Dual polarity accurate mass calibration for electrospray ionization and matrix-assisted laser desorption/ionization mass spectrometry using maltooligosaccharides

2-Nitro-4-Carboxyphenylhydrazine and 2,4-Dicarboxylphenylhydrazine as a Pair of Novel Reactive MALDI Matrices for Rapid and Accurate Profiling of N-Glycome in Dual Ion Modes

N-glycosylation is closely linked to a wide range of biological functions in organisms. Owing to the constriction of awful crystals formed by conventional MALDI matrices and the extremely inferior ionization efficiency of N-glycans, the traditional direct detection of N-glycans by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been gradually replaced by postderivatization detection using reactive matrices. Nevertheless, the laborious identification of complex spectral peaks remains the major difficulty in N-glycan profiling. Hence, we logically designed and synthesized two novel reactive matrices, 2-nitro-4-carboxylphenylhydrazine (NCPH) and 2,4-dicarboxylphenylhydrazine (DCPH), and separately combined them with the acidic matrix 2,5-dihydroxybenzoic acid (DHB) to constitute two composite matrices with high on-target derivatization efficiency and significant promotion of N-glycan ionization for productive MALDI analysis in dual ion modes. Using both composite matrices, we can actualize MALDI-MS and MS2 mass calibration in dual ion modes by postderivatization detection and fragmentation of dextrans and selectively enhance the ionization effect of oligosaccharides in mixed systems. Quite homogeneous cocrystals can ensure N-glycan quantification with decent linearity and reproducibility. A fixed mass difference derived from the identical N-glycan in two ion modes is available for rapid identification in complex biological samples. Ultimately, the developed strategy was triumphantly employed to identify and quantify the relative content and alteration tendency of peach N-glycans, which can be referable to the latent correlation between N-glycan expression and peach ripening.

Amyrel, a novel glucose-forming α-amylase from Drosophila with 4-α-glucanotransferase activity by disproportionation and hydrolysis of maltooligosaccharides

The α-amylase paralogue Amyrel present in true flies (Diptera Muscomorpha) has been classified as a glycoside hydrolase in CAZy family GH13 on the basis of its primary structure. Here we report that, in fact, Amyrel is currently unique amongst Animals as it possesses both the hydrolytic α-amylase activity (EC 3.2.1.1) and a 4-α-glucanotransferase (EC 2.4.1.25) transglycosylation activity. Amyrel reacts specifically on α-(1-4) glycosidic bonds of starch and related polymers but produces a complex mixture of maltooligosaccharides, in sharp contrast with canonical animal α-amylases. With model maltooligosaccharides G2 (maltose) to G7, the Amyrel reaction starts by a disproportionation leading to Gn-1 and Gn + 1 products, which become themselves substrates for new disproportionation cycles. As a result, all detectable odd- and even-numbered maltooligosaccharides at least up to G12 were observed. However, hydrolysis of these products proceeds simultaneously, as shown by p-nitrophenyl-tagged oligosaccharides and microcalorimetry, and upon prolonged reaction, glucose is the major end product followed by maltose. The main structural determinant of these atypical activities was found to be a Gly-His-Gly-Ala deletion in the so-called flexible loop bordering the active site. Indeed, engineering this deletion in pig pancreatic and D. melanogaster α-amylases results in reaction patterns similar to those of Amyrel. It is proposed that this deletion provides more freedom to the substrate for subsites occupancy and allows a less constrained action pattern resulting in versatile activities at the active site.

Variations in porcine colostrum oligosaccharide composition between breeds and in association with sow maternal performance

Background

Oligosaccharides (OS) are indigestible carbohydrates naturally found in milk. The composition of porcine colostrum OS may influence the growth and the health of the neonate and consuming optimal concentrations of OS may reduce piglet susceptibility to illness. In this manner, targeted supplementation of animal feed with OS is being explored as a health management tool in the livestock industry. The variation in OS composition between different breeds of pig and its association with the litter performance is currently unknown. The aim of this study was to characterize the colostrum OS composition from sows of different breed and parity and correlate this data with sow maternal traits.

Methods

Eighty-three colostrum samples from parities 1 to 8 were gathered from 3 different breeds of sow: 44 Large White sows, 27 Landrace sows and 12 Duroc sows. Samples were taken between the birth of the first and the last piglet from sows that were not pharmacologically induced to farrow. OS were purified from the samples and analysed by MALDI-ToF mass spectrometry (21 OS compositions detected). The farrowing season and the maternal data were recorded for each sow, including the number of live piglets and the litter body weight at birth, at day (d) 3 and at weaning.

Results

Five OS compositions, including isomers of the bifidogenic Sialyllactose, Lacto-N-Tetraose and Lacto-N-Hexaose series, were detected in all the samples. Twelve other OS were identified in at least 50% of samples, and their abundances were affected by breed (P < 0.05; 6 of 12), marginally affected by season (P < 0.10; 3 of 12) and never by parity number. The abundances of each OS component were standardized by Z-score scaling (μ = 0 and SD = 1), transformed by principal component analysis, and four similarity clusters were generated. Cluster membership was associated with litter weight gain within 3 days (P = 0.063) and at weaning (P < 0.05), but not with piglet mortality within 3 days.

Conclusions

OS composition of colostrum may partially explain the variability in maternal performance within and between different breeds of sow. The obtained OS data can provide useful information for the development of novel prebiotic food supplements for suckling and weaning pigs.

Parallel On-Target Derivatization for Mass Calibration and Rapid Profiling of N-Glycans by MALDI-TOF MS

Glycosylation is an important post-translational modification of proteins, and abnormal glycosylation is involved in a variety of diseases. Accurate and rapid profiling of N-glycans by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) is still technically challenging and hampered mainly by mass drift of instrument, manual identification of spectrum peaks, and poor cocrystallization with traditional matrices besides low ionization efficiency of analytes. In the present study, a parallel on-target derivatization strategy (POTDS), on the basis of two rationally combined matrices, i.e., 3-hydrazinobenzoic acid plus DHB (DHB/3HBA) and quinoline-3-carbohydrazide plus DHB (DHB/Q3CH), was proposed for mass calibration and rapid detection of reducing N-glycans. Both DHB/3HBA and DHB/Q3CH show high derivatization efficiency and can improve the ionization efficiency of reducing N-glycans significantly. For mass calibration, in combination with dextrans, DHB/3HBA and DHB/Q3CH prove to be highly sensitive matrices facilitating both MS and MS² calibration for N-glycans in dual polarities. For rapid identification, the regular mass difference observed for each N-glycan labeled with Q3CH and 3HBA respectively can eliminate the occurrence of false positives and promote automated identification of N-glycans in complex samples. For relative quantitation, the acid-base pair of DHB/Q3CH generates a concentrated cocrystallization of glycan-matrix mixtures at the edge of the droplet uniformly, exhibiting good linearity (R² > 0.998) and accuracy (RSD ≤ 10%). Furthermore, the established POTDS was successfully utilized to assess N-glycans of serum from HCC patients, revealing potential for biomarker discovery in clinical practice.

Dual Polarity Ion Confinement and Mobility Separations

Here, we present simulations and describe the initial implementation of a device capable of performing simultaneous ion mobility (IM) separations of positive and negative ions based upon the structures for lossless ion manipulations (SLIM). To achieve dual polarity ion confinement, the DC fields used for lateral confinement in previous SLIM were replaced with RF fields. Concurrent ion transport and mobility separation in the SLIM device are shown possible due to the nature of the traveling wave (TW) voltage profile which has potential minima at opposite sides of the wave for each ion polarity. We explored the potential for performing simultaneous IM separations of cations and anions over the same SLIM path and the impacts on the achievable IM resolution and resolving power. Initial results suggest comparable IM performance with previous single-polarity SLIM separations can be achieved. We also used ion trajectory simulations to investigate the capability to manipulate the spatial distributions of ion populations based on their polarities by biasing the RF fields and TW potentials on each SLIM surface so as to limit the interactions between opposite polarity ions. Graphical Abstract.

Dual-Polarity Ion Trap Mass Spectrometry: Dynamic Monitoring and Controlling Gas-phase Ion-Ion Reactions

A dual-polarity linear ion trap (LIT) mass spectrometer was developed in this study, and the method for simultaneously controlling and detecting cations and anions was proposed and realized in the LIT. With the application of an additional dipolar DC field on the ejection electrodes of an LIT, dual-polarity mass spectra could be obtained, which include both the mass-to-charge (m/z) ratio and charge polarity information of an ion. Compared with conventional method, the ion ejection and detection efficiency could also be improved by about one-fold. Furthermore, ion-ion reactions within the LIT could be dynamically controlled and monitored by manipulating the distributions of ions with opposite charge polarities. This method was then used to control and study the reaction kinetics of ion-ion reactions, including electron transfer dissociation (ETD) and charge inversion reactions. A dual-polarity collision-induced dissociation (CID) experiment was proposed and performed to enhance the sequence coverage of a peptide ion. Ion trajectory simulations were also carried out for concept validation and system optimization. Graphical Abstract ᅟ.

Organosolv Lignin-Based Wood Adhesive. Influence of the Lignin Extraction Conditions on the Adhesive Performance

Ethanol organosolv alfa grass lignins were extracted in the presence of sulfuric acid or Lewis acids (Sc(OTf)₃, FeCl₃) as catalysts and subjected to a comprehensive structural characterization by solid state ¹³C NMR, GPC, MALDI-TOF, and ASAP-MS/MS. The impact of the severity of the treatment and of the nature of the acid catalyst on the recovered lignin structure was investigated. The lignins isolated at high severity were highly recondensed and partly composed of regular structures composed of furan-like rings. The alfa (Stipa tenacissima L.) organosolv lignins were used for the preparation of formaldehyde-free adhesives which were characterized by TMA and used for the preparation of particleboard without any addition of synthetic resin. It has been demonstrated for the first time that: (1) the addition of 10% to 30% of organosolv alfa lignin in a tannin-based adhesive improved the adhesive performance; and (2) the conditions of the lignin extraction strongly impact the lignin-based adhesive performances. The highly recondensed lignin extracted with sulfuric acid as a catalyst allowed the production of resins with improved performances. Formulations composed of 50% glyoxalated alfa lignin and 50% of Aleppo Pine tannins yielded good internal bond strength results for the panels (IB = 0.45 MPa) and satisfied relevant international standard specifications for interior-grade panels.

Extraction, isolation and MALDI-QTOF MS/MS analysis of β-d-Glucan from the fruiting bodies of Daedalea quercina

We report for the first time the extraction, isolation, and the proposed structure of a polysaccharide from the fruiting bodies of Daedalea quercina. The monosaccharide composition of D. quercina isolate (DQW1Pa1) was mainly glucose as identified using GC-MS. FTIR-ATR spectroscopy and absolute configuration studies showed that this polysaccharide is a β-d-glucan. Its average molecular weight obtained using size exclusion chromatography was 1.6×10⁴Da, consistent with glucans derived from the order Polyporaceae. MALDI-QTOF MS/MS was carried out to identify the linkage and connectivity of the glucose units. Collision Induced Dissociation (CID) of selected parent ions of different oligosaccharide lengths showed the presence of characteristic glycosidic bond cleavages B_n/C_n, the linear backbone by 1-6 linkage, and the cross-ring fragment, ^0,3A_n. Presence of branching unit was identified from high intensity ^0,3A₄ fragment and verified from diagnostic ion of [D] and [D-H₂O] types. To confirm the linkage assignment obtained using MALDI-QTOF MS/MS, DQW1Pa1 was subjected to methylation analysis. Results showed the presence of 1-3, 1-6, 1- and 1-3-6 linked glucose in the order of decreasing abundance, respectively. The repeating unit of isolate DQW1Pa1 was deduced as 1-3 linked linear glucose backbone with branches composed of three 1-3 linked glucose units connected to backbone by 1-6 linkage.

A comparison of energy-resolved vibrational activation/dissociation characteristics of protonated and sodiated high mannose N-glycopeptides

Fragmentation of glycopeptides in tandem mass spectrometry (MS/MS) plays a pivotal role in site-specific protein glycosylation profiling by allowing specific oligosaccharide compositions and connectivities to be associated with specific loci on the corresponding protein. Although MS/MS analysis of glycopeptides has been successfully performed using a number of distinct ion dissociation methods, relatively little is known regarding the fragmentation characteristics of glycopeptide ions with various charge carriers. In this study, energy-resolved vibrational activation/dissociation was examined via collision-induced dissociation for a group of related high mannose tryptic glycopeptides as their doubly protonated, doubly sodiated, and hybrid protonated sodium adduct ions. The doubly protonated glycopeptide ions with various compositions were found to undergo fragmentation over a relatively low but wide range of collision energies compared with the doubly sodiated and hybrid charged ions, and were found to yield both glycan and peptide fragmentation depending on the applied collision energy. By contrast, the various doubly sodiated glycopeptides were found to dissociate over a significantly higher but narrow range of collision energies, and exhibited only glycan cleavages. Interestingly, the hybrid protonated sodium adduct ions were consistently the most stable of the precursor ions studied, and provided fragmentation information spanning both the glycan and the peptide moieties. Taken together, these findings illustrate the influence of charge carrier over the energy-resolved vibrational activation/dissociation characteristics of glycopeptides, and serve to suggest potential strategies that exploit the analytically useful features uniquely afforded by specific charge carriers or combinations thereof.

Letter: The potential of amine-containing dendrimer mass standards for internal calibration of peptides

In order to ensure accurate mass determinations, MALDI-TOF mass spectrometers must be calibrated regularly. While peptides and proteins represent the most widely used calibration standards due to their monodispersity, known masses and availability, their limited shelf-life complicates their use. Recently, polyester dendrimer calibrants have been introduced as an alternative because, in addition to monodispersity and relative molecular masses as high as 30,000, they exhibit vastly improved stability and broad compatibility with both matrices and solvents. However, the use of these initially reported polyester dendrimers as internal calibrants for the analysis of peptides or proteins presents a unique problem because these dendrimers typically require ionization with metal cations, while amino acid-based compounds preferentially ionize via protonation of an amine. To address this complication, dendrimers bearing a single amine were prepared which demonstrate the ability to easily ionize via protonation with either acidic matrices or dilute solutions of trifluoroacetic acid. This class of amine-containing dendrimers shows promise as a calibrant system specifically designed for the internal calibration of peptides.

Advantages of monodisperse and chemically robust "SpheriCal" polyester dendrimers as a "universal" MS calibrant

The utilization of dendrimer calibrants as an alternative to peptides and proteins for high mass calibration is explored. These synthetic macromolecules exhibited a number of attractive advantages, including exceptional shelf-lives, broad compatibility with a wide range of matrices and solvents, and evenly spaced calibration masses across the mass range examined, 700-30,000 u. The exceptional purity of these dendrimers and the technical simplicity of this calibration platform validate their broad relevance for high molecular weight mass spectrometry.

Impact of glutathione-enriched inactive dry yeast preparations on the stability of terpenes during model wine aging

The impact of the addition of glutathione-enriched Inactive dry yeast preparations (g-IDYs) on the stability of some typical wine terpenes (linalool, α-terpineol, β-citronellol, and nerol) stored under accelerated oxidative conditions was evaluated in model wines. Additionally, the effects of a second type of IDY preparation with a different claim (fermentative nutrient) and the sole addition of commercial glutathione into the model wines were also assessed. Model wines were spiked with the low molecular weight fraction (<3 kDa permeate) isolated from the IDYs, avoiding the interaction of aroma compounds with other yeast components. An exhaustive chemical characterization of both IDY permeates was carried out by using targeted and nontargeted metabolomics approaches using CE-MS and FT-ICR-MS analytical platforms. The findings suggest that the addition of <3 kDa permeate isolated from any of the IDYs employed decreases the loss of typical wine terpenes in model wines submitted to accelerated aging conditions. The g-IDY preparation did indeed release reduced GSH into the model wines, although this compound did not seem exclusively related to the protective effect on some aroma compounds determined in both model wines. The presence of other sulfur-containing compounds from yeast origin in g-IDY, and also the presence of small yeast peptides, such as methionine/tryptophan/tyrosine-containing tripeptide in both types of IDYs, seemed to be related to the antioxidant activity determined in the two permeates and to the minor loss of some terpenes in the model wines spiked with them.

New strategies for resolving oligosaccharide isomers by exploiting mechanistic and thermochemical aspects of fragment ion formation

Three complementary experimental approaches for elucidating human milk oligosaccharide (HMOs) isomers by Fourier Transform Ion Cyclotron Resonance mass spectrometry (FT-ICR) are described: tandem-MS disruption by double resonance to distinguish different fragmentation pathways, examination of fragment intensity ratios arising from differential alkali metal ion affinities and monitoring competitive fragmentation rates. The interpretation of the fragmentation pattern from a mechanistic and thermochemical point of view permits the assignment of not only pure isomers but, in some cases, mixtures of them. Methodologically the procedures are simple, reliable and rapid making unnecessary both the use of previous separation techniques and tedious chemical modifications of the HMOs. In principle, the rationale can be expanded to resolve other isomeric mixtures of biological nature.

A quantitative and comprehensive method to analyze human milk oligosaccharide structures in the urine and feces of infants

Human milk oligosaccharides (HMOs), though non-nutritive to the infant, shape the intestinal microbiota and protect against pathogens during early growth and development. Infant formulas with added galacto-oligosaccharides have been developed to mimic the beneficial effects of HMOs. Premature infants have an immature immune system and a leaky gut and are thus highly susceptible to opportunistic infections. A method employing nanoflow liquid chromatography time-of-flight mass spectrometry (MS) is presented to simultaneously identify and quantify HMOs in the feces and urine of infants, of which 75 HMOs have previously been fully structurally elucidated. Matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance MS was employed for high-resolution and rapid compositional profiling. To demonstrate this novel method, samples from mother-infant dyads as well as samples from infants receiving infant formula fortified with dietary galacto-oligosaccharides or probiotic bifidobacteria were analyzed. Ingested oligosaccharides are demonstrated in high abundance in the infant feces and urine. While the method was developed to examine specimens from preterm infants, it is of general utility and can be used to monitor oligosaccharide consumption and utilization in term infants, children, and adults. This method may therefore provide diagnostic and therapeutic opportunities.

Analytical platform for glycomic characterization of recombinant erythropoietin biotherapeutics and biosimilars by MS

Background: Erythropoietin is a therapeutic glycoprotein that stimulates red blood cell production. The quality, safety and potency of recombinant erythropoietins are determined largely by their glycosylation. Small variations in cell culture conditions can significantly affect the glycosylation, and therefore the efficacy, of recombinant erythropoietins. Thus, detailed glycomic analyses are necessary to assess biotherapeutic quality. We have developed a platform for qualitative and quantitative glycomic analysis of recombinant erythropoietins. Results: The platform was used to profile native N-glycans from three production batches of darbepoetin alfa (also known as NESP), a common form of recombinant erythropoietin. Darbepoetin alfa was found to contain an abundance of large, multi-antennary N-glycans with high levels of sialylation, O-acetylation and dehydration. Results were verified by independent orthogonal analysis with both MALDI-TOF and nano-LC/Q-TOF MS. Conclusion: This platform may be applied to QC and batch analysis of not only recombinant erythropoietin, but also other complex, glycosylated biotherapeutics and biosimilars.

Investigating the thermal decomposition of starch and cellulose in model systems and toasted bread using domino tandem mass spectrometry

Many dietary products containing polysaccharides, mostly starch and cellulose, are processed by thermal treatment. Similarly to the formation of caramel from mono- and disaccharides, the chemical structure of the carbohydrates is dramatically altered by heat treatment. This contribution investigates the products of thermal decomposition of pure starch and cellulose as model systems followed by an investigation of bread obtained at comparable conditions using a combination of modern mass spectrometry techniques. From both starch and cellulose, dehydrated oligomers of glucose and dehydrated glucose have been predominately observed, with oligomers of more than four glucose moieties dominating. Moreover, disproportionation and oligomers with up to six carbohydrates units are formed through unselective glycosidic bond breakage. MALDI-MS data confirm the presence of the majority of products in toasted bread.

Lacto-N-tetraose, fucosylation, and secretor status are highly variable in human milk oligosaccharides from women delivering preterm

Breast milk is the ideal nutrition for term infants but must be supplemented to provide adequate growth for most premature infants. Human milk oligosaccharides (HMOs) are remarkably abundant and diverse in breast milk and yet provide no nutritive value to the infant. HMOs appear to have at least two major functions: prebiotic activity (stimulation of the growth of commensal bacteria in the gut) and protection against pathogens. Investigations of HMOs in milk from women delivering preterm have been limited. We present the first detailed mass spectrometric analysis of the fucosylation and sialylation in HMOs in serial specimens of milk from 15 women delivering preterm and 7 women delivering at term using nanohigh performance liquid chromatography chip/time-of-flight mass spectrometry. A mixed-effects model with Levene's test was used for the statistical analyses. We find that lacto-N-tetraose, a core HMO, is both more abundant and more highly variable in the milk of women delivering preterm. Furthermore, fucosylation in preterm milk is not as well regulated as in term milk, resulting in higher within and between mother variation in women delivering preterm vs term. Of particular clinical interest, the α1,2-linked fucosylated oligosaccharide 2'-fucosyllactose, an indicator of secretor status, is not consistently present across lactation of several mothers that delivered preterm. The immaturity of HMO production does not appear to resolve over the time of lactation and may have relevance to the susceptibility of premature infants to necrotizing enterocolitis, late onset sepsis, and related neurodevelopmental impairments.

Endo-β-N-acetylglucosaminidases from infant gut-associated bifidobacteria release complex N-glycans from human milk glycoproteins

Breastfeeding is one of the main factors guiding the composition of the infant gut microbiota in the first months of life. This process is shaped in part by the high amounts of human milk oligosaccharides that serve as a carbon source for saccharolytic bacteria such as Bifidobacterium species. Infant-borne bifidobacteria have developed various molecular strategies for utilizing these oligosaccharides as a carbon source. We hypothesized that these species also interact with N-glycans found in host glycoproteins that are structurally similar to free oligosaccharides in human milk. Endo-β-N-acetylglucosaminidases were identified in certain isolates of Bifidobacterium longum subsp. longum, B. longum subsp. infantis, and Bifidobacterium breve, and their presence correlated with the ability of these strains to deglycosylate glycoproteins. An endoglycosidase from B. infantis ATCC 15697, EndoBI-1, was active toward all major types of N-linked glycans found in glycosylated proteins. Its activity was not affected by core fucosylation or extensive fucosylation, antenna number, or sialylation, releasing several N-glycans from human lactoferrin and immunoglobulins A and G. Extensive N-deglycosylation of whole breast milk was also observed after coincubation with this enzyme. Mutation of the active site of EndoBI-1 did not abolish binding to N-glycosylated proteins, and this mutant specifically recognized Man(3)GlcNAc(2)(α1-6Fuc), the core structure of human N-glycans. EndoBI-1 is constitutively expressed in B. infantis, and incubation of the bacterium with human or bovine lactoferrin led to the induction of genes associated to import and consumption of human milk oligosaccharides, suggesting linked regulatory mechanisms among these glycans. This work reveals an unprecedented interaction of bifidobacteria with host N-glycans and describes a novel endoglycosidase with broad specificity on diverse N-glycan types, potentially a useful tool for glycoproteomics studies.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for 2007-2008

This review is the fifth update of the original review, published in 1999, on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2008. The first section of the review covers fundamental studies, fragmentation of carbohydrate ions, use of derivatives and new software developments for analysis of carbohydrate spectra. Among newer areas of method development are glycan arrays, MALDI imaging and the use of ion mobility spectrometry. The second section of the review discusses applications of MALDI MS to the analysis of different types of carbohydrate. Specific compound classes that are covered include carbohydrate polymers from plants, N- and O-linked glycans from glycoproteins, biopharmaceuticals, glycated proteins, glycolipids, glycosides and various other natural products. There is a short section on the use of MALDI mass spectrometry for the study of enzymes involved in glycan processing and a section on the use of MALDI MS to monitor products of the chemical synthesis of carbohydrates with emphasis on carbohydrate-protein complexes and glycodendrimers. Corresponding analyses by electrospray ionization now appear to outnumber those performed by MALDI and the amount of literature makes a comprehensive review on this technique impractical. However, most of the work relating to sample preparation and glycan synthesis is equally relevant to electrospray and, consequently, those proposing analyses by electrospray should also find material in this review of interest.

AHL signals induce rubrifacine production in a bruI mutant of Brenneria rubrifaciens

Several members of the bacterial genus Brenneria are pathogenic on different tree species. Cell-free extracts from the bacterial phytopathogens Brenneria rubrifaciens, B. salicis, and B. nigrifluens induced production of the red pigment rubrifacine in the B. rubrifaciens bruI insertional mutant Br-212. Analysis of the bruI locus identified an adjacent open reading frame, designated bruR, with homology to luxR. High-performance liquid chromatography and mass spectrometry analysis of ethyl acetate extracts from wild-type B. rubrifaciens and Escherichia coli expressing the bruI gene identified two acyl homoserine lactone (AHL) peaks, N-(3-oxohexanoyl)-homoserine lactone (3OC6HSL) and N-hexanoyl-homoserine lactone (C6HSL). Addition of synthetic 3OC6HSL and C6HSL at 10 μM to the bruI mutant, strain Br-212, induced rubrifacine production and the ability to elicit a hypersensitive reaction (HR) in tobacco leaves. Synthetic C6HSL was less effective at inducing pigment production than 3OC6HSL at 10 μM. The bruI mutant Br-212 did not produce detectable AHLs, indicating that C6HSL and 3OC6HSL are the major AHLs produced by this species. The AHLs N-heptanoyl-DL-homoserine lactone (C7HSL), N-octanoyl-DL-homoserine lactone (C8HSL), and N-(3-oxooctanoyl)-DL-homoserine lactone (3OC8HSL) also induced pigment production in Br-212 and restored its ability to elicit an HR in tobacco, suggesting that cross-talk with other bacterial species may be possible.

Rapid Profiling of Bovine and Human Milk Gangliosides by Matrix-Assisted Laser Desorption/Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

Gangliosides are anionic glycosphingolipids widely distributed in vertebrate tissues and fluids. Their structural and quantitative expression patterns depend on phylogeny and are distinct down to the species level. In milk, gangliosides are exclusively associated with the milk fat globule membrane. They may participate in diverse biological processes but more specifically to host-pathogen interactions. However, due to the molecular complexities, the analysis needs extensive sample preparation, chromatographic separation, and even chemical reaction, which makes the process very complex and time-consuming. Here, we describe a rapid profiling method for bovine and human milk gangliosides employing matrix-assisted desorption/ionization (MALDI) Fourier transform ion cyclotron resonance (FTICR) mass spectrometry (MS). Prior to the analyses of biological samples, milk ganglioside standards GM3 and GD3 fractions were first analyzed in order to validate this method. High mass accuracy and high resolution obtained from MALDI FTICR MS allow for the confident assignment of chain length and degree of unsaturation of the ceramide. For the structural elucidation, tandem mass spectrometry (MS/MS), specifically as collision-induced dissociation (CID) and infrared multiphoton dissociation (IRMPD) were employed. Complex ganglioside mixtures from bovine and human milk were further analyzed with this method. The samples were prepared by two consecutive chloroform/methanol extraction and solid phase extraction. We observed a number of differences between bovine milk and human milk. The common gangliosides in bovine and human milk are NeuAc-NeuAc-Hex-Hex-Cer (GD3) and NeuAc-Hex-Hex-Cer (GM3); whereas, the ion intensities of ganglioside species are different between two milk samples. Kendrick mass defect plot yields grouping of ganglioside peaks according to their structural similarities. Gangliosides were further probed by tandem MS to confirm the compositional and structural assignments. We found that only in human milk gangliosides was the ceramide carbon always even numbered, which is consistent with the notion that differences in the oligosaccharide and the ceramide moieties confer to their physiological distinctions.

An infant-associated bacterial commensal utilizes breast milk sialyloligosaccharides

Lactating mothers secrete milk sialyloligosaccharides (MSOs) that function as anti-adhesives once provided to the neonate. Particular infant-associated commensals, such as Bifidobacterium longum subsp. infantis, consume neutral milk oligosaccharides, although their ability to utilize acidic oligosaccharides has not been assessed. Temporal glycoprofiling of acidic HMO consumed during fermentation demonstrated a single composition, with several isomers, corresponding to sialylated lacto-N-tetraose. To utilize MSO, B. longum subsp. infantis deploys a sialidase that cleaves α2-6 and α2-3 linkages. NanH2, encoded within the HMO catabolic cluster is up-regulated during HMO fermentation and is active on sialylated lacto-N-tetraose. These results demonstrate that commensal microorganisms do utilize MSO, a substrate that may be enriched in the distal gastrointestinal tract.

Enhanced detection and identification of glycopeptides in negative ion mode mass spectrometry

A combined mass spectrometry (MS) and tandem mass spectrometry (MS/MS) approach implemented with matrix-assisted laser desorption ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI FTICR MS) in the negative ion mode is described for enhanced glycopeptide detection and MS/MS analysis. Positive ion mode MS analysis is widely used for glycopeptide characterization, but the analyses are hampered by potential charge-induced fragmentation of the glycopeptides and poor detection of the glycopeptides harboring sialic acids. Furthermore, tandem MS analysis (MS/MS) via collision-induced dissociation (CID) of glycopeptides in the positive ion mode predominantly yields glycan fragmentation with minimal information to verify the connecting peptide moiety. In this study, glycoproteins such as, bovine lactoferrin (b-LF) for N-glycosylation and kappa casein (k-CN) for O-glycosylation were analyzed in both the positive- and negative ion modes after digestion with bead-immobilized Pronase. For the b-LF analysis, 44 potential N-linked glycopeptides were detected in the positive ion mode while 61 potential N-linked glycopeptides were detected in the negative ion mode. By the same token, more O-linked glycopeptides mainly harboring sialic acids from k-CN were detected in the negative ion mode. The enhanced glycopeptide detection allowed improved site-specific analysis of protein glycosylation and superior to positive ion mode detection. Overall, the negative ion mode approach is aimed toward enhanced N- and O-linked glycopeptide detection and to serve as a complementary tool to positive ion mode MS/MS analysis.

Method for the identification of lipid classes based on referenced Kendrick mass analysis

A rapid method for the determination of lipid classes with high sensitivity is described. The referenced Kendrick mass defect (RKMD) and RKMD plots are novel adaptations of the Kendrick mass defect analysis that allows for the rapid identification of members of a homologous series in addition to identifying the lipid class. Assignment of lipid classes by the RKMD method is accomplished by conversion of the lipid masses to the Kendrick mass scale and then referencing the converted masses to each lipid class. Referencing of the masses to a given lipid class is achieved by first subtracting the heteroatom and lipid backbone contributions to the mass defect, leaving behind the contribution to the mass by the fatty acid constituents. The final step in the referencing makes use of spacing differences in mass defects between members of the same Kendrick class to identify members of the lipid class being referenced. The end result of this is that a lipid belonging to the class being referenced will have an integer RKMD with the value of the integer being the degrees of unsaturation in the lipid. The RKMD method was able to successfully identify the lipids in an idealized data set consisting of 160 lipids drawn from the glyceride and phosphoglyceride classes. As a real world example the lipid extract from bovine milk was analyzed using both accurate mass measurements and the RKMD method.

Glycoprotein expression in human milk during lactation

While milk proteins have been studied for decades, strikingly little effort has been applied to determining how the post-translational modifications (PTMs) of these proteins may change during the course of lactation. PTMs, particularly glycosylation, can greatly influence protein structure, function, and stability and can particularly influence the gut where their degradation products are potentially bioactive. In this work, previously undiscovered temporal variations in both expression and glycosylation of the glycoproteome of human milk are observed. Lactoferrin, one of the most abundant glycoproteins in human milk, is shown to be dynamically glycosylated during the first 10 days of lactation. Variations in expression or glycosylation levels are also demonstrated for several other abundant whey proteins, including tenascin, bile salt-stimulated lipase, xanthine dehydrogenase, and mannose receptor.

Laser desorption ionization of red phosphorus clusters and their use for mass calibration in time-of-flight mass spectrometry

Phosphorus clusters P(n) (n = 1-89) are easily formed from red phosphorus by laser desorption ionization (LDI) and they cover a range of up to approx. m/z 3000 in both positive and negative ion mode. The clusters are singly charged and the spectra are simple because phosphorus is monoisotopic. The mass spectra can be measured with an acceptable resolution and intensity. The use of positively charged P(n) clusters for calibration in mass spectrometry was examined and it was demonstrated that in external calibration a standard deviation of +/-0.04 m/z units can be achieved even when using a common commercial matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) instrument. When used as internal standards the P(n) clusters react with some analytes - C(60) and C(70) fullerenes and cucurbituril[8], for example. It was also found that red phosphorus is a suitable MALDI matrix for peptides and proteins, illustrated by the examples of a Calmix mixture of bradykinin, angiotensin, renin, adrenocorticotropic hormone ACTH fragment 18-359 and insulin, and of insulin alone.

Analytical performance of immobilized pronase for glycopeptide footprinting and implications for surpassing reductionist glycoproteomics

A fully developed understanding of protein glycosylation requires characterization of the modifying oligosaccharides, elucidation of their covalent attachment sites, and determination of the glycan heterogeneity at specific sites. Considering the complexity inherent to protein glycosylation, establishing these features for even a single protein can present an imposing challenge. To meet the demands of glycoproteomics, the capability to screen far more complex systems of glycosylated proteins must be developed. Although the proteome wide examination of carbohydrate modification has become an area of keen interest, the intricacy of protein glycosylation has frustrated the progress of large-scale, systems oriented research on site-specific protein-glycan relationships. Indeed, the analytical obstacles in this area have been more instrumental in shaping the current glycoproteomic paradigm than have the diverse functional roles and ubiquitous nature of glycans. This report describes the ongoing development and analytically salient features of bead immobilized pronase for glycosylation site footprinting. The present work bears on the ultimate goal of providing analytical tools capable of addressing the diversity of protein glycosylation in a more comprehensive and efficient manner. In particular, this approach has been assessed with respect to reproducibility, sensitivity, and tolerance to sample complexity. The efficiency of pronase immobilization, attainable pronase loading density, and the corresponding effects on glycoprotein digestion rate were also evaluated. In addition to being highly reproducible, the immobilized enzymes retained a high degree of proteolytic activity after repeat usage for up to 6 weeks. This method also afforded a low level of chemical background and provided favorable levels of sensitivity with respect to traditional glycoproteomic strategies. Thus, the application of immobilized pronase shows potential to contribute to the advancement of more comprehensive glycoproteomic research methods that are capable of providing site-specific glycosylation and microheterogeneity information across many proteins.