Automating mass spectrometry-based quantitative glycomics using aminoxy tandem mass tag reagents with SimGlycan

Coupling an ion chromatography to high resolution mass spectrometry (IC-MS) for the discovery of potentially prebiotic oligosaccharides in Chardonnay grape marc

Oligosaccharides are carbohydrates made of three to twenty monosaccharide units linked through glycosidic bonds. Emerging research into the potential prebiotic activity of oligosaccharides is creating opportunities to use industrial byproducts as value-added products. Grape marc is a residue left after winemaking and has been shown to provide health benefits to humans. In this study, we analyzed the oligosaccharides in Chardonnay grape marc by utilizing a hyphenated platform in which an ion chromatography (IC) system is coupled to an Orbitrap mass spectrometer (MS). With this platform, we obtained a structural library including 32 oligosaccharides with unique compositions of monosaccharides and 61 oligosaccharide structures. Notably, the ion chromatographic separation provided resolution of charged isomers while maintaining separation capacity for small, neutral oligosaccharides. High-quality tandem MS also facilitated the identification of oligosaccharides with structural modifications including methylation and the presence of sugar alditols and hexuronic acids. The data acquired by the IC-MS system were also compared with previously published LC-MS data. We found that these two platforms are largely complementary and, in combination, provide a more comprehensive characterization of oligosaccharides than either platform achieves alone.

Toolbox Accelerating Glycomics (TAG): Improving Large-Scale Serum Glycomics and Refinement to Identify SALSA-Modified and Rare Glycans

Glycans are involved in many fundamental cellular processes such as growth, differentiation, and morphogenesis. However, their broad structural diversity makes analysis difficult. Glycomics via mass spectrometry has focused on the composition of glycans, but informatics analysis has not kept pace with the development of instrumentation and measurement techniques. We developed Toolbox Accelerating Glycomics (TAG), in which glycans can be added manually to the glycan list that can be freely designed with labels and sialic acid modifications, and fast processing is possible. In the present work, we improved TAG for large-scale analysis such as cohort analysis of serum samples. The sialic acid linkage-specific alkylamidation (SALSA) method converts differences in linkages such as α2,3- and α2,6-linkages of sialic acids into differences in mass. Glycans modified by SALSA and several structures discovered in recent years were added to the glycan list. A routine to generate calibration curves has been implemented to explore quantitation. These improvements are based on redefinitions of residues and glycans in the TAG List to incorporate information on glycans that could not be attributed because it was not assumed in the previous version of TAG. These functions were verified through analysis of purchased sera and 74 spectra with linearity at the level of R2 > 0.8 with 81 estimated glycan structures obtained including some candidate of rare glycans such as those with the N,N’-diacetyllactosediamine structure, suggesting they can be applied to large-scale analyses.

A Reciprocal Best-hit Approach to Characterize Isomeric N-Glycans Using Tandem Mass Spectrometry

Glycosylation is a post-translational modification involved in many important biological functions. The aberrant alteration of glycan structure is implicit with malfunction of cells and possess potential significance in medical diagnosis of complex diseases such as cancer. Liquid chromatography tandem mass spectrometry (LC-MS/MS) has been commonly applied to the analysis of complex glycomic samples. However, the characterization of isomeric glycans from their MS/MS spectra in complex biological samples remains challenging. In this paper, we present a novel reciprocal best-hit glycan-spectrum matching (RB-GSM) approach toward characterizing N-glycans. In this method, the MS/MS spectra in the input data set are evaluated against all glycans with the matched precursor mass using customized scoring functions, where a glycan-spectrum matching (GSM) is considered to be true if it is a reciprocal best-hit, that is, it receives the highest score among not only the GSMs between the respective spectrum and all matched glycans, but also the GSMs between the respective glycan and all matched MS/MS spectra in the input data set. We evaluated this RB-GSM approach on N-glycan identification using MS/MS spectra acquired from glycan standards as well as those released from the model glycoprotein fetuin, immunoglobulin G, and human serum samples, which showed the RB-GSM is capable of distinguishing isomeric glycans.

Dietary Fiber to Starch Ratio Affects Bovine Milk Oligosaccharide Profiles

Background

Bovine milk oligosaccharides (BMOs) have several demonstrated and hypothesized benefits including roles in cognitive development and antipathogenic activities, making them promising ingredients for infant formulas and nutraceutical applications. BMO extraction from bovine milk is challenged by low concentrations relative to nonbioactive simple sugars like lactose. BMO abundances are known to vary with a cow's lactation stage, breed, and parity, but these characteristics are difficult to modify in existing dairy herds. In contrast, diet modification is an accessible target, and is already known to influence milk yield, lipid content, protein levels, and monosaccharide compositions.

Objectives

To determine the impact of a low starch high fiber versus a high starch low fiber diet on overall BMO profiles and individual BMO abundances in Holstein dairy cattle.

Methods

Milk samples were collected from 59 midlactation Holsteins in a crossover study featuring dietary modification with either a low starch high fiber or high starch low fiber feed. BMO profiles were evaluated by nano-LC quadrupole time-of-flight tandem MS, and differences in BMO abundances between diets were evaluated using linear mixed effects modeling.

Results

A total of 19 BMOs were identified across the sample set, including 4 large fucosylated compounds. Seven BMOs were found to have significantly more positive percent changes in yield-adjusted abundance from the pre-experiment baseline period for milk samples collected during feeding with the low starch high fiber diet compared with the high starch low fiber diet.

Conclusions

Consuming the low starch high fiber diet promoted greater overall BMO production than the high starch low fiber diet in a population of midlactation Holsteins. Additionally, this study afforded the opportunity to investigate the impact of other factors potentially influencing BMO abundances, furthering understanding of how dairy herd management practices can positively impact milk composition and support the potential use of BMOs as functional ingredients.

Analysis of Viral Spike Protein N-Glycosylation Using Ultraviolet Photodissociation Mass Spectrometry

Characterization of protein glycosylation by tandem mass spectrometry remains challenging owing to the vast diversity of oligosaccharides bound to proteins, the variation in monosaccharide linkage patterns, and the lability of the linkage between the glycan and protein. Here, we have adapted an HCD-triggered-ultraviolet photodissociation (UVPD) approach for the simultaneous localization of glycosites and full characterization of both glycan compositions and intersaccharide linkages, the latter provided by extensive cross-ring cleavages enabled by UVPD. The method is applied to study glycan compositions based on analysis of glycopeptides from proteolytic digestion of recombinant human coronaviruse spike proteins from SARS-CoV-2 and HKU1. UVPD reveals unique intersaccharide linkage information and is leveraged to localize N-linked glycoforms with confidence.

GlycoHunter: An Open-Source Software for the Detection and Relative Quantification of INLIGHT-Labeled N-Linked Glycans

Glycans are responsible for many biological activities; however, their structures are incredibly diverse and complex, often rendering the field of glycomics unsolvable by a single analytical technique. The development of multiple chemical derivatization strategies and bioinformatic software is responsible for some of the greatest analytical gains in the field of glycomics. The INLIGHT strategy is a chemical derivatization technique using hydrazide chemistry to derivatize the reducing end of N-linked glycans and incorporates either a natural (NAT, ¹²C₆) or a stable-isotope label (SIL, ¹³C₆) to carry out relative quantification. Here we present GlycoHunter, a user-friendly software created in MATLAB that enables researchers to accurately and efficiently process MS1 glycomics data where a NAT and SIL pair is generated for relative quantification, including but not limited to, INLIGHT. GlycoHunter accepts the commonly used data file formats imzML and mzXML and effectively identifies all peak pairs associated with NAT- and SIL-labeled N-linked glycans using MS1 data. It also includes the ability to tailor the search parameters and export the results for further analysis using Skyline or Excel.

Structures and functions of invertebrate glycosylation

Glycosylation refers to the covalent attachment of sugar residues to a protein or lipid, and the biological importance of this modification has been widely recognized. While glycosylation in mammals is being extensively investigated, lower level animals such as invertebrates have not been adequately interrogated for their glycosylation. The rich diversity of invertebrate species, the increased database of sequenced invertebrate genomes and the time and cost efficiency of raising and experimenting on these species have enabled a handful of the species to become excellent model organisms, which have been successfully used as tools for probing various biologically interesting problems. Investigation on invertebrate glycosylation, especially on model organisms, not only expands the structural and functional knowledgebase, but also can facilitate deeper understanding on the biological functions of glycosylation in higher organisms. Here, we reviewed the research advances in invertebrate glycosylation, including N- and O-glycosylation, glycosphingolipids and glycosaminoglycans. The aspects of glycan biosynthesis, structures and functions are discussed, with a focus on the model organisms Drosophila and Caenorhabditis. Analytical strategies for the glycans and glycoconjugates are also summarized.

Towards a standardized bioinformatics infrastructure for N- and O-glycomics

The mass spectrometry (MS)-based analysis of free polysaccharides and glycans released from proteins, lipids and proteoglycans increasingly relies on databases and software. Here, we review progress in the bioinformatics analysis of protein-released N- and O-linked glycans (N- and O-glycomics) and propose an e-infrastructure to overcome current deficits in data and experimental transparency. This workflow enables the standardized submission of MS-based glycomics information into the public repository UniCarb-DR. It implements the MIRAGE (Minimum Requirement for A Glycomics Experiment) reporting guidelines, storage of unprocessed MS data in the GlycoPOST repository and glycan structure registration using the GlyTouCan registry, thereby supporting the development and extension of a glycan structure knowledgebase.

Profiling of aminoxyTMT-labeled bovine milk oligosaccharides reveals substantial variation in oligosaccharide abundance between dairy cattle breeds

Free milk oligosaccharides are bioactive molecules that function as prebiotics and prevent infections that commonly afflict developing infants. To date, few publications have examined the factors affecting bovine milk oligosaccharide production among cattle in the dairy industry. Here we have applied a high-throughput isobaric labeling technique to measure oligosaccharide abundances in milk collected from Danish Holstein-Friesian and Jersey dairy cattle by liquid chromatography-mass spectrometry. With a total of 634 milk samples, this collection represents the largest sample set used for milk oligosaccharide profiling in the current literature. This study is also the first to use isobaric labeling for the purpose of measuring free oligosaccharides in a real sample set. We have identified 13 oligosaccharides that vary significantly by breed, with most structures being more abundant in the milk of Jersey cattle. The abundances of several oligosaccharides were increased in second-parity cows, and correlations between the abundances of oligosaccharide pairs were identified, potentially indicating similarities in their synthetic pathways. Fucosylated oligosaccharide structures were widely identified among both breeds. Improving our understanding of oligosaccharide production will aid in developing strategies to recover these compounds from processing streams and may enable their use as a functional ingredient in foods for infants and adults.

Quantitative glycomics using liquid phase separations coupled to mass spectrometry

Post-translational modification of proteins by the attachment of glycans is governed by a variety of highly specific enzymes and is associated with fundamental impacts on the parent protein's physical, chemical and biological properties. The inherent connection between cellular physiology and specific glycosylation patterns has been shown to offer potential for diagnostic and prognostic monitoring of altered glycosylation in the disease state. Conversely, glycoprotein based biopharmaceuticals have emerged as dominant therapeutic strategies in the treatment of intricate diseases. Glycosylation present on these biopharmaceuticals represents a major critical quality attribute with impacts on both pharmacokinetics and pharmacodynamics. The structural variety of glycans, based upon their non-template driven assembly, poses a significant analytical challenge for both qualitative and quantitative analysis. Labile monosaccharide constituents, isomeric species and often low sample availability from biological sources necessitates meticulous sample handling, ultra-high-resolution analytical separation and sensitive detection techniques, respectively. In this article a critical review of analytical quantitation approaches using liquid phase separations coupled to mass spectrometry for released glycans of biopharmaceutical and biomedical significance is presented. Considerations associated with sample derivatisation strategies, ionisation, relative quantitation through isotopic as well as isobaric labelling, metabolic/enzymatic incorporation and targeted analysis are all thoroughly discussed.

Screening for biomarkers reflecting the progression of Babesia microti infection

Background

Babesiosis is caused by the invasion of erythrocytes by parasites of the Babesia spp. Babesia microti is one of the primary causative agents of human babesiosis. To better understand the status of the disease, discovering key biomarkers of the different infection stages is crucial.

Results

This study investigated B. microti infection in the mouse model from 0 to 270 days post-infection (dpi), using blood smears, PCR assays and ELISA. PCR assays showed a higher sensitivity when compared to microscopic examination. Specific IgG antibodies could be detected from 7 days to 270 dpi. Two-dimensional electrophoresis was combined with western blotting and mass spectrometric analysis to screen for specific reactive antigens during both the peak parasitaemia period (7 dpi) and IgG antibody response peak period (30 dpi) by the infected mice plasma. The 87 positive reactive proteins were identified and then expressed with the wheat germ cell-free system. Protein microarrays of all 87 targeted proteins were produced and hybridized with the serial plasma of infected mice model. Based on the antigen reaction profile during the infection procedure, 6 antigens were selected and expressed in Escherichia coli. Due to an early response to IgM, lower immunoreactivity levels of IgG after two months and higher immunoreactivity level IgG during nine months, four recombinant proteins were selected for further characterization, namely rBm2D97(CCF75281.1), rBm2D33(CCF74637.1), rBm2D41(CCF75408.1) and rBm7(CCF73510.1). The diagnostic efficacy of the four recombinant protein candidates was evaluated in a clinical setting using babesiosis patient plasma. The rBm2D33 showed the highest sensitivity with a positive rate of 62.5%. Additional characterization of the two candidate proteins using a mouse vaccination assay, demonstrated that rBm2D41 could reduce peak parasitaemia by 37.4%, indicating its efficacy in preventing severe babesiosis.

Conclusions

The detection technologies of microscopic examination, PCR assays and antibody tests showed different sensitivities and accuracy during the different stages of B. microti infection. Antibody detection has a unique significance for B. microti infection in the asymptomatic stages. Using immunoreactivity profiles, biomarkers for disease progression were identified and represent useful information for future the diagnosis and vaccine development for this serious disease of public health significance.

Electronic supplementary material

The online version of this article (10.1186/s13071-018-2951-0) contains supplementary material, which is available to authorized users.

Multiplexed bovine milk oligosaccharide analysis with aminoxy tandem mass tags

Milk oligosaccharides (OS) are a key factor that influences the infant gut microbial composition, and their importance in promoting healthy infant development and disease prevention is becoming increasingly apparent. Investigating the structures, properties, and sources of these compounds requires a host of complementary analytical techniques. Relative compound quantification by mass spectral analysis of isobarically labeled samples is a relatively new technique that has been used mainly in the proteomics field. Glycomics applications have so far focused on analysis of protein-linked glycans, while analysis of free milk OS has previously been conducted only on analytical standards. In this paper, we extend the use of isobaric glycan tags to the analysis of bovine milk OS by presenting a method for separation of labeled OS on a porous graphitized carbon liquid chromatographic column with subsequent analysis by quadrupole time-of-flight tandem mass spectrometry. Abundances for 15 OS extracted from mature bovine milk were measured, with replicate injections providing coefficients of variation below 15% for most OS. Isobaric labeling improved ionization efficiency for low-abundance, high-molecular weight fucosylated OS, which are known to exist in bovine milk but have been only sporadically reported in the literature. We compared the abundances of four fucosylated OS in milk from Holstein and Jersey cattle and found that three of the compounds were more abundant in Jersey milk, which is in general agreement with a previous study. This novel method represents an advancement in our ability to characterize milk OS and provides the advantages associated with isobaric labeling, including reduced instrumental analysis time and increased analyte ionization efficiency. This improved ability to measure differences in bioactive OS abundances in large datasets will facilitate exploration of OS from all food sources for the purpose of developing health-guiding products for infants, immune-compromised elderly, and the population at large.

Human disease glycomics: technology advances enabling protein glycosylation analysis - part 1

INTRODUCTION

Protein glycosylation is recognized as an important post-translational modification, with specific substructures having significant effects on protein folding, conformation, distribution, stability and activity. However, due to the structural complexity of glycans, elucidating glycan structure-function relationships is demanding. The fine detail of glycan structures attached to proteins (including sequence, branching, linkage and anomericity) is still best analysed after the glycans are released from the purified or mixture of glycoproteins (glycomics). The technologies currently available for glycomics are becoming streamlined and standardized and many features of protein glycosylation can now be determined using instruments available in most protein analytical laboratories. Areas covered: This review focuses on the current glycomics technologies being commonly used for the analysis of the microheterogeneity of monosaccharide composition, sequence, branching and linkage of released N- and O-linked glycans that enable the determination of precise glycan structural determinants presented on secreted proteins and on the surface of all cells. Expert commentary: Several emerging advances in these technologies enabling glycomics analysis are discussed. The technological and bioinformatics requirements to be able to accurately assign these precise glycan features at biological levels in a disease context are assessed.

Quantitative Glycomics: A Combined Analytical and Bioinformatics Approach

Glycosylation is one of the most common and essential protein modifications. Glycans conjugated to biomolecules modulate the function of such molecules through both direct recognition of glycan structures and indirect mechanisms that involve the control of protein turnover rates, stability, and conformation. The biological attributes of glycans in numerous biological processes and implications in a number of diseases highlight the necessity for comprehensive characterization of protein glycosylation. This chapter reviews cutting-edge methods and tools developed to facilitate quantitative glycomics. This chapter highlights the different methods employed for the release and purification of glycans from biological samples. The most effective labeling methods developed for sensitive quantitative glycomics are also described and discussed. The chromatographic approaches that have been used effectively in glycomics are also highlighted.

Analysis of Permethylated Glycan by Liquid Chromatography (LC) and Mass Spectrometry (MS)

The development of a reliable and high-throughput glycomic profiling strategy is in high demand due to the biological roles of glycans and their association with different diseases. Native analysis can be quite difficult because of the low ionization efficiency and microheterogeneity of glycans. In this chapter, the sample preparation protocols and LC-MS analysis of permethylated glycan strategies are introduced. Solid-phase permethylation is a fast, convenient, and high-yield method to stabilize sialic acid and improve glycan ionization efficiency and analysis in positive mode; this results in a more sensitive and reliable glycomic profiling strategy. Several modifications in the LC method are also mentioned in this chapter. Online purification simplifies sample preparation and reduces sample loss. Elevating the column temperature significantly improves the peak shape of permethylated glycans and results in isomeric separation. The identification and quantification of permethylated glycans can be achieved through high resolution MS and MS/MS experiments using a MRM method; both approaches are reliable, sensitive, and conducive to high-throughput glycomic studies.

Molecular labels for analysis of amines and diols by spray based ionization-mass spectrometry

A family of imidazolium and pyridinium salts was synthesized for the purpose of labeling amines and 1,2-diols for highly sensitivite analysis by mass spectrometry. The chosen mass labels are shown to serve as effective reporters when bound to particles functionalized with amines or 1,2-diols and the binding is reversible. The straightforward synthetic route allows analogous internal standards to be generated quickly. Solvents amenable to electrospray ionization facilitate the rapid liberation of imidazolium and pyridinium mass labels from particles by hydrolysis in aqueous acid, while the acetal bond remains stable in anhydrous or buffered aqueous solution. Detection of the labels is demonstrated at 1 nM and quantitation of mass labels released from particles is also demonstrated.

Quantitative profiling of glycans and glycopeptides: an informatics' perspective

Experimental techniques to identify and quantify glycan structures in a given sample are continuously improving. However, as they advance data analysis and annotation seems to become more complex. To address this issue, much progress has been made in developing software for interpretation of quantitative glycan profiles. Here, we focus on these informatics tools for high/ultra performance liquid chromatography (H/UPLC), mass spectrometry (MS), tandem mass spectrometry (MSⁿ) and combinations thereof. Software for biomarker discovery, pathway, genomic and disease analysis and a final note on some future prospects for glycoinformatics are also mentioned.

N-linked glycosite profiling and use of Skyline as a platform for characterization and relative quantification of glycans in differentiating xylem of Populus trichocarpa

Our greater understanding of the importance of N-linked glycosylation in biological systems has spawned the field of glycomics and development of analytical tools to address the many challenges regarding our ability to characterize and quantify this complex and important modification as it relates to biological function. One of the unmet needs of the field remains a systematic method for characterization of glycans in new biological systems. This study presents a novel workflow for identification of glycans using Individuality Normalization when Labeling with Isotopic Glycan Hydrazide Tags (INLIGHT™) strategy developed in our lab. This consists of monoisotopic mass extraction followed by peak pair identification of tagged glycans from a theoretical library using an in-house program. Identification and relative quantification could then be performed using the freely available bioinformatics tool Skyline. These studies were performed in the biological context of studying the N-linked glycome of differentiating xylem of the poplar tree, a widely studied model woody plant, particularly with respect to understanding lignin biosynthesis during wood formation. Through our workflow, we were able to identify 502 glycosylated proteins including 12 monolignol enzymes and 1 peroxidase (PO) through deamidation glycosite analysis. Finally, our novel semi-automated workflow allowed for rapid identification of 27 glycans by intact mass and by NAT/SIL peak pairing from a library containing 1573 potential glycans, eliminating the need for extensive manual analysis. Implementing Skyline for relative glycan quantification allowed for improved accuracy and precision of quantitative measurements over current processing tools which we attribute to superior algorithms correction for baseline variation and MS1 peak filtering. Graphical abstract Workflow for FANGS-INLIGHT glycosite profiling of plant xylem and monolignol proteins followed by INLIGHT tagging with semi-automated identification of glycans by light-heavy peak pairs. Finally, manual validation and relative quantification was performed in Skyline.

Maturing Glycoproteomics Technologies Provide Unique Structural Insights into the N-glycoproteome and Its Regulation in Health and Disease

The glycoproteome remains severely understudied because of significant analytical challenges associated with glycoproteomics, the system-wide analysis of intact glycopeptides. This review introduces important structural aspects of protein N-glycosylation and summarizes the latest technological developments and applications in LC-MS/MS-based qualitative and quantitative N-glycoproteomics. These maturing technologies provide unique structural insights into the N-glycoproteome and its synthesis and regulation by complementing existing methods in glycoscience. Modern glycoproteomics is now sufficiently mature to initiate efforts to capture the molecular complexity displayed by the N-glycoproteome, opening exciting opportunities to increase our understanding of the functional roles of protein N-glycosylation in human health and disease.