Automatic annotation of matrix-assisted laser desorption/ionizationN-glycan spectra

Emerging glycomics technologies

The nascent field of glycomics is currently undergoing rapid development, largely as a result of advances in technologies for analyzing glycan structure, unraveling glycan-protein interactions and establishing the functional significance of glycans. A meeting was held in November 2006 to explore the challenges and opportunities ahead for this emerging 'omics' domain.

Laser-induced dissociation/high-energy collision-induced dissociation fragmentation using MALDI-TOF/TOF-MS instrumentation for the analysis of neutral and acidic oligosaccharides

Producing detailed mass spectrometric fragmentation data of native oligosaccharides for the purpose of basic structure elucidation has become a readily accessible tool since the availability of enhanced technical equipment. In this report, high-energy collision-induced dissociation (heCID) in combination with MALDI-TOF/TOF technology for analysis of native neutral and acidic oligosaccharides is described. By providing complementary data, heCID-MALDI-TOF/TOF adds a variety of valuable cross-ring fragmentation information to the information of glycosidic fragmentation obtained preferably by laser-induced dissociation (LID). We examined parameters influencing fragmentation behavior of both-acidic and neutral-compounds. Results show a dependency of the fragmentation pattern for the employed matrix as well as the laser intensity provided for the ionization of the analytes and the complexity of the analytes. Due to instrument-specific settings, protonated glycosidic ion series within spectra of sodiated compounds could also be identified. Furthermore, acquired spectra could be readily used to identify compounds by comparison to existing glycan databases such as GlycoSuiteDB and GlycosciencesDB. The results show a better scoring of heCID data sets in comparison to LID-derived data. heCID-MALDI-TOF/TOF analysis in combination with database search algorithms is demonstrated to be suitable for an initial identification/classification of carbohydrates.

Strategies for analysis of glycoprotein glycosylation

Glycoproteins are known to exhibit multiple biological functions. In order to assign distinct functional properties to defined structural features, detailed information on the respective carbohydrate moieties is required. Chemical and biochemical analyses, however, are often impeded by the small amounts of sample available and the vast structural heterogeneity of these glycans, thus necessitating highly sensitive and efficient methods for detection, separation and structural investigation. The aim of this article is to briefly review suitable strategies for characterization of glycosylation at the levels of intact proteins, glycopeptides and free oligosaccharides. Furthermore, methods commonly used for isolation, fractionation and carbohydrate structure analysis of liberated glycoprotein glycans are discussed in the context of potential applications in glycoproteomics.

Glycoproteomics based on tandem mass spectrometry of glycopeptides

Next to the identification of proteins and the determination of their expression levels, the analysis of post-translational modifications (PTM) is becoming an increasingly important aspect in proteomics. Here, we review mass spectrometric (MS) techniques for the study of protein glycosylation at the glycopeptide level. Enrichment and separation techniques for glycoproteins and glycopeptides from complex (glyco-)protein mixtures and digests are summarized. Various tandem MS (MS/MS) techniques for the analysis of glycopeptides are described and compared with respect to the information they provide on peptide sequence, glycan attachment site and glycan structure. Approaches using electrospray ionization and matrix-assisted laser desorption/ionization (MALDI) of glycopeptides are presented and the following fragmentation techniques in glycopeptide analysis are compared: collision-induced fragmentation on different types of instruments, metastable fragmentation after MALDI ionization, infrared multi-photon dissociation, electron-capture dissociation and electron-transfer dissociation. This review discusses the potential and limitations of tandem mass spectrometry of glycopeptides as a tool in structural glycoproteomics.

The use of mass spectrometry for the proteomic analysis of glycosylation

Of all protein PTMs, glycosylation is by far the most common, and is a target for proteomic research. Glycosylation plays key roles in controlling various cellular processes and the modifications of the glycan structures in diseases highlight the clinical importance of this PTM. Glycosylation analysis remains a difficult task. MS, in combination with modern separation methodologies, is one of the most powerful and versatile techniques for the structural analysis of glycoconjugates. This review describes methodologies based on MS for detailed characterization of glycoconjugates in complex biological samples at the sensitivity required for proteomic work.

Activation of murine CD4+ and CD8+ T lymphocytes leads to dramatic remodeling of N-linked glycans

Differentiation and activation of lymphocytes are documented to result in changes in glycosylation associated with biologically important consequences. In this report, we have systematically examined global changes in N-linked glycosylation following activation of murine CD4 T cells, CD8 T cells, and B cells by MALDI-TOF mass spectrometry profiling, and investigated the molecular basis for those changes by assessing alterations in the expression of glycan transferase genes. Surprisingly, the major change observed in activated CD4 and CD8 T cells was a dramatic reduction of sialylated biantennary N-glycans carrying the terminal NeuGcalpha2-6Gal sequence, and a corresponding increase in glycans carrying the Galalpha1-3Gal sequence. This change was accounted for by a decrease in the expression of the sialyltransferase ST6Gal I, and an increase in the expression of the galactosyltransferase, alpha1-3GalT. Conversely, in B cells no change in terminal sialylation of N-linked glycans was evident, and the expression of the same two glycosyltransferases was increased and decreased, respectively. The results have implications for differential recognition of activated and unactivated T cells by dendritic cells and B cells expressing glycan-binding proteins that recognize terminal sequences of N-linked glycans.

Automatic determination of O-glycan structure from fragmentation spectra

Glycosylation is one of the most important classes of post-translational protein modifications, but the identification of glycans is difficult because of their branched structures and numerous isomers. We describe an algorithm called CartoonistTwo that proposes structures for O-linked glycans by automatically analyzing fragmentation mass spectra. CartoonistTwo improves upon previous glycan identification software primarily in its scoring function, which can more successfully distinguish among a number of similar structures. CartoonistTwo was designed and tested with FTICR mass spectra, and includes automatic recalibration and peak selection especially tuned for such data, yet it can be easily adapted to fragmentation spectra (MS2 or MSn) from other instrument types. On a validated test set of 34 SORI-CID MSn FTICR spectra from Xenopus egg jelly, CartoonistTwo gave the manually determined structural assignment either the first or second highest score over 90% of the time. And for over 50% of these spectra, CartoonistTwo selected a unique highest scoring structure that agreed with the manually determined one.

Glycomic profiling of cells and tissues by mass spectrometry: fingerprinting and sequencing methodologies

Over the past decade, rapid, high-sensitivity mass spectrometric strat-egies have been developed and optimized for screening for the types of N- and O-glycans present in a diverse range of biological material, including secretions, cell lines, tissues, and organs. These glycomic strategies are based on matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass fingerprinting of permethylated derivatives, combined with electrospray (ES) or MALDI tandem mass spectrometry (MS/MS) sequencing and gas chromatography (GC)-MS linkage analysis, complemented by chemical and enzymatic degradations. Protocols for these methods are described in the first part of this chapter. Glycomic experiments yield large volumes of MS data, and interpretation of the resulting spectra remains a time-consuming bottleneck in the process. In the second part of this chapter, we describe the use and operation of a mass spectral viewer program capable of displaying and automatically labeling spectra arising from MALDI fingerprinting of N-glycans.

The role of informatics in glycobiology research with special emphasis on automatic interpretation of MS spectra

This paper reviews the current status of bioinformatics applications and databases in glycobiology, which are based on bioinformatics approaches as well as informatics for glycobiology where an explicit encoding of glycan structures is required. The availability of the complete sequence of the human genome has accelerated the systematic identification of so far unidentified glycogenes considerably in many areas of glycobiology using well-established bioinfomatics tools. Although there has been an immense development of new glyco-related data collections as well as informatics tools and several efforts have been started to cross-link and reference the various data deposited in distributed databases, informatics for glycobiology and glycomics is still poorly developed compared to the genomics and proteomics area. The development of algorithms for the automatic interpretation of MS spectra - currently, a severe bottleneck, which hampers the rapid and reliable interpretation of MS data in high-throughput glycomics projects - is reviewed. A comprehensive list of web resources is given. Several lines of progression are discussed. There is an urgent need for the development of decentralised input facilities of experimentally determined glycan structures. Simultaneously, agreements of standards for the structural description of glycans as well as formats for the related data have to be established. The integration of glycomics with genomics/proteomics has to increase.

Glycomics: an integrated systems approach to structure-function relationships of glycans

In comparison with genomics and proteomics, the advancement of glycomics has faced unique challenges in the pursuit of developing analytical and biochemical tools and biological readouts to investigate glycan structure-function relationships. Glycans are more diverse in terms of chemical structure and information density than are DNA and proteins. This diversity arises from glycans' complex nontemplate-based biosynthesis, which involves several enzymes and isoforms of these enzymes. Consequently, glycans are expressed as an 'ensemble' of structures that mediate function. Moreover, unlike protein-protein interactions, which can be generally viewed as 'digital' in regulating function, glycan-protein interactions impinge on biological functions in a more 'analog' fashion that can in turn 'fine-tune' a biological response. This fine-tuning by glycans is achieved through the graded affinity, avidity and multivalency of their interactions. Given the importance of glycomics, this review focuses on areas of technologies and the importance of developing a bioinformatics platform to integrate the diverse datasets generated using the different technologies to allow a systems approach to glycan structure-function relationships.

Prospects for glycoinformatics

High-throughput and automated techniques (mass spectrometry in particular) allow increasingly rapid structural analysis of complex glycans. Information concerning the primary structure (composition, sequence and linkages), three-dimensional structure (including dynamics) and interactions of glycans is now available in sufficient quantity to justify the maintenance of databases and search facilities. Several such resources (both commercial and open access) are now available as web tools. To derive the full value of glycan databases, it will be necessary to develop a universally accepted machine-readable structural representation of glycans.