The Aristotle Classifier: Using the Whole Glycomic Profile To Indicate a Disease State.

"The totality is not, as it were, a mere heap, but the whole is something besides the parts."-Aristotle. We built a classifier that uses the totality of the glycomic profile, not restricted to a few glycoforms, to differentiate samples from two different sources. This approach, which relies on using thousands of features, is a radical departure from current strategies, where most of the glycomic profile is ignored in favor of selecting a few features, or even a single feature, meant to capture the differences in sample types. The classifier can be used to differentiate the source of the material; applicable sources may be different species of animals, different protein production methods, or, most importantly, different biological states (disease vs healthy). The classifier can be used on glycomic data in any form, including derivatized monosaccharides, intact glycans, or glycopeptides. It takes advantage of the fact that changing the source material can cause a change in the glycomic profile in many subtle ways: some glycoforms can be upregulated, some downregulated, some may appear unchanged, yet their proportion-with respect to other forms present-can be altered to a detectable degree. By classifying samples using the entirety of their glycan abundances, along with the glycans' relative proportions to each other, the "Aristotle Classifier" is more effective at capturing the underlying trends than standard classification procedures used in glycomics, including PCA (principal components analysis). It also outperforms workflows where a single, representative glycomic-based biomarker is used to classify samples. We describe the Aristotle Classifier and provide several examples of its utility for biomarker studies and other classification problems using glycomic data from several sources.

DrawGlycan-SNFG: a robust tool to render glycans and glycopeptides with fragmentation information.

Glycan or carbohydrate structures can be pictorially represented using symbolic nomenclatures. The symbol nomenclature for glycans (SNFG) contains 67 different monosaccharides represented using various colors and geometric shapes. A simple tool to convert International Union of Pure and Applied Chemistry (IUPAC) format text to SNFG will be useful for sketching glycans and glycopeptides. Such code can also enable the development of more sophisticated applications, where the visual representation of carbohydrate structures is necessary. To address this need, the current manuscript describes DrawGlycan-SNFG, a freely available, platform-independent, open-source tool. It allows: i. the display of glycans and glycopeptides from IUPAC-condensed text inputs and ii. the depiction of glycan and glycopeptide fragments. The online version of this program is provided with a user-friendly web interface at www.virtualglycome.org/DrawGlycan. Downloadable, stand-alone GUI (Graphical User Interface) version and the program source code are also available from this repository. DrawGlycan-SNFG will be useful for experimentalists looking for a ready to use, simple program for sketching carbohydrates and for software developers interested in incorporating SNFG into their program suite.

Differentiation of underivatized monosaccharides by atmospheric pressure chemical ionization quadrupole time-of-flight mass spectrometry.

RATIONALE: Differentiation of underivatized monosaccharides is essential in the structural elucidation of oligosaccharides which are closely involved in many life processes. So far, such differentiation has been usually achieved by electrospray ionization mass spectrometry (ESI-MS). As an alternative to ESI-MS, atmospheric pressure chemical ionization mass spectrometry (APCI-MS) should provide complementary results. METHODS: A quadrupole time-of-flight (QTOF) mass spectrometer with accurate mass measurement ability was used with an APCI heated nebulizer ion source because we believe that a recently published article using a single quadrupole mass spectrometer assigned incorrect identities for APCI ions from hexoses. Using APCI-QTOF, the MS(2) and pseudo-MS(3) mass spectra of 11 underivatized monosaccharides were obtained under various collision voltages. The mass spectra were carefully interpreted after accurate mass measurement. RESULTS: Differentiation of three hexoses was achieved by different MS(2) spectra of their [M + NH(4)](+) and [M - H](-) ions. The MS(2) spectra of the [M + NH(4)](+) ions were also used to distinguish methyl α-D-glucose and methyl ß-D-glucose, while the pseudo-MS(3) spectra of the [M + H](+) ions were utilized to differentiate the three hexosamine and N-acetylhexosamine stereoisomers. Unique [M + O(2)](-) ions were observed and their distinctive fragmentation patterns were utilized to differentiate the three hexosamine stereoisomers. CONCLUSIONS: Although ESI coupled with single or triple quadrupole and ion trap mass spectrometers has been widely utilized in the differentiation of monosaccharides, this report demonstrated that APCI-QTOF-MS had its own advantages in achieving the same goal.

Comprehensive evaluation of alkali-extracted polysaccharides from Agrocybe cylindracea: Comparison on structural characterization.

Agrocybe cylindracea is a common source of active polysaccharides, but their fine structures are not clearly elucidated. In the present study, four fractions were purified from the alkaline extract of A. cylindracea (JACP), and their chemical components and structures were compared by HPAEC-PAD, methylation combined with GC-MS, and 1D/2D NMR analysis. Results showed the purified fractions' physicochemical properties, including monosaccharide compositions, molecular weights, viscosities and surface morphology considerably varied. JACP-30 was identified as a fucoglucogalactan with a α-(1 → 6)-galactopyranosyl as main chain. JACP-50p and JACP-80r were characterized as ß-(1 → 6)-glucans with side chains composed of terminal and 3-substituted ß-glucopyranosyl residues attached at O-3 for every three residues. Similarly, the backbone of JACP-80 was ß-(1 → 6)-linked glucopyranosyl and ß-(1 → 3,6)-linked glucopyranosyl residues at a ratio of 4:1. This work provides more information to the understanding of polysaccharides from A. cylindracea, further guiding its biological researches and developing the application in food and biomedicine industries.

Extraction, characterisation and antioxidant activity of polysaccharides from Chinese watermelon.

Extraction and antioxidant activity of polysaccharides from the Chinese watermelon was investigated. The polysaccharides were obtained by hot water extraction, ethanol precipitation, and deproteinization with HCl, respectively. The molecular weight was 3.02 × 104. It showed by high performance liquid chromatography (HPLC) and TLC that Chinese watermelon polysaccharides consisted of six monosaccharides, namely glucose, galactose, mannose, xylose, arabinose, and rhamnose. The polysaccharides contained the ß-glycosidic bond. Moreover, it was proved that the polysaccharides had high scavenging ability to superoxide anions.

Rapid Identification and Assignation of the Active Ingredients in Fufang Banbianlian Injection Using HPLC-DAD-ESI-IT-TOF-MS.

Fufang Banbianlian Injection (FBI) is a well-known traditional Chinese medicine formula composed of three herbal medicines. However, the systematic investigation on its chemical components has not been reported yet. In this study, a high-performance liquid chromatography combined with diode-array detector, and coupled to an electrospray ionization with ion-trap time-of-flight mass spectrometry (HPLC-DAD-ESI-IT-TOF-MS) method, was established for the identification of chemical profile in FBI. Sixty-six major constituents (14 phenolic acids, 14 iridoids, 20 flavonoids, 2 benzylideneacetone compounds, 3 phenylethanoid glycosides, 1 coumarin, 1 lignan, 3 nucleosides, 1 amino acids, 1 monosaccharides, 2 oligosaccharides, 3 alduronic acids and citric acid) were identified or tentatively characterized by comparing their retention times and MS spectra with those of standards or literature data. Finally, all constituents were further assigned in the individual herbs (InHs), although some of them were from multiple InHs. As a result, 11 compounds were from Lobelia chinensis Lour, 33 compounds were from Scutellaria barbata D. Don and 38 compounds were from Hedyotis diffusa Willd. In conclusion, the developed HPLC-DAD-ESI-IT-TOF-MS method is a rapid and efficient technique for analysis of FBI sample, and could be a valuable method for the further study on the quality control of the FBI.

The distinction of underivatized monosaccharides using electrospray ionization ion trap mass spectrometry.

A convenient method for distinguishing underivatized isomeric monosaccharides has been established using electrospray ionization ion trap mass spectrometry (ESI-ITMS). Mass spectra of hexoses (glucose, galactose, and mannose), N-acetylhexosamines (N-acetylglucosamine, N-acetylgalactosamine, and N-acetylmannosamine) and hexosamines (glucosamine, galactosamine, and mannosamine) dissolved in solvent containing 1 mM ammonium acetate were obtained in the positive ion mode. Glucose was distinguished from galactose and mannose in the MS(2) spectrum of the [M+NH(4)](+) ion at m/z 198. The MS(3) spectra generated from [M+NH(4)-H(2)O-NH(3)](+) at m/z 163 showed that galactose and mannose could be distinguished by the ratio of peak intensities at m/z 145 and 127, while the three N-acetylhexosamine and hexosamine stereochemical isomers could be identified by the relative abundance ratios of product ions observed in MS(3) spectra. The investigation of MS and MS(2) spectra from complexes of these monosaccharides with Na(+) and Pb(2+) failed to distinguish these monosaccharide isomers. Therefore, multiple stage mass analysis by ESI-ITMS using either [M+NH(4)](+) or [M+H](+) was useful to distinguish between the isomers of monosaccharides.

Cell wall composition in Corynebacterium bovis and some other corynebacteria.

The cell wall compositions of two strains of Corynebacterium bovis were found to differ: one contained lysine, rhamnose, mannose, and glucose, the other meso-alpha, epsilon, diaminopimelic acid (DAP), arabinose, galactose, and mannose. The walls of a strain of C. nephridii were characterized by l-DAP and galactose. Those of a strain of C. paurometabolum and of two strains of "lipophilic diphtheroids" contained meso-DAP, arabinose, galactose, and mannose as did walls of a reference strain of C. xerosis. The results are discussed in relation to the taxonomy of the organisms examined.