Creating a Mass Spectral Reference Library for Oligosaccharides in Human Milk

MilkOligoThesaurus, a dataset of mammalian milk oligosaccharide synonyms

There is a growing interest in milk oligosaccharides (MOs) because of their numerous benefits for newborns' and long-term health. A large number of MO structures have been identified in mammalian milk. Mostly described in human milk, the oligosaccharide richness, although less broad, has also been reported for a wide range of mammalian species. The structure of MOs is particularly difficult to report as it results from the combination of 5 monosaccharides linked by various glycosidic bonds forming structurally diverse and complex matrices of linear and branched oligosaccharides. Exploring the literature and extracting relevant information on MO diversity within or across species appears promising to elucidate structure-function role of MOs. Currently, given the complexity of these molecules, the main issues in exploring literature to extract relevant information on MO diversity within or across species relate to the heterogeneity in the way authors refer to these molecules. Herein, we provide a thesaurus (MilkOligoThesaurus) including the names and synonyms of MOs collected from key selected articles on mammalian milk analyses. MilkOligoThesaurus gathers the names of the MOs with a complete description of their monosaccharide composition and structures. When available, each unique MO molecule is linked to its ID from the NCBI PubChem and ChEBI databases. MilkOligoThesaurus is provided in a tabular format. It gathers 245 unique oligosaccharide structures described by 22 features (columns) including the name of the molecule, its abbreviation, the chemical database IDs if available, the monosaccharide composition, chemical information (molecular formula, monoisotopic mass), synonyms, its formula in condensed form, and in abbreviated condensed form, the abbreviated systematic name, the systematic name, the isomer group, and scientific article sources. MilkOligoThesaurus is also provided in the SKOS (Simple Knowledge Organization System) format. This thesaurus is a valuable resource gathering MO naming variations that are not found elsewhere for (i) Text and Data Mining to enable automatic annotation and rapid extraction of milk oligosaccharide data from scientific papers; (ii) biology researchers aiming to search for or decipher the structure of milk oligosaccharides based on any of their names, abbreviations or monosaccharide compositions and linkages.

Unlocking the mysteries of milk oligosaccharides: Structure, metabolism, and function

Milk oligosaccharides (MOs), complex carbohydrates prevalent in human breast milk, play a vital role in infant nutrition. Serving as prebiotics, they inhibit pathogen adherence, modulate the immune system, and support newborn brain development. Notably, MOs demonstrate significant variations in concentration and composition, both across different species and within the same species. These characteristics of MOs lead to several compelling questions: (i) What distinct beneficial functions do MOs offer and how do the functions vary along with their structural differences? (ii) In what ways do MOs in human milk differ from those in other mammals, and what factors drive these unique profiles? (iii) What are the emerging applications of MOs, particularly in the context of their incorporation into infant formula? This review delves into the structural characteristics, quantification methods, and species-specific concentration differences of MOs. It highlights the critical role of human MOs in infant growth and their potential applications, providing substantial evidence to enhance infant health and development.

Simulated digestions of free oligosaccharides and mucin-type O-glycans reveal a potential role for Clostridium perfringens

The development of a stable human gut microbiota occurs within the first year of life. Many open questions remain about how microfloral species are influenced by the composition of milk, in particular its content of human milk oligosaccharides (HMOs). The objective is to investigate the effect of the human HMO glycome on bacterial symbiosis and competition, based on the glycoside hydrolase (GH) enzyme activities known to be present in microbial species. We extracted from UniProt a list of all bacterial species catalysing glycoside hydrolase activities (EC 3.2.1.-), cross-referencing with the BRENDA database, and obtained a set of taxonomic lineages and CAZy family data. A set of 13 documented enzyme activities was selected and modelled within an enzyme simulator according to a method described previously in the context of biosynthesis. A diverse population of experimentally observed HMOs was fed to the simulator, and the enzymes matching specific bacterial species were recorded, based on their appearance of individual enzymes in the UniProt dataset. Pairs of bacterial species were identified that possessed complementary enzyme profiles enabling the digestion of the HMO glycome, from which potential symbioses could be inferred. Conversely, bacterial species having similar GH enzyme profiles were considered likely to be in competition for the same set of dietary HMOs within the gut of the newborn. We generated a set of putative biodegradative networks from the simulator output, which provides a visualisation of the ability of organisms to digest HMO and mucin-type O-glycans. B. bifidum, B. longum and C. perfringens species were predicted to have the most diverse GH activity and therefore to excel in their ability to digest these substrates. The expected cooperative role of Bifidobacteriales contrasts with the surprising capacities of the pathogen. These findings indicate that potential pathogens may associate in human gut based on their shared glycoside hydrolase digestive apparatus, and which, in the event of colonisation, might result in dysbiosis. The methods described can readily be adapted to other enzyme categories and species as well as being easily fine-tuneable if new degrading enzymes are identified and require inclusion in the model.

Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics

Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpreting unannotated spectra, we created a nearest neighbor suspect spectral library, consisting of 87,916 annotated MS/MS spectra derived from hundreds of millions of MS/MS spectra originating from published untargeted metabolomics experiments. Entries in this library, or "suspects," were derived from unannotated spectra that could be linked in a molecular network to an annotated spectrum. Annotations were propagated to unknowns based on structural relationships to reference molecules using MS/MS-based spectrum alignment. We demonstrate the broad relevance of the nearest neighbor suspect spectral library through representative examples of propagation-based annotation of acylcarnitines, bacterial and plant natural products, and drug metabolism. Our results also highlight how the library can help to better understand an Alzheimer's brain phenotype. The nearest neighbor suspect spectral library is openly available for download or for data analysis through the GNPS platform to help investigators hypothesize candidate structures for unknown MS/MS spectra in untargeted metabolomics data.

Inferring the Nominal Molecular Mass of an Analyte from Its Electron Ionization Mass Spectrum

The performance of three algorithms for predicting nominal molecular mass from an analyte's electron ionization mass spectrum is presented. The Peak Interpretation Method (PIM) attempts to quantify the likelihood that a molecular ion peak is contained in the mass spectrum, whereas the Simple Search Hitlist Method (SS-HM) and iterative Hybrid Search Hitlist Method (iHS-HM) leverage results from mass spectral library searching. These predictions can be employed in combination (recommended) or independently. The methods were tested on two sets of query mass spectra searched against libraries that did not contain the reference mass spectra of the same compounds: 19,074 spectra of various organic molecules searched against the NIST17 mass spectral library and 162 spectra of small molecule drugs searched against SWGDRUG version 3.3. Individually, each molecular mass prediction method had computed precisions (the fraction of positive predictions that were correct) of 91, 89, and 74%, respectively. The methods become more valuable when predictions are taken together. When all three predictions were identical, which occurred in 33% of the test cases, the predicted molecular mass was almost always correct (>99%).

Breast Milk Oligosaccharides Contain Immunomodulatory Glucuronic Acid and LacdiNAc

Breast milk is abundant with functionalized milk oligosaccharides (MOs) to nourish and protect the neonate. Yet we lack a comprehensive understanding of the repertoire and evolution of MOs across Mammalia. We report ∼400 MO-species associations (>100 novel structures) from milk glycomics of nine mostly understudied species: alpaca, beluga whale, black rhinoceros, bottlenose dolphin, impala, L'Hoest's monkey, pygmy hippopotamus, domestic sheep, and striped dolphin. This revealed the hitherto unknown existence of the LacdiNAc motif (GalNAcβ1-4GlcNAc) in MOs of all species except alpaca, sheep, and striped dolphin, indicating the widespread occurrence of this potentially antimicrobial motif in MOs. We also characterize glucuronic acid-containing MOs in the milk of impala, dolphins, sheep, and rhinoceros, previously only reported in cows. We demonstrate that these GlcA-MOs exhibit potent immunomodulatory effects. Our study extends the number of known MOs by >15%. Combined with >1900 curated MO-species associations, we characterize MO motif distributions, presenting an exhaustive overview of MO biodiversity.

An Overview of Sugar Nucleotide-Dependent Glycosyltransferases for Human Milk Oligosaccharide Synthesis

Human milk oligosaccharides (HMOs) have received increasing attention because of their special effects on infant health and commercial value as the new generation of core components in infant formula. Currently, large-scale production of HMOs is generally based on microbial synthesis using metabolically engineered cell factories. Introduction of the specific glycosyltransferases is essential for the construction of HMO-producing engineered strains in which the HMO-producing glycosyltransferases are generally sugar nucleotide-dependent. Four types of glycosyltransferases have been used for typical glycosylation reactions to synthesize HMOs. Soluble expression, substrate specificity, and regioselectivity are common concerns of these glycosyltransferases in practical applications. Screening of specific glycosyltransferases is an important research topic to solve these problems. Molecular modification has also been performed to enhance the catalytic activity of various HMO-producing glycosyltransferases and to improve the substrate specificity and regioselectivity. In this article, various sugar nucleotide-dependent glycosyltransferases for HMO synthesis were overviewed, common concerns of these glycosyltransferases were described, and the future perspectives of glycosyltransferase-related studies were provided.

Human Milk Oligosaccharide Profile across Lactation Stages in Israeli Women-A Prospective Observational Study

Human milk oligosaccharides (HMOs) stimulate the growth of gut commensals, prevent the adhesion of enteropathogens and modulate host immunity. The major factors influencing variations in the HMO profile are polymorphisms in the secretor (Se) or Lewis (Le) gene, which affect the activity of the enzymes fucoslytransferase 2 and 3 (FUT2 and FUT3) that lead to the formation of four major fucosylated and non-fucosylated oligosaccharides (OS). This pilot study aimed to determine the HMO profile of Israeli breastfeeding mothers of 16 term and 4 preterm infants, from a single tertiary center in the Tel Aviv area. Fifty-two human milk samples were collected from 20 mothers at three-time points: colostrum, transitional milk and mature milk. The concentrations of nine HMOs were assessed using liquid chromatography coupled with mass spectra chromatograms. Fifty-five percent of the mothers were secretors and 45% were non-secretors. Infant sex affected HMO levels depending on the maternal secretor status. Secretor mothers to boys had higher levels of FUT2-dependent OS and higher levels of disialyllacto-N-tetraose in the milk of mothers to girls, whereas non-secretor mothers to girls had higher levels of 3'-sialyllactose. In addition, the season at which the human milk samples were obtained affected the levels of some HMOs, resulting in significantly lower levels in the summer. Our findings provide novel information on the irregularity in the HMO profile among Israeli lactating women and identify several factors contributing to this variability.

Determinants of human milk oligosaccharides profiles of participants in the STRONG kids 2 cohort

Introduction

Human milk oligosaccharides (HMOS) are indigestible carbohydrates that support infant development by establishing a healthy microbiota, preventing infectious diseases, and promoting immune and cognitive development. Individual HMOS have distinct functions based on their chemical structures. HMO profiles can vary largely among mothers, but the research on factors other than genetic background affecting HMO composition are limited.

Methods

In the present analysis, we examined the relationships between maternal characteristics and the HMO profiles of breastfeeding mothers (n = 392) in the STRONG kids 2 with the following demographic characteristics: average age: 30.8 y, 74.5% White, and 75.5% exclusively breastfeeding. Human milk samples were collected at 6 weeks postpartum and maternal information was obtained from self-reported surveys. Information on dietary intake changes since the participants have been breastfeeding was collected. HMO profiles were analyzed by high performance liquid chromatography coupled with mass spectrometry and secretor status was determined by the presence of four secretor markers [2′-fucosyllactose (2′-FL), LNFP I, LDFT, and TFLNH]. Spearmen correlation test was utilized to determine the relationships between individual HMOS and associations with maternal factors. Between-group differences in HMO relative abundances were examined with Kruskal-Wallis test.

Results

Among all participants, 71.9% were secretors and 28.1% were non-secretors. The relative abundances of all HMOS differed (p < 0.05) by secretor status, with the exception for 6′-SL and 3′-SL. Positive correlations were observed among HMOS with similar structures, such as the 1,2-fucosylated HMOS. The abundances of selected HMOS were associated with maternal body weight, pregnancy complications, and dietary characteristics. Based on pre-pregnancy BMI, in all mothers, relative abundance of 3′-SL was significantly higher in overweight mothers than obese mothers (p = 0.013). In milk produced by non-secretor mothers, LNPF I + III abundances were greater in overweight than normal weight mothers (p = 0.020). Several HMO abundances were found to be associated with Gestational diabetes mellitus (GDM). Variations of HMO abundances were also observed with dietary food intake. In all mothers, egg consumption was positively correlated with LNT + LNnT (R = 0.13; p = 0.012) and cheese intake was positively associated with 2′-FL (R = 0.10; p = 0.046) and S-LNnH II (R = 0.11; p = 0.026) abundances.

Discussion

HMO profiles were found to be associated with maternal characteristics and intake. Future research will investigate associations between HMOS and maternal and infant outcomes.

Efficient production of lacto-N-fucopentaose III in engineered Escherichia coli using α1,3-fucosyltransferase from Parabacteroides goldsteinii

Lacto-N-fucopentaose III (LNFP III) is a human milk oligosaccharide (HMO) with potential health benefits in infants, including in immune development and modulation of the intestinal environment. Low-cost fermentative production of various HMOs from lactose by engineered Escherichia coli has attracted attention, but few reports have investigated long-chain HMO production, such as of the pentasaccharide LNFP III. LNFP III is synthesized by α1,3-fucosyltransfer reaction to the glucosamine (GlcNAc) moiety in the lacto-N-neotetraose (LNnT) skeleton by α1,3-fucosyltransferase (α1,3-FucT). However, the known α1,3-FucTs also transfer fucose to the reducing terminal glucose moiety of LNnT or the starting material lactose, resulting in various byproducts. Here, we found a useful α1,3-FucT from Parabacteroides goldsteinii (PgsFucT), which is only reactive for GlcNAc in the N-acetyllactosamine (LacNAc) skeleton in vivo. On the basis of sequence alignment with a FucT of known structure, we also generated α1,3-FucT variants with altered reactivity for LacNAc or lactose. An E. coli strain heterologously expressing PgsFucT accumulated 3.84 g/L of LNFP III after 48 h of culture in a 3-L jar-fermenter. The amounts of various byproduct sugars were remarkably decreased compared with a strain expressing the previously characterized α1,3-fucT from Bacteroides fragilis.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018

This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.

Fact-based nutrition for infants and lactating mothers-The NUTRISHIELD study

Background

Human milk (HM) is the ideal source of nutrients for infants. Its composition is highly variable according to the infant's needs. When not enough own mother's milk (OMM) is available, the administration of pasteurized donor human milk (DHM) is considered a suitable alternative for preterm infants. This study protocol describes the NUTRISHIELD clinical study. The main objective of this study is to compare the % weight gain/month in preterm and term infants exclusively receiving either OMM or DHM. Other secondary aims comprise the evaluation of the influence of diet, lifestyle habits, psychological stress, and pasteurization on the milk composition, and how it modulates infant's growth, health, and development.

Methods and design

NUTRISHIELD is a prospective mother-infant birth cohort in the Spanish-Mediterranean area including three groups: preterm infants <32 weeks of gestation (i) exclusively receiving (i.e., >80% of total intake) OMM, and (ii) exclusively receiving DHM, and (iii) term infants exclusively receiving OMM, as well as their mothers. Biological samples and nutritional, clinical, and anthropometric characteristics are collected at six time points covering the period from birth and until six months of infant's age. The genotype, metabolome, and microbiota as well as the HM composition are characterized. Portable sensor prototypes for the analysis of HM and urine are benchmarked. Additionally, maternal psychosocial status is measured at the beginning of the study and at month six. Mother-infant postpartum bonding and parental stress are also examined. At six months, infant neurodevelopment scales are applied. Mother's concerns and attitudes to breastfeeding are registered through a specific questionnaire.

Discussion

NUTRISHIELD provides an in-depth longitudinal study of the mother-infant-microbiota triad combining multiple biological matrices, newly developed analytical methods, and ad-hoc designed sensor prototypes with a wide range of clinical outcome measures. Data obtained from this study will be used to train a machine-learning algorithm for providing dietary advice to lactating mothers and will be implemented in a user-friendly platform based on a combination of user-provided information and biomarker analysis. A better understanding of the factors affecting milk's composition, together with the health implications for infants plays an important role in developing improved strategies of nutraceutical management in infant care.

Clinical trial registration

https://register.clinicaltrials.gov, identifier: NCT05646940.

The critical role that spectral libraries play in capturing the metabolomics community knowledge

BACKGROUND

Spectral library searching is currently the most common approach for compound annotation in untargeted metabolomics. Spectral libraries applicable to liquid chromatography mass spectrometry have grown in size over the past decade to include hundreds of thousands to millions of mass spectra and tens of thousands of compounds, forming an essential knowledge base for the interpretation of metabolomics experiments.

AIM OF REVIEW

We describe existing spectral library resources, highlight different strategies for compiling spectral libraries, and discuss quality considerations that should be taken into account when interpreting spectral library searching results. Finally, we describe how spectral libraries are empowering the next generation of machine learning tools in computational metabolomics, and discuss several opportunities for using increasingly accessible large spectral libraries.

KEY SCIENTIFIC CONCEPTS OF REVIEW

This review focuses on the current state of spectral libraries for untargeted LC-MS/MS based metabolomics. We show how the number of entries in publicly accessible spectral libraries has increased more than 60-fold in the past eight years to aid molecular interpretation and we discuss how the role of spectral libraries in untargeted metabolomics will evolve in the near future.

In silico analysis of the human milk oligosaccharide glycome reveals key enzymes of their biosynthesis

Human milk oligosaccharides (HMOs) form the third most abundant component of human milk and are known to convey several benefits to the neonate, including protection from viral and bacterial pathogens, training of the immune system, and influencing the gut microbiome. As HMO production during lactation is driven by enzymes that are common to other glycosylation processes, we adapted a model of mucin-type GalNAc-linked glycosylation enzymes to act on free lactose. We identified a subset of 11 enzyme activities that can account for 206 of 226 distinct HMOs isolated from human milk and constructed a biosynthetic reaction network that identifies 5 new core HMO structures. A comparison of monosaccharide compositions demonstrated that the model was able to discriminate between two possible groups of intermediates between major subnetworks, and to assign possible structures to several previously uncharacterised HMOs. The effect of enzyme knockouts is presented, identifying β-1,4-galactosyltransferase and β-1,3-N-acetylglucosaminyltransferase as key enzyme activities involved in the generation of the observed HMO glycosylation patterns. The model also provides a synthesis chassis for the most common HMOs found in lactating mothers.

Structure and function of non-digestible carbohydrates in the gut microbiome

Together with proteins and fats, carbohydrates are one of the macronutrients in the human diet. Digestible carbohydrates, such as starch, starch-based products, sucrose, lactose, glucose and some sugar alcohols and unusual (and fairly rare) α-linked glucans, directly provide us with energy while other carbohydrates including high molecular weight polysaccharides, mainly from plant cell walls, provide us with dietary fibre. Carbohydrates which are efficiently digested in the small intestine are not available in appreciable quantities to act as substrates for gut bacteria. Some oligo- and polysaccharides, many of which are also dietary fibres, are resistant to digestion in the small intestines and enter the colon where they provide substrates for the complex bacterial ecosystem that resides there. This review will focus on these non-digestible carbohydrates (NDC) and examine their impact on the gut microbiota and their physiological impact. Of particular focus will be the potential of non-digestible carbohydrates to act as prebiotics, but the review will also evaluate direct effects of NDC on human cells and systems.

Quality Markers of Dendrobium officinale by “Oligosaccharide-Spectrum-Effect” Relationships

Dendrobium officinale Kimura et Migo has been used as a traditional Chinese medicine (TCM) and a functional food for thousands of years. Carbohydrate is one of the most important effective substances and indicative components in D. officinale. However, since the qualitative and quantitative analysis of polysaccharides in D. officinale remains a challenge and limitation, herein, an oligosaccharide-quality marker approach was newly developed for quality assessment of D. officinale by spectrum–effect relationships between high performance liquid chromatographic (HPLC) fingerprints and anti-inflammatory effects. The HPLC fingerprints of 48 batches of oligosaccharides from D. officinale (DOOS) were developed and analyzed with similarity analysis (SA) and hierarchical cluster analysis (HCA), and eight common peaks were identified. In vitro screening experiment indicated that DOOS potentially inhibited nitric oxide (NO) production and effectively reduced the release of inflammatory cytokines, such as TNF-α, IL-6, and IL-1β in RAW 264.7 cells, thereby reducing the inflammatory response of cells. Finally, the HPLC fingerprint of different batches of DOOS was combined with in vitro anti-inflammatory activity to assess the spectrum–effect relationships of DOOS by gray correlation analysis (GCA), in addition, the purified oligosaccharide components were identified and validated for NO inhibitory activity. Our results showed four DOOS (maltotetraose, maltopentaose, maltohexaose, and mannohexaose) were relevant to anti-inflammatory effects and could be as quality markers for the quality control of D. officinale. It suggests that the “oligosaccharide-spectrum-effect” relationships approach is a simple and reliable method for the quality control of herb medicines or nutritious foods.

Chemoenzymatic Synthesis of Asymmetrically Branched Human Milk Oligosaccharide Lacto-N-Hexaose

We herein reported the first chemoenzymatic synthesis of lacto-N-hexaose (LNH) by combining chemical carbohydrate synthesis with a selectively enzymatic glycosylation strategy. A tetrasaccharide core structure GlcNH₂β1→3 (GlcNAcβ1→6) Galβ1→4Glc, a key precursor for subsequent enzymatic glycan extension toward asymmetrically branched human milk oligosaccharides, was synthesized in this work. When the order of galactosyltransferase-catalyzed reactions was appropriately arranged, the β1,4-galactosyl and β1,3-galactosyl moieties could be sequentially assembled on the C6-arm and C3-arm of the tetrasaccharide, respectively, to achieve an efficient LNH synthesis. Lacto-N-neotetraose (LNnH), another common human milk oligosaccharide, was also synthesized en route to the target LNH.

Structural characterization of human milk oligosaccharides using ultrahigh performance liquid chromatography-helium charge transfer dissociation mass spectrometry

The combination of helium charge transfer dissociation mass spectrometry (He-CTD-MS) with ultrahigh performance liquid chromatography (UHPLC) is presented for the analysis of a complex mixture of acidic and neutral human milk oligosaccharides (HMOs). The research focuses on the identification of the monosaccharide sequence, the branching patterns, the sialylation/fucosylation arrangements, and the differentiation of isomeric oligosaccharides in the mixture. Initial studies first optimized the conditions for the UHPLC separation and the He-CTD-MS conditions. Results demonstrate that He-CTD is compatible with UHPLC timescales and provides unambiguous glycosidic and cross-ring cleavages from both the reducing and the nonreducing ends, which is not typically possible using collision-induced dissociation. He-CTD produces informative fragments, including 0,3An and 0,4An ions, which have been observed with electron transfer dissociation, electron detachment dissociation, and ultraviolet photodissociation (UVPD) and are crucial for differentiating the α-2,3- versus α-2,6-linked sialic acid (Neu5Ac) residues present among sialyllacto-N-tetraose HMOs. In addition to the linkage positions, He-CTD is able to differentiate structural isomers for both sialyllacto-N-tetraoses and lacto-N-fucopentaoses structures by providing unique, unambiguous cross-ring cleavages of types 0,2An, 0,2Xn, and 1,5An while preserving most of the labile Neu5Ac and fucose groups.

Mass Spectrometry-Based Techniques to Elucidate the Sugar Code

Cells encode information in the sequence of biopolymers, such as nucleic acids, proteins, and glycans. Although glycans are essential to all living organisms, surprisingly little is known about the "sugar code" and the biological roles of these molecules. The reason glycobiology lags behind its counterparts dealing with nucleic acids and proteins lies in the complexity of carbohydrate structures, which renders their analysis extremely challenging. Building blocks that may differ only in the configuration of a single stereocenter, combined with the vast possibilities to connect monosaccharide units, lead to an immense variety of isomers, which poses a formidable challenge to conventional mass spectrometry. In recent years, however, a combination of innovative ion activation methods, commercialization of ion mobility-mass spectrometry, progress in gas-phase ion spectroscopy, and advances in computational chemistry have led to a revolution in mass spectrometry-based glycan analysis. The present review focuses on the above techniques that expanded the traditional glycomics toolkit and provided spectacular insight into the structure of these fascinating biomolecules. To emphasize the specific challenges associated with them, major classes of mammalian glycans are discussed in separate sections. By doing so, we aim to put the spotlight on the most important element of glycobiology: the glycans themselves.

Longitudinal Profiles of Dietary and Microbial Metabolites in Formula- and Breastfed Infants

The early-life metabolome of the intestinal tract is dynamically influenced by colonization of gut microbiota which in turn is affected by nutrition, i.e. breast milk or formula. A detailed examination of fecal metabolites was performed to investigate the effect of probiotics in formula compared to control formula and breast milk within the first months of life in healthy neonates. A broad metabolomics approach was conceptualized to describe fecal polar and semi-polar metabolites affected by feeding type within the first year of life. Fecal metabolomes were clearly distinct between formula- and breastfed infants, mainly originating from diet and microbial metabolism. Unsaturated fatty acids and human milk oligosaccharides were increased in breastfed, whereas Maillard products were found in feces of formula-fed children. Altered microbial metabolism was represented by bile acids and aromatic amino acid metabolites. Elevated levels of sulfated bile acids were detected in stool samples of breastfed infants, whereas secondary bile acids were increased in formula-fed infants. Microbial co-metabolism was supported by significant correlation between chenodeoxycholic or lithocholic acid and members of Clostridia. Fecal metabolites showed strong inter- and intra-individual behavior with features uniquely present in certain infants and at specific time points. Nevertheless, metabolite profiles converged at the end of the first year, coinciding with solid food introduction.

Creation and filtering of a recurrent spectral library of CHO cell metabolites and media components

This paper reports the first implementation of a new type of mass spectral library for the analysis of Chinese hamster ovary (CHO) cell metabolites that allows users to quickly identify most compounds in any complex metabolite sample. We also describe an annotation methodology developed to filter out artifacts and low‐quality spectra from recurrent unidentified spectra of metabolites. CHO cells are commonly used to produce biological therapeutics. Metabolic profiles of CHO cells and media can be used to monitor process variability and look for markers that discriminate between batches of product. We have created a comprehensive library of both identified and unidentified metabolites derived from CHO cells that can be used in conjunction with tandem mass spectrometry to identify metabolites. In addition, we present a workflow that can be used for assigning confidence to a NIST MS/MS Library search match based on prior probability of general utility. The goal of our work is to annotate and identify (when possible), all liquid chromatography‐mass spectrometry generated metabolite ions as well as create automatable library building and identification pipelines for use by others in the field.

Recent advances in the analysis of human milk oligosaccharides by liquid phase separation methods

Human milk is a complex, dynamically changing biological fluid, which contains a large amount of non-conjugated carbohydrates, referred to as human milk oligosaccharides (HMOs). These HMOs are very important for the infants as they play important roles in the formation of the gut microbiome, the immune system and support brain development. HMOs show highly complex structural diversity due to numerous linkage possibilities of the building monosaccharides. In order to elucidate their structure-function relationship and to develop more effective infant formulas, cutting-edge analytical technologies are in great demand. In this paper, we review the current strategies for HMO analysis based on liquid phase separation methods. High performance liquid chromatography, capillary electrophoresis and their hyphenation with mass spectrometry are critically reviewed, emphasizing their advantages and disadvantages from practical point of views. Recent advances of the methods are categorized according to their application fields.

Insights into Bioinformatic Applications for Glycosylation: Instigating an Awakening towards Applying Glycoinformatic Resources for Cancer Diagnosis and Therapy

Glycosylation plays a crucial role in various diseases and their etiology. This has led to a clear understanding on the functions of carbohydrates in cell communication, which eventually will result in novel therapeutic approaches for treatment of various disease. Glycomics has now become one among the top ten technologies that will change the future. The direct implication of glycosylation as a hallmark of cancer and for cancer therapy is well established. As in proteomics, where bioinformatics tools have led to revolutionary achievements, bioinformatics resources for glycosylation have improved its practical implication. Bioinformatics tools, algorithms and databases are a mandatory requirement to manage and successfully analyze large amount of glycobiological data generated from glycosylation studies. This review consolidates all the available tools and their applications in glycosylation research. The achievements made through the use of bioinformatics into glycosylation studies are also presented. The importance of glycosylation in cancer diagnosis and therapy is discussed and the gap in the application of widely available glyco-informatic tools for cancer research is highlighted. This review is expected to bring an awakening amongst glyco-informaticians as well as cancer biologists to bridge this gap, to exploit the available glyco-informatic tools for cancer.

Increasing the Coverage of a Mass Spectral Library of Milk Oligosaccharides Using a Hybrid-Search-Based Bootstrapping Method and Milks from a Wide Variety of Mammals

This study significantly expands both the scope and method of identification for construction of a previously reported tandem mass spectral library of 74 human milk oligosaccharides (HMOs) derived from results of combined LC-MS/MS experiments and comprehensive structural analysis of HMOs. In the present work, a hybrid search "bootstrap" identification method was employed that substantially broadens the coverage of milk oligosaccharides and thereby increases utility use of a spectrum library-based method for the rapid tentative identification of all distinguishable glycans in milk. This involved hybrid searching of the previous library, which was itself constructed using the hybrid search of oligosaccharide spectra in the NIST 17 Tandem MS Library. The general approach appears applicable to library construction of other classes of compounds. The coverage of oligosaccharides was significantly extended using milks from a variety of mammals, including bovine, Asian buffalo, African lion, and goat. This new method led to the identification of another 145 oligosaccharides, including an additional 80 HMOs from reanalysis of human milk. The newly identified compounds were added to a freely available mass spectral reference database of 219 milk oligosaccharides. We also provide suggestions to overcome several limitations and pitfalls in the interpretation of spectra of unknown oligosaccharides.

Glycomics and glycoproteomics of viruses: Mass spectrometry applications and insights toward structure-function relationships

The advancement of viral glycomics has paralleled that of the mass spectrometry glycomics toolbox. In some regard the glycoproteins studied have provided the impetus for this advancement. Viral proteins are often highly glycosylated, especially those targeted by the host immune system. Glycosylation tends to be dynamic over time as viruses propagate in host populations leading to increased number of and/or "movement" of glycosylation sites in response to the immune system and other pressures. This relationship can lead to highly glycosylated, difficult to analyze glycoproteins that challenge the capabilities of modern mass spectrometry. In this review, we briefly discuss five general areas where glycosylation is important in the viral niche and how mass spectrometry has been used to reveal key information regarding structure-function relationships between viral glycoproteins and host cells. We describe the recent past and current glycomics toolbox used in these analyses and give examples of how the requirement to analyze these complex glycoproteins has provided the incentive for some advances seen in glycomics mass spectrometry. A general overview of viral glycomics, special cases, mass spectrometry methods and work-flows, informatics and complementary chemical techniques currently used are discussed. © 2020 The Authors. Mass Spectrometry Reviews published by John Wiley & Sons Ltd. Mass Spec Rev.

Mass spectral similarity mapping applied to fentanyl analogs

This manuscript outlines a straight-forward procedure for generating a map of similarity between spectra of a set. When applied to a reference set of spectra for Type I fentanyl analogs (molecules differing from fentanyl by a single modification), the map illuminates clustering that is applicable to automated structure assignment of unidentified molecules. An open-source software implementation that generates mass spectral similarity mappings of unknowns against a library of Type I fentanyl analog spectra is available at http://github.com/asm3-nist/FentanylClassifier.

New strategies for profiling and characterization of human milk oligosaccharides

Human breast milk is an incredibly rich and complex biofluid composed of proteins, lipids and complex carbohydrates, including a diverse repertoire of free human milk oligosaccharides (HMOs). Strikingly, HMOs are not digested by the infant but function as prebiotics for bacterial strains associated with numerous benefits. Considering the broad variety of beneficial effects of HMOs, and the vast number of factors that affect breast milk composition, the analysis of HMO diversity and complexity is of utmost relevance. Using human milk samples from a cohort of Bangladeshi mothers participating in a study on malnutrition and stunting in children, we have characterized breast milk oligosaccharide composition by means of permethylation followed by liquid chromatography coupled with high-resolution tandem mass spectrometry (LC-MS/MS) analysis. This approach identified over 100 different glycoforms and showed a wide diversity of milk composition, with a predominance of fucosylated and sialylated HMOs over nonmodified HMOs. We observed that these samples contain on average 80 HMOs, with the highest permethylated masses detected being >5000 mass units. Here we report an easily implemented method developed for the separation, characterization and relative quantitation of large arrays of HMOs, including higher molecular weight sialylated HMOs. Our ultimate goal is to create a simple, high-throughput method, which can be used for full characterization of sialylated and/or fucosylated HMOs. These results demonstrate how current analytical techniques can be applied to characterize human milk composition, providing new tools to help the scientific community shed new light on the impact of HMOs during infant development.

Neutral Human Milk Oligosaccharides Are Associated with Multiple Fixed and Modifiable Maternal and Infant Characteristics

We aimed to identify if maternal and infant factors were associated with neutral human milk oligosaccharides (HMOs) variability and examined the associations between HMOs concentration and infant growth and disease status in healthy Chinese mothers over a 6-month lactation period. We recruited mothers and their full-term infants as our subjects. At 1–5 days, 8–14 days, 4 weeks, and 6 months postpartum, all participants were interviewed to collect breast milk samples, obtain follow-up data and measure infant length and weight at their local hospital. A total of 23 neutral HMOs were analyzed by high performance liquid chromatography (HPLC)- mass spectrometer (MS). Secretor and Lewis phenotype were determined by the concentration of 2′-fucosyllactose (2′-FL) and Lacto-N-fucopentaose (LNFP)-II. The associations between maternal and infant factors with HMOs concentrations were investigated. A total of 464 human breast milk samples were collected from 116 mothers at four different time points. In total, 76.7% mothers were found to be Secretor and Lewis positive phenotype (Se+Le+), 17.2% were Se-Le+, 4.3% were Se+Le-, and 1.7% were Se-Le-. Several individual HMOs, including 2′-FL, Lactodifucotetraose (LDFT), LNFP-I were determined by Secretor phenotype. Most individual HMOs decreased at the later stage of lactation, except 3′-FL. We suggest that Secretor phenotype and lactation stage could influence most of the neutral HMOs. Concentrations of specific HMOs may be associated with maternal age, allergic history, pre-pregnancy body mass index (BMI), parity, delivery mode, infant gestational age and gender.

Chemical Synthesis of Human Milk Oligosaccharides: Lacto-N-hexaose Galβ1→3GlcNAcβ1→3 [Galβ1→4GlcNAcβ1→6] Galβ1→4Glc

The first synthesis of lacto-N-hexaose (LNH) has been completed using a convergent strategy. The donor-acceptor protecting-leaving group combinations were found to be of paramount significance for achieving successful glycosylations and minimizing side reactions. Lacto-N-tetraose, another common human milk oligosaccharide, was also obtained en route to the target LNH.

The chemical synthesis of human milk oligosaccharides: Lacto-N-tetraose (Galβ1→3GlcNAcβ1→3Galβ1→4Glc)

The total chemical synthesis of lacto-N-tetraose (LNT) has been completed using both convergent and linear strategies. Similarly to that of our previous HMO syntheses, the donor-acceptor protecting-leaving group combinations were found to be of paramount significance to achieving successful glycosylations and minimizing side reactions.

The chemical synthesis of human milk oligosaccharides: Lacto-N-neotetraose (Galβ1→4GlcNAcβ1→3Galβ1→4Glc)

The discovery of innovative methods that offer new capabilities for obtaining individual oligosaccharides from human milk will help to improve understanding their roles and boost practical applications. The total chemical synthesis of lacto-N-neotetraose (LNnT) has been completed using both linear and convergent strategies. The donor and acceptor protecting and leaving group combinations were found to be of paramount significance to successful couplings.

glypy: An Open Source Glycoinformatics Library

Glycoinformatics is a critical resource for the study of glycobiology, and glycobiology is a necessary component for understanding the complex interface between intra- and extracellular spaces. Despite this, there is limited software available to scientists studying these topics, requiring each to create fundamental data structures and representations anew for each of their applications. This leads to poor uptake of standardization and loss of focus on the real problems. We present glypy, a library written in Python for reading, writing, manipulating, and transforming glycans at several levels of precision. In addition to understanding several common formats for textual representation of glycans, the library also provides application programming interfaces (APIs) for major community databases, including GlyTouCan and UnicarbKB. The library is freely available under the Apache 2 common license with source code available at https://github.com/mobiusklein/ and documentation at https://glypy.readthedocs.io/ .

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.

Fucosylated Human Milk Oligosaccharides and N-Glycans in the Milk of Chinese Mothers Regulate the Gut Microbiome of Their Breast-Fed Infants during Different Lactation Stages

Human milk glycans provide a broad range of carbon sources for gut microbes in infants. Levels of protein glycosylation in human milk vary during lactation and may also be affected by the stages of gestation and lactation and by the secretor status of the mother. This was the first study to evaluate systematically dynamic changes in human milk oligosaccharides and fucosylated N-glycans in the milk of Chinese mothers with different secretor statuses during 6 months of lactation. Given the unique single nucleotide polymorphism site (rs1047781, A385T) on the fucosyltransferase 2 gene among Chinese populations, our report provides a specific insight into the milk glycobiome of Chinese mothers, which may exert effects on the gut microbiota of infants that differ from findings from other study cohorts.

The milk glycobiome has a significant impact on the gut microbiota of infants, which plays a pivotal role in health and development. Fucosylated human milk oligosaccharides (HMOs) and N-glycans on milk proteins are beneficial for the development of healthy gut microbiota, and the fucosylation levels of these glycans can be affected by the maternal fucosyltransferase 2 gene (FUT2). Here, we present results of longitudinal research on paired milk and stool samples from 56 Chinese mothers (CMs) and their breast-fed children. Changes of HMOs and fucosylated N-glycans in milk of CMs at different lactation stages were detected, which allowed characterization of the major differences in milk glycans and consequential effects on the gut microbiome of infants according to maternal FUT2 status. Significant differences in the abundance of total and fucosylated HMOs between secretor and nonsecretor CMs were noted, especially during early lactation. Despite a tendency toward decreasing milk protein concentrations, the fucosylation levels of milk N-glycans increased during late lactation. The changes in the levels of fucosylated HMOs and milk N-glycans were highly correlated with the growth of Bifidobacterium spp. and Lactobacillus spp. in the gut of infants during early and later lactation, respectively. Enriched expression of genes encoding glycoside hydrolases, glycosyl transferases, ATP-binding cassette (ABC) transporters, and permeases in infants fed by secretor CMs contributed to the promotion of these bacteria in infants. Our data highlight the important role of fucosylated milk glycans in shaping the gut microbiome of infants and provide a solid foundation for development of “personalized” nutrition for Chinese infants.

IMPORTANCE Human milk glycans provide a broad range of carbon sources for gut microbes in infants. Levels of protein glycosylation in human milk vary during lactation and may also be affected by the stages of gestation and lactation and by the secretor status of the mother. This was the first study to evaluate systematically dynamic changes in human milk oligosaccharides and fucosylated N-glycans in the milk of Chinese mothers with different secretor statuses during 6 months of lactation. Given the unique single nucleotide polymorphism site (rs1047781, A385T) on the fucosyltransferase 2 gene among Chinese populations, our report provides a specific insight into the milk glycobiome of Chinese mothers, which may exert effects on the gut microbiota of infants that differ from findings from other study cohorts.