectively. This selective HPLC method could be applied to the determination of FA in various water samples. It was found that only APD among the derivatizing reagents containing two secondary diamines was useful for the selective determination of FA.

MS-based glycomics and glycoproteomics methods enabling isomeric characterization

Glycosylation is one of the most significant and abundant posttranslational modifications in mammalian cells. It mediates a wide range of biofunctions, including cell adhesion, cell communication, immune cell trafficking, and protein stability. Also, aberrant glycosylation has been associated with various diseases such as diabetes, Alzheimer's disease, inflammation, immune deficiencies, congenital disorders, and cancers. The alterations in the distributions of glycan and glycopeptide isomers are involved in the development and progression of several human diseases. However, the microheterogeneity of glycosylation brings a great challenge to glycomic and glycoproteomic analysis, including the characterization of isomers. Over several decades, different methods and approaches have been developed to facilitate the characterization of glycan and glycopeptide isomers. Mass spectrometry (MS) has been a powerful tool utilized for glycomic and glycoproteomic isomeric analysis due to its high sensitivity and rich structural information using different fragmentation techniques. However, a comprehensive characterization of glycan and glycopeptide isomers remains a challenge when utilizing MS alone. Therefore, various separation methods, including liquid chromatography, capillary electrophoresis, and ion mobility, were developed to resolve glycan and glycopeptide isomers before MS. These separation techniques were coupled to MS for a better identification and quantitation of glycan and glycopeptide isomers. Additionally, bioinformatic tools are essential for the automated processing of glycan and glycopeptide isomeric data to facilitate isomeric studies in biological cohorts. Here in this review, we discuss commonly employed MS-based techniques, separation hyphenated MS methods, and software, facilitating the separation, identification, and quantitation of glycan and glycopeptide isomers.

Simultaneous analysis of paralytic shellfish toxins and tetrodotoxins in human serum by liquid chromatography coupled to Q-Exactive high-resolution mass spectrometry

Paralytic shellfish toxins (PSTs) and tetrodotoxins (TTXs) are powerful neurotoxins. Previous research reported that PSTs and TTXs are found together in seafoods and may pose a serious hazard to public health. In this study, a new analytical method combining modified QuEChERS (Quick, Easy, Cheap, Effective, Rugged, Safe) with high-performance liquid chromatography coupled to Q-Exactive Orbitrap high-resolution mass spectrometry was developed and validated for the quantification of 10 PSTs and 2 TTXs in human serum. Chromatographic separation was achieved using the HILIC TSK-Gel Amide-80 column. The mass spectrometer was operated in full scan/dd-MS²(data-dependent MS²) mode, and for quantification analysis. The dd-MS² resolution was set to 17,500 fullwidthat halfmaximum （FWHM）. Results showed that methanol with 1 % (v/v) acetic acid extraction combined with 50 mg graphitized carbon black (GCB) and 50 mg octadecyl bonded silica gel (C18) was most suitable for purification. The mean recovery for all toxins ranged from 85.3 % to 118.2 % (RSD < 12 %). The limits of detection and quantification for human serum were in the ranges of 0.67-2.61 and 2.23-8.69 ng mL^-1, respectively. The method was applied to analyze toxins in serum samples obtained from three poisoned patients in a case of poisoning caused by consumption of toxin-contaminated gastropoda (Bullacta exerata). The study has important application for rapid and accurate diagnosis of PSTs and TTXs toxin poisoning patients in clinic.

Comparison of Solid-Phase Extraction Sorbents for Monitoring the In Vivo Intestinal Survival and Digestion of Kappa-Casein-Derived Caseinomacropeptide

Kappa-casein-derived caseinomacropeptide (CMP)-a 64-amino-acid peptide-is released from kappa-casein after rennet treatment and is one of the major peptides in whey protein isolate (WPI). CMP has anti-inflammatory and antibacterial activities. It also has two major amino acid sequences with different modifications, including glycosylation, phosphorylation, and oxidation. To understand the potential biological role of CMP within the human body, there is a need to examine the extent to which CMP and CMP-derived fragments survive across the digestive tract, where they can exert these functions. In this study, three solid-phase extraction (SPE) methods-porous graphitized carbon (PGC), hydrophilic interaction liquid chromatography (HILIC), and C18 chromatography-were evaluated to determine which SPE sorbent is the most efficient to extract intact CMP and CMP-derived peptides from WPI and intestinal digestive samples prior to LC-MS/MS acquisition. The C18 SPE sorbent was the most efficient in extracting intact CMP and CMP-derived peptides from WPI, whereas the PGC SPE sorbent was the most efficient in extracting CMP-derived peptides from intestinal digesta samples.

Liquid chromatography and capillary electrophoresis in glycomic and glycoproteomic analysis

Glycosylation is one of the most significant and abundant post-translational modifications in cells. Glycomic and glycoproteomic analyses involve the characterization of oligosaccharides (glycans) conjugated to proteins. Glycomic and glycoproteomic analysis is highly challenging because of the large diversity of structures, low abundance, site-specific heterogeneity, and poor ionization efficiency of glycans and glycopeptides in mass spectrometry (MS). MS is a key tool for characterization of glycans and glycopeptides. However, MS alone does not always provide full structural and quantitative information for many reasons, and thus MS is combined with some separation technique. This review focuses on the role of separation techniques used in glycomic and glycoproteomic analyses, liquid chromatography and capillary electrophoresis. The most important separation conditions and results are presented and discussed.

Graphical abstract

Evaluation of the Tasso-SST® capillary blood microsampling device for the measurement of endogenous uracil levels

BACKGROUND

Uracil (U) plasma or serum levels can be used as surrogates of dihydropyrimidine dehydrogenase (DPD) activity, which is strongly related to the occurrence of severe or fatal toxicity after administration of fluoropyrimidines (FP) chemotherapy. Obtaining blood plasma or serum for U measurement usually requires a phlebotomy procedure by a qualified professional. An alternative to conventional blood drawn is the use of the Tasso-SST® device, which allows the collection of a small blood volume from skin capillaries. This study aimed to implement a sensitive liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay for the determination of U in small serum samples and to compare U concentrations measured in venous plasma, obtained after phlebotomy, and serum obtained with the Tasso-SST® device.

METHODS

Fifty microliter samples were prepared through simple protein precipitation with trichloroacetic acid. Chromatographic separation was performed with a porous graphitic carbon stationary phase and mass spectrometric detection used positive electrospray ionization. The assay was validated according to international guidelines.

RESULTS

The linear range of the assay was 5-250 ng/mL. Measurement accuracy was in the range of 98.8-108.2%, inter-assay precision was 4.3-7.3%, and intra-assay precision was 3.4-6.1%. The average matrix effect was -6.42%. The extraction yield was 95-103.3%. U concentrations measured in serum obtained with the Tasso-SST® device and venous blood plasma were highly correlated (rs = 0.910, P < 0.0001), and no systematic or proportional bias between U levels measured in both matrices was found.

CONCLUSIONS

The use of blood microsampling with the Tasso-SST® device is a useful alternative for the measurement of U and the identification of patients with DPD deficiency.

Glycomic and Glycoproteomic Techniques in Neurodegenerative Disorders and Neurotrauma: Towards Personalized Markers

The proteome represents all the proteins expressed by a genome, a cell, a tissue, or an organism at any given time under defined physiological or pathological circumstances. Proteomic analysis has provided unparalleled opportunities for the discovery of expression patterns of proteins in a biological system, yielding precise and inclusive data about the system. Advances in the proteomics field opened the door to wider knowledge of the mechanisms underlying various post-translational modifications (PTMs) of proteins, including glycosylation. As of yet, the role of most of these PTMs remains unidentified. In this state-of-the-art review, we present a synopsis of glycosylation processes and the pathophysiological conditions that might ensue secondary to glycosylation shortcomings. The dynamics of protein glycosylation, a crucial mechanism that allows gene and pathway regulation, is described. We also explain how-at a biomolecular level-mutations in glycosylation-related genes may lead to neuropsychiatric manifestations and neurodegenerative disorders. We then analyze the shortcomings of glycoproteomic studies, putting into perspective their downfalls and the different advanced enrichment techniques that emanated to overcome some of these challenges. Furthermore, we summarize studies tackling the association between glycosylation and neuropsychiatric disorders and explore glycoproteomic changes in neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Huntington disease, multiple sclerosis, and amyotrophic lateral sclerosis. We finally conclude with the role of glycomics in the area of traumatic brain injury (TBI) and provide perspectives on the clinical application of glycoproteomics as potential diagnostic tools and their application in personalized medicine.

High-performance nano-flow liquid chromatography column combined with high- and low-collision energy data-independent acquisition enables targeted and discovery identification of modified ribonucleotides by mass spectrometry

Over 170 post-transcriptional RNA modifications have been described and are common in all kingdoms of life. These modifications range from methylation to complex chemical structures, with methylation being the most abundant. RNA modifications play a key role in RNA folding and function and their dysregulation in humans has been linked to several diseases such as cancer, metabolic diseases or neurological disorder. Nowadays, liquid chromatography-tandem mass spectrometry is considered the gold standard method for the identification and quantification of these modifications due to its sensitivity and accuracy. However, the analysis of modified ribonucleosides by mass spectrometry is complex due to the presence of positional isomers. In this scenario, optimal separation of these compounds by highly sensitive liquid chromatography combined with the generation of high-information spectra is critical to unequivocally identify them, especially in high-complex mixtures. Here we present an analytical method that comprises a new type of mixed-mode nano-flow liquid chromatography column combined with high- and low-collision energy data-independent mass spectrometric acquisition for the identification and quantitation of modified ribonucleosides. The method produces content-rich spectra and combines targeted and screening capabilities thus enabling the identification of a variety of modified nucleosides in biological matrices by single-shot liquid chromatographic analysis coupled to mass spectrometry.

Chromatographic analysis of oxidized cello-oligomers generated by lytic polysaccharide monooxygenases using dual electrolytic eluent generation

Research on oligosaccharides, including the complicated product mixtures generated by lytic polysaccharide monooxygenases (LPMOs), is growing at a rapid pace. LPMOs are gaining major interest, and the ability to efficiently and accurately separate and quantify their native and oxidized products chromatographically is essential in furthering our understanding of these oxidative enzymes. Here we present a novel set of methods based on dual electrolytic eluent generation, where the conventional sodium acetate/sodium hydroxide (NaOAc/NaOH) eluents in high-performance anion-exchange chromatography (HPAEC) are replaced by electrolytically-generated potassium methane sulfonate/potassium hydroxide (KMSA/KOH). The new methods separate all compounds of interest within 24-45 min and with high sensitivity; limits of detection and quantification were in the range of 0.0001-0.0032 mM and 0.0002-0.0096 mM, respectively. In addition, an average of 3.5 times improvement in analytical CV was obtained. This chromatographic platform overcomes drawbacks associated with manual preparation of eluents and offers simplified operation and rapid method optimization, with increased precision for less abundant LPMO-derived products.

Cell-free multi-enzyme synthesis and purification of uridine diphosphate galactose

High costs and low availability of UDP‐galactose hampers the enzymatic synthesis of valuable oligosaccharides such as human milk oligosaccharides. Here, we report the development of a platform for the scalable, biocatalytic synthesis and purification of UDP‐galactose. UDP‐galactose was produced with a titer of 48 mM (27.2 g/L) in a small‐scale batch process (200 μL) within 24 h using 0.02 g_enzyme/g_product. Through in‐situ ATP regeneration, the amount of ATP (0.6 mM) supplemented was around 240‐fold lower than the stoichiometric equivalent required to achieve the final product yield. Chromatographic purification using porous graphic carbon adsorbent yielded UDP‐galactose with a purity of 92 %. The synthesis was transferred to 1 L preparative scale production in a stirred tank bioreactor. To further reduce the synthesis costs here, the supernatant of cell lysates was used bypassing expensive purification of enzymes. Here, 23.4 g/L UDP‐galactose were produced within 23 h with a synthesis yield of 71 % and a biocatalyst load of 0.05 g_{total_protein}/g_product. The costs for substrates per gram of UDP‐galactose synthesized were around 0.26 €/g.

Advances in mass spectrometry-based glycomics-An update covering the period 2017-2021

The wide variety of chemical properties and biological functions found in proteins is attained via post-translational modifications like glycosylation. Covalently bonded to proteins, glycans play a critical role in cell activity. Complex structures with microheterogeneity, the glycan structures that are associated with proteins are difficult to analyze comprehensively. Recent advances in sample preparation methods, separation techniques, and MS have facilitated the quantitation and structural elucidation of glycans. This review focuses on highlighting advances in MS-based techniques for glycomic analysis that occurred over the last 5 years (2017-2021) as an update to the previous review on the subject. The topics of discussion will include progress in glycomic workflow such as glycan release, purification, derivatization, and separation as well as the topics of ionization, tandem MS, and separation techniques that can be coupled with MS. Additionally, bioinformatics tools used for the analysis of glycans will be described.

Solid-phase extraction of alkylphosphonic and O-alkyl alkylphosphonic acids followed by HPLC separation using porous graphitic carbon sorbent

An HPLC separation of alkyl phosphonic acids on porous graphitic carbon adsorbent Hypercarb, based upon a step gradient of formic acid concentration in an aqueous mobile phase, was evaluated in this study. Analytes were detected by single quadrupole and triple quadrupole MS. Good separation was achieved for methyl phosphonic acid, ethylphosphonic acid, n-propylphosphonic acid, isopropylphosphonic acid, ethyl methylphosphonic acid, isopropyl methylphosphonic acid, isobutyl methylphosphonic acid, pinacolyl methylphosphonic acid. Solid-phase extraction of these analytes on Hypercarb was also proposed, desorption was carried out with aqueous ammonium formate and water-methanol mixtures. LODs were 0.1-0.2 ng mL-1 for these analytes without SPE; solid-phase extraction resulted in the decrease of LODs at least 100-fold. Accuracy was proven by analyses of spiked samples of river water and snow meltwater.

Recent advances in metal-free heteroatom-doped carbon heterogonous catalysts

The development of cost-effective, efficient, and novel catalytic systems is always an important topic for heterogeneous catalysis from academia and industrial points of view. Heteroatom-doped carbon materials have gained more and more attention as effective heterogeneous catalysts to replace metal-based catalysts, because of their excellent physicochemical properties, outstanding structure characteristics, environmental compatibility, low cost, inexhaustible resources, and low energy consumption. Doping of heteroatoms can tailor the properties of carbons for different utilizations of interest. In comparison to pure carbon catalysts, these catalysts demonstrate superior catalytic activity in many organic reactions. This review highlights the most recent progress in synthetic strategies to fabricate metal-free heteroatom-doped carbon catalysts including single and multiple heteroatom-doped carbons and the catalytic applications of these fascinating materials in various organic transformations such as oxidation, hydrogenation, hydrochlorination, dehydrogenation, etc.

Recent advances in metal-free heteroatom-doped carbon heterogeneous catalysts including the preparation methods and their catalytic applications in various organic reactions have been reported.

In-House Packed Porous Graphitic Carbon Columns for Liquid Chromatography-Mass Spectrometry Analysis of N-Glycans

Protein glycosylation is a common post-translational modification that modulates biological processes such as the immune response and protein trafficking. Altered glycosylation profiles are associated with cancer and inflammatory diseases, as well as impacting the efficacy of therapeutic monoclonal antibodies. Consisting of oligosaccharides attached to asparagine residues, enzymatically released N-linked glycans are analytically challenging due to the diversity of isomeric structures that exist. A commonly used technique for quantitative N-glycan analysis is liquid chromatography-mass spectrometry (LC-MS), which performs glycan separation and characterization. Although many reversed and normal stationary phases have been utilized for the separation of N-glycans, porous graphitic carbon (PGC) chromatography has become desirable because of its higher resolving capability, but is difficult to implement in a robust and reproducible manner. Herein, we demonstrate the analytical properties of a 15 cm fused silica capillary (75 µm i.d., 360 µm o.d.) packed in-house with Hypercarb PGC (3 µm) coupled to an Agilent 6550 Q-TOF mass spectrometer for N-glycan analysis in positive ion mode. In repeatability and intermediate precision measurements conducted on released N-glycans from a glycoprotein standard mixture, the majority of N-glycans reported low coefficients of variation with respect to retention times (≤4.2%) and peak areas (≤14.4%). N-glycans released from complex samples were also examined by PGC LC-MS. A total of 120 N-glycan structural and compositional isomers were obtained from formalin-fixed paraffin-embedded ovarian cancer tissue sections. Finally, a comparison between early- and late-stage formalin-fixed paraffin-embedded ovarian cancer tissues revealed qualitative changes in the α2,3- and α2,6-sialic acid linkage of a fucosylated bi-antennary complex N-glycan. Although the α2,3-linkage was predominant in late-stage ovarian cancer, the alternate α2,6-linkage was more prevalent in early-stage ovarian cancer. This study establishes the utility of in-house packed PGC columns for the robust and reproducible LC-MS analysis of N-glycans.

Development of LC-HRMS methods for evaluation of metabolic conversion of 5-fluorocytosine at GDEPT procedure

Gene-directed enzyme/prodrug therapy represents one of the experimental treatment approaches. The system based on conversion of nontoxic prodrug 5-fluorocytosine to chemotherapeutic 5-fluorouracil by cytosine deaminase or fusion cytosine deaminase::uracil phosphoribosyl transferase belongs to the most frequently used. The detailed analysis of 5-fluorocytosine, 5-fluorouracil and its metabolites enables to understand various responses of tumour cells to treatment as well as mechanisms of resistance. A fast, sensitive and accurate methods based on liquid chromatography with high-resolution mass spectrometry (LC-HRMS) for the identification and quantification of 5-fluorocytosine, 5-fluorouracil and its major metabolites were developed. Two different hybrid high-resolution mass spectrometers sufficient for study of metabolic pathways were used. The LC-ESI IT-TOF MS method was successfully used for identification of 5-fluorocytosine, 5-fluorouracil and its metabolites in complex biological matrices (mesenchymal stromal cells and tumour cells media) and for confirmation of the metabolic conversion of 5-fluorocytosine even in chemoresistant tumour cells media samples. For quantification, the LC-HESI QExactive MS method was developed and validated. The developed method demonstrated a very good linear range for 5-fluorocytosine from 1 ng/mL to 1000 ng/mL and for its major metabolites from 5 ng/mL to 1000 ng/mL. The limits of detection and limits of quantification ranged from 1.1 to 26 ng/mL and from 3.6 to 87 ng/mL, respectively. Both developed methods confirmed the ability of gene-directed enzyme prodrug therapy to metabolically convert 5-fluorocytosine to 5-fluorouracil and its major metabolites in real samples of tumour cell media and mesenchymal stromal cells.

Solution-processable porous graphitic carbon from bottom-up synthesis and low-temperature graphitization

It is urgently desired yet challenging to synthesize porous graphitic carbon (PGC) in a bottom-up manner while circumventing the need for high-temperature pyrolysis. Here we present an effective and scalable strategy to synthesize PGC through acid-mediated aldol triple condensation followed by low-temperature graphitization. The deliberate structural design enables its graphitization in situ in solution and at low pyrolysis temperature. The resulting material features ultramicroporosity characterized by a sharp pore size distribution. In addition, the pristine homogeneous composition of the reaction mixture allows for solution-processability of the material for further characterization and applications. Thin films of this PGC exhibit several orders of magnitude higher electrical conductivity compared to analogous control materials that are carbonized at the same temperatures. The integration of low-temperature graphitization and solution-processability not only allows for an energy-efficient method for the production and fabrication of PGC, but also paves the way for its wider employment in applications such as electrocatalysis, sensing, and energy storage.

Determination of Isomeric Glycan Structures by Permethylation and Liquid Chromatography-Mass Spectrometry (LC-MS)

The existence of glycans in isomeric forms is responsible for the multifariousness of their properties and biological functions. Their altered expression has been associated with various diseases and cancers. Analysis of native glycans is not very sensitive due to the low ionization efficiency of glycans. These facts necessitate their comprehensive structural studies and establishes a high demand for sensitive and reliable techniques. In this chapter, we discuss the strategies for effective separation and identification of permethylated isomeric glycans. The sample preparation for permethylated glycans derived from model glycoproteins and complex biological samples, analyzed using LC-MS/MS, is delineated. We introduce protein extraction and release of glycans, followed by strategies to purify the released glycans, which are reduced and permethylated to improve ionization efficiency and stabilize sialic acid residues. High-temperature LC-based separation on PGC (porous graphitized carbon) column is conducive to isomeric separation of glycans and allows their sensitive identification and quantification using MS/MS.

Polysaccharide identification through oligosaccharide fingerprinting

The identification of polysaccharide structures in complex samples remains a unique challenge complicated by the lack of specific tools for polymeric mixtures. In this work, we present a method that depolymerizes polysaccharides to generate diagnostic oligosaccharide markers that are then analyzed by high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (HPLC-QTOF MS). Rapid identification of food polysaccharides was performed by aligning the identified oligosaccharides with a library of oligosaccharide markers generated from standard polysaccharides. Measurements of standard and food polysaccharides were performed to obtain the contributions of the identified polysaccharides using percent peak coverage and angle cosine methods. The method was validated using a synthetic mixture of standard polysaccharides while the reproducibility was confirmed with experimental triplicates of butternut squash samples, where standard deviation was less than 3% for the relative abundance of oligosaccharides. The method was further employed to examine diverse set of food samples.

Mass Spectrometry-Based Methods for Immunoglobulin G N-Glycosylation Analysis

Mass spectrometry and its hyphenated techniques enabled by the improvements in liquid chromatography, capillary electrophoresis, novel ionization, and fragmentation modes are truly a cornerstone of robust and reliable protein glycosylation analysis. Boost in immunoglobulin G (IgG) glycan and glycopeptide profiling demands for both applied biomedical and research applications has brought many new advances in the field in terms of technical innovations, sample preparation, improved throughput, and confidence in glycan structural characterization. This chapter summarizes mass spectrometry basics, focusing on IgG and monoclonal antibody N-glycosylation analysis on several complexity levels. Different approaches, including antibody enrichment, glycan release, labeling, and glycopeptide preparation and purification, are covered and illustrated with recent breakthroughs and examples from the literature omitting excessive theoretical frameworks. Finally, selected highly popular methodologies in IgG glycoanalytics such as liquid chromatography-mass spectrometry and matrix-assisted laser desorption ionization are discussed more thoroughly yet in simple terms making this text a practical starting point either for the beginner in the field or an experienced clinician trying to make sense out of the IgG glycomic or glycoproteomic dataset.

A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-Based Glycoproteomics

Glycosylation is a prevalent, yet heterogeneous modification with a broad range of implications in molecular biology. This heterogeneity precludes enrichment strategies that can be universally beneficial for all glycan classes. Thus, choice of enrichment strategy has profound implications on experimental outcomes. Here we review common enrichment strategies used in modern mass spectrometry-based glycoproteomic experiments, including lectins and other affinity chromatographies, hydrophilic interaction chromatography and its derivatives, porous graphitic carbon, reversible and irreversible chemical coupling strategies, and chemical biology tools that often leverage bioorthogonal handles. Interest in glycoproteomics continues to surge as mass spectrometry instrumentation and software improve, so this review aims to help equip researchers with the necessary information to choose appropriate enrichment strategies that best complement these efforts.

Extraction Improvement of the Bioactive Blue-Green Pigment "Marennine" from Diatom Haslea ostrearia's Blue Water: A Solid-Phase Method Based on Graphitic Matrices

The compound “marennine” is a blue–green pigment produced by the benthic microalgae Haslea ostrearia, with pathogenicity reduction activities against some bacteria and promising potential as a natural pigment in seafood industries. After decades of research, the chemical family of this compound still remains unclear, mainly because structural studies were impaired by the presence of co-extracted compounds in marennine isolates. To improve the purity of marennine extract, we developed a novel extraction method using a graphitic stationary phase, which provides various advantages over the previous procedure using tandem ultrafiltration. Our method is faster, more versatile, provides a better crude yield (66%, compared to 57% for ultrafiltration) and is amenable to upscaling with continuous photobioreactor cultivation. Our goal was to take advantage of the modulable surface properties of the graphitic matrix by optimizing its interactions with marennine. As such, the effects of organic modifiers, pH and reducing agents were studied. With this improvement on marennine purification, we achieved altogether the isolation of a fucoidan-related, sulfated polysaccharide from blue water. Characterization of the polysaccharides fraction suggests that roughly half of UV-absorbing compounds could be isolated from the marennine crude extracts. The identification of sulfated polysaccharides could be a major breakthrough for marennine purification, providing targeted isolation techniques. Likewise, the added value of Haslea ostrearia and the role of polysaccharides in previous marennine chemical characterization and bioactivity studies remain to be determined.

Bullet points to evaluate the performance of the middle-down proteomics workflow for histone modification analysis

Middle-down proteomics has emerged as the method of choice to study combinatorial histone post translational modifications (PTMs). In the common bottom-up workflow, histones are digested into relatively short peptides (4-20 aa), separated using reversed-phase chromatography and analyzed using typical proteomics methods in mass spectrometry. In middle-down, histones are cleaved into longer polypeptides (50-60 aa) mostly corresponding to their N-terminal tails, resolved using weak cation exchange-hydrophilic interaction liquid chromatography (WCX-HILIC) and analyzed with less conventional mass spectrometry, i.e. using Electron Transfer Dissociation (ETD) for analyte fragmentation. Middle-down is not nearly as utilized as bottom-up for PTM analysis, partially due to its limited reproducibility and robustness. This has also limited the establishment of rigorous benchmarks to discriminate good vs poor quality experiments. Here, we describe critical aspects of the middle-down workflow to assist the user in evaluating the presence of biased and misleading results. Specifically, we tested the use of porous graphitic carbon (PGC) during the desalting step, demonstrating that desalting using only C18 material leads to sample loss. We also tested different salts in the WCX-HILIC buffers for their effect on retention, selectivity, and reproducibility of analysis of variants of histone tail fragments, in particular replacing ammonium ion with ethylenediammonium ion in buffer A. These substitutions had marked effects on selectivity and retention. Our results provide a streamlined way to evaluate middle-down performance to identify and quantify combinatorial histone PTMs.

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.

Enhanced protocol for quantitative N-linked glycomics analysis using Individuality Normalization when Labeling with Isotopic Glycan Hydrazide Tags (INLIGHT)™

The analysis of N-linked glycans using liquid chromatography and mass spectrometry (LC-MS) presents significant challenges, particularly owing to their hydrophilic nature. To address these difficulties, a variety of derivatization methods have been developed to facilitate improved ionization and detection sensitivity. One such method, the Individuality Normalization when Labeling with Isotopic Glycan Hydrazide Tags (INLIGHT)™ strategy for labeling glycans, has previously been utilized in the analysis of N- and O-linked glycans in biological samples. To assess the maximum sensitivity and separability of the INLIGHT™ preparation and analysis pipeline, several critical steps were investigated. First, recombinant and nonrecombinant sources of PNGase F were compared to assess variations in the released glycans. Second, modifications in the INLIGHT™ derivatization step were evaluated including temperature optimization, solvent composition changes, reaction condition length and tag concentration. Optimization of the modified method resulted in 20-100 times greater peak areas for the detected N-linked glycans in fetuin and horseradish peroxidase compared with the standard method. Furthermore, the identification of low-abundance glycans, such as (Fuc)1(Gal)2(GlcNAc)4(Man)3(NeuAc)1 and (Gal)3(GlcNAc)5(Man)3(NeuAc)3, was possible. Finally, the optimal LC setup for the INLIGHT™ derivatized N-linked glycan analyses was found to be a C18 reverse-phase (RP) column with mobile phases typical of RPLC.

Systematic examination of protein extraction, proteolytic glycopeptide enrichment and MS/MS fragmentation techniques for site-specific profiling of human milk N-glycoproteins

Human milk contains numerous N-glycoproteins with functions that provide protection to the infant. Increasing understanding of the functional role of human milk glycoproteins within the infant requires toolsets to comprehensively profile their site-specific glycosylation patterns. However, optimized methods for site-specific glycosylation analysis across the entire human milk proteome are not available. Therefore, we performed a systematic analysis of techniques for profiling the sites and compositions of N-glycans in human milk using liquid chromatography/mass spectrometry. To decrease interference from non-target molecules, we compared techniques for protein extraction, including ethanol (EtOH) precipitation, trichloroacetic acid precipitation, molecular weight cut-off filtration and techniques for tryptic glycopeptide enrichment, including C18-, porous graphitized carbon and hydrophilic interaction liquid chromatography (HILIC)-solid phase extraction (SPE) and acetone precipitation. We compared the capacity of higher-energy collision dissociation, electron-transfer dissociation and electron-transfer/higher-energy collision dissociation (EThcD) to produce fragment ions that would enable effective identification of the glycan composition, peptide sequence and glycosylation site. Of these methods, a combination of EtOH precipitation, HILIC-SPE and EThcD-fragmentation was the most effective for human milk N-glycopeptide profiling. This optimized approach significantly increased the number of N-glycopeptides and precursor N-glycoproteins (246 N-glycopeptides from 29 glycoproteins) compared with a more common extraction approach with no protein extraction and C18 clean-up (62 N-glycopeptides from 11 glycoproteins). The advancement in methods for human milk N-glycoproteins provided by this study represents a key step for better understanding the function of glycoproteins within the breast milk-fed infant.

Porous graphite as stationary phase for the chromatographic separation of polymer additives - determination of adsorption capability by Raman spectroscopy and physisorption

Additives are added to polymers in small concentration to achieve desired application properties widely used to tailor the properties. The rapid diversification of their molecular structures, with often only minute differences, necessitates the development of adequate chromatographic techniques. While modified silica so far is the workhorse as stationary phase we have probed the potential of porous graphitic carbon (Hypercarb^TM) for this purpose. The results show that the multitude of physicochemical interactions between analyte molecules and the graphitic surface enables separations of polyolefin stabilizers with unprecedented selectivity. To support the chromatographic results the adsorption capability of Hypercarb^TM for selected antioxidants and UV absorbers has been determined by Raman spectroscopy and argon physisorption measurements. The shift of the Graphite-band in the Raman spectra of Hypercarb^TM upon infusion with additives correlates with the changes in the Adsorption Potential Distributions. The results of argon physisorption measurements go hand in hand with the chronology of desorption of the additives in liquid chromatography experiments. The elution sequence can be explained by van der Waals or London forces, π-π-interactions and electron lone pair donor-acceptor interactions between the graphite surface and analyte functional groups.

Separation of saccharides using fullerene-bonded silica monolithic columns via π interactions in liquid chromatography

We report on a potential method to separate sugars by using the specific interaction between fullerenes and saccharides in liquid chromatography (LC). Aromatic rings with high electron density are believed to interact strongly with saccharides due to CH–π and/or OH–π interactions. In this study, the fullerene-bonded columns were used to separate saccharides by LC under aqueous conditions. As a result, 2-aminobenzamide-labeled glucose homopolymer (Glcs) was effectively separated by both C60 and C70 columns in the range of Glc-1 to Glc-20 and high blood glucose level being retained in greater quantity. Furthermore, similar separations were identified by LC–mass spectrometry with non-labeled glucose homopolymers. Theoretical study based on molecular dynamics and DFT calculation demonstrated that a supramolecular complex of saccharide–fullerene was formed through CH–π and/or OH–π interactions, and that the interactions between saccharide and fullerene increase with the increase units of the saccharide. Additionally, the C60 column retained disaccharides containing maltose, trehalose, and sucrose. In this case, it was assumed that the retention rates were determined by the difference of the dipole moment in each saccharide. These results suggest that the dipole-induced dipole interaction was dominant, and that maltose—with the higher dipole moment—was more strongly retained compared to other disaccharides having lower dipole moment.

Purification of natural neutral N-glycans by using two-dimensional hydrophilic interaction liquid chromatography × porous graphitized carbon chromatography for glycan-microarray assay

Glycan microarray for studying carbohydrate-protein interactions requires diverse classes of well-defined glycan standards. In this study, a purification strategy was established based on two-dimensional hydrophilic interaction liquid chromatography and porous graphitized carbon chromatography (HILIC × PGC) for the acquisition of neutral N-glycan standards from natural source. A total of thirty-one N-glycan compounds including seven pairs of isomers with the amounts from 0.7 to 230.0 nmol were isolated from ovalbumin as the model glycoconjugate. The purified N-glycans covered high-mannose, hybrid as well as multi-antenna asymmetric complex types. The purity of majority of these N-glycans was higher than 90%. Detailed structures of the N-glycan compounds were verified via negative ion tandem MS analysis, in which specific diagnostic ions including D- and E-ions were used to identify isomeric and terminal fine structures. The tag-free glycan compounds with well-defined structures, purity and amounts were finally assembled on the glass slide through neoglycolipid technology. Microarray binding assay of purified glycans with WGA lectin indicated the potential of the established strategy in glycan library expansion and functional glycomics.

Isomeric Separation of N-Glycopeptides Derived from Glycoproteins by Porous Graphitic Carbon (PGC) LC-MS/MS

Protein glycosylation is involved in many biological processes and physiological functions. Despite the recent advances in LC-MS/MS methodologies, the profiling of site-specific glycosylation is one of the major analytical challenges of glycoprotein analysis. Herein, we report that the separation of glycopeptide isomers on porous graphitic carbon (PGC)-LC was significantly improved by elevating the separation temperature under basic mobile phases. These findings permitted the isomeric separation of glycopeptides resulting from highly specific enzymatic digestions. The selectivity for different glycan types was studied using bovine fetuin, asialofetuin, IgG, ribonuclease B, and alpha-1 acid glycoprotein (AGP) by PGC-LC-MS. Comprehensive structural isomeric separation of glycopeptides was observed by high-resolution MS and confirmed by MS/MS. The specific structures of the glycopeptide isomers were identified and confirmed through exoglycosidase digestions. Glycosylation analysis of human AGP revealed the potential use of PGC-LC-MS for extensive glycoprotein analysis for biomarker discovery. This newly developed separation technique was shown as a reproducible and useful analytical method to study site-specific isomeric glycosylation.

Preparation of Complex Glycans From Natural Sources for Functional Study

One major barrier in glycoscience is the lack of diverse and biomedically relevant complex glycans in sufficient quantities for functional study. Complex glycans from natural sources serve as an important source of these glycans and an alternative to challenging chemoenzymatic synthesis. This review discusses preparation of complex glycans from several classes of glycoconjugates using both enzymatic and chemical release approaches. Novel technologies have been developed to advance the large-scale preparation of complex glycans from natural sources. We also highlight recent approaches and methods developed in functional and fluorescent tagging and high-performance liquid chromatography (HPLC) isolation of released glycans.

Quantitative Analysis of the Positional Distribution of Hydroxyproline in Collagenous Gly-Xaa-Yaa Sequences by LC-MS with Partial Acid Hydrolysis and Precolumn Derivatization

Collagen is extensively modified by various enzymes, including prolyl hydroxylases. Pro residues at the Yaa position of repeating Gly-Xaa-Yaa amino acid sequences are mostly hydroxylated to 4-hydroxyproline (4Hyp), which is essential for the thermal stability of collagen triple helix. In contrast, Pro residues at the Xaa position are rarely modified to 3Hyp and 4Hyp, the biological function of which is poorly understood. Overall estimation of prolyl hydroxylation with discrimination of the position (Xaa or Yaa) and hydroxylation type (4Hyp or 3Hyp) has been difficult to perform using traditional methods. In the present study, we developed a novel position-specific analytical method featuring LC-MS detection of collagenous Gly-containing dipeptides, including Gly-Pro, Pro-Gly, Gly-4Hyp, Gly-3Hyp, and 4Hyp-Gly, after partial acid hydrolysis and precolumn derivatization using 3-aminopyridyl-N-hydroxysuccinimidyl carbamate (APDS). We performed acid hydrolysis at 55 °C with HCl/trifluoroacetic acid/water (2:1:1, v/v) to avoid peptide inversion and imbalanced peptide generation observed for collagenous model peptides. The positional distribution of Pro, 4Hyp, and 3Hyp can be calculated from the relative concentrations of the APDS-derivatized dipeptides, and in combination with amino acid analysis, we can determine their absolute contents at the Xaa and Yaa positions. Bovine type I, III, and V collagens were analyzed by the established method, and the amount of 4Hyp was higher than that of 3Hyp at the Xaa position in type I and III collagens. In addition, we clearly showed that collagen extracted from earthworm cuticles has an extremely high content of Xaa position 4Hyp, reaching over 10% of the total amino acids.

Direct formation and isolation of unprotected α-and β-d-ribopyranosyl urea, α-and β-d-ribofuranosyl urea, and a ribosyl-1,2-cyclic carbamate in carbohydrate melts

Solvent-free melts of unprotected d-ribose and urea generated mainly C₁- substituted ribosyl products. The remarkable resolving power of a graphitised-carbon HPLC column allowed products of the reaction formed over a range of heating times and temperatures to be monitored. Heating an uncatalysed mixture of d-ribose and urea at temperatures between 75 °C and 90 °C resulted in complex mixtures of compounds; after 19 h heating at 90 °C, up to ten components could be resolved. At shorter heating times and lower temperatures, the composition and distribution of products varied. By manipulation of the reaction time and temperature, and with the addition of an acid catalyst, it was possible to optimise the yields of selected products. Thus, the acid-catalysed reaction after 1-2 h at 80 °C gave optimal yields of α- and β-d-ribopyranosyl urea, whereas the uncatalysed reaction after 22 h at 75-78 °C in addition produced significant amounts of α-d-ribofuranosyl-1,2- cyclic carbamate [glyco-1,2-oxazolidin-2-one] plus the α- and β-ribofuranosyl ureas. The five compounds were isolated and characterised, demonstrating the significant advantages of this approach; its simplicity, and the ability to produce multiple compounds of biological interest in a single step. LC/MS was used to identify tentatively several other components of the reaction mixture. The unprotected title compounds were prepared, isolated and characterised with water as the only solvent.

Development of ion pairing LC-MS/MS method for itaconate and cis-aconitate in cell extract and cell media

Accumulation of Immune Responsive Gene 1(IRG1) in macrophage induced by lipopolysaccharide (LPS) and interferon gamma (IFN-γ) leads to production of itaconate by decarboxylation of cis-aconitate. The biology associated with IRG1 and itaconate is not fully understood. A rapid and sensitive method for measurement of itaconate will benefit the study of IRG1 biology. Multiple HPLC and derivatization methods were tested. An ion pairing LC-MS/MS method using tributylamine/formic acid as ion pairing agents and a Hypercarb^TM guard column we proposed demonstrated better peak shape and better sensitivity for itaconate. The current protocol allows baseline separation of itaconate, citraconate, and cis-aconitate without derivatization and direct analysis of analytes in 80% methanol/water solution to avoid the dry-down step. It provides the limit of quantitation (LOQ) of 30 pg itaconate on column with a 4.5-minute run time. This method is validated for measurement of itaconate and cis-aconitate in RAW264.7 cell extract and cell media in a 96-well plate format. We applied this method to successfully measure the increase of itaconate and the decrease of cis-aconitate in RAW cell extract and cell media after LPS/IFN-γ treatment.