Catherine A. Cooper

GlycoMod - A software tool for determining glycosylation compositions from mass spectrometric data

GlycoMod (http://www.expasy.ch/tools/glycomod/) is a software tool designed to find all possible compositions of a glycan structure from its experimentally determined mass. The program can be used to predict the composition of any glycoprotein‐derived oligosaccharide comprised of either underivatised, methylated or acetylated monosaccharides, or with a derivatised reducing terminus. The composition of a glycan attached to a peptide can be computed if the sequence or mass of the peptide is known. In addition, if the protein is known and is contained in the SWISS‐PROT or TrEMBL databases, the program will match the experimentally determined masses against all the predicted protease‐produced peptides (including any post‐translational modifications annotated in these databases) which have the potential to be glycosylated with either N‐ or O‐linked oligosaccharides. Since many possible glycan compositions can be generated from the same mass, the program can apply compositional constraints to the output if the user supplies either known or suspected monosaccharide constituents. Furthermore, known oligosaccharide structural constraints on monosaccharide composition are also incorporated into the program to limit the output.

GlycoSuiteDB: a curated relational database of glycoprotein glycan structures and their biological sources. 2003 update

GlycoSuiteDB is an annotated and curated relational database of glycan structures reported in the literature. It contains information on the glycan type, core type, linkages and anomeric configurations, mass, composition and the analytical methods used by the researchers to determine the glycan structure. Native and recombinant sources are detailed, including species, tissue and/or cell type, cell line, strain, life stage, disease, and if known the protein to which the glycan structures are attached. There are links to SWISS-PROT/TrEMBL and PubMed where applicable. Recent developments include the implementation of searching by 2D structure and substructure, disease and reference. The database is updated twice a year, and now contains over 7650 entries. Access to GlycoSuiteDB is available at http://www.glycosuite.com.

GlycoSuiteDB: a new curated relational database of glycoprotein glycan structures and their biological sources

GlycoSuiteDB is a relational database that curates information from the scientific literature on glyco-protein derived glycan structures, their biological sources, the references in which the glycan was described and the methods used to determine the glycan structure. To date, the database includes most published O:-linked oligosaccharides from the last 50 years and most N:-linked oligosaccharides that were published in the 1990s. For each structure, information is available concerning the glycan type, linkage and anomeric configuration, mass and composition. Detailed information is also provided on native and recombinant sources, including tissue and/or cell type, cell line, strain and disease state. Where known, the proteins to which the glycan structures are attached are reported, and cross-references to the SWISS-PROT/TrEMBL protein sequence databases are given if applicable. The GlycoSuiteDB annotations include literature references which are linked to PubMed, and detailed information on the methods used to determine each glycan structure are noted to help the user assess the quality of the structural assignment. GlycoSuiteDB has a user-friendly web interface which allows the researcher to query the database using mono-isotopic or average mass, monosaccharide composition, glycosylation linkages (e.g. N:- or O:-linked), reducing terminal sugar, attached protein, taxonomy, tissue or cell type and GlycoSuiteDB accession number. Advanced queries using combinations of these parameters are also possible. GlycoSuiteDB can be accessed on the web at http://www.glycosuite.com.

Amino acid analysis protocols

Amino Acid Analysis: An Overview, Margaret I. Tyler. Amino Acid Analysis, Using Postcolumn Ninhydrin Detection, in a Biotechnology Laboratory, Frank D. Macchi, Felicity J. Shen, Rodney G. Keck, and Reed J. Harris. Purification of Proteins Using UltraMacro Spin Columns or ProSorb Sample Preparation Cartridges for Amino Acid Analysis, Li Zhang and Nancy Denslow. Amino Acid Analysis Using Precolumn Derivatization with 6-Aminoquinolyl-N-Hydroxysuccinimidyl Carbamate Steven A. Cohen. Amino Acid Analysis by High-Performance Liquid Chromatography after Derivatization with 1-Fluoro-2,4-Dinitrophenyl-5-l-Alanine Amide (Marfeys Reagent), Sunil Kochhar, Barbara Mouratou, and Philipp Christen. The Analysis of Amino Acids Using Precolumn Derivatization, HPLC, and Electrochemical Detection, C. David Forster and Charles A. Marsden. Anion Exchange Chromatography and Intergrated Amperometric Detection of Amino Acids, Petr Jandik, Christopher Pohl, Victor Barreto, and Nebojsa Avdalovic. Ion-Pair Chromatography for Identification of Picomolar-Order Protein on a PVDF Membrane, Noriko Shindo, Tsutomu Fujimura, Saiko Kazuno, and Kimie Murayama. Capillary Gas Chromatographic Analysis of Protein and Nonprotein Amino Acids in Biological Samples, Hiroyuki Kataoka, Sayuri Matsumura, Shigeo Yamamoto, and Masami Makita. Measurement of Blood Plasma Amino Acids in Ultrafiltrates by High-Performance Liquid Chromatography with Automatic Precolumn O-Phthaldialdehyde Derivatization, Hua Liu. Determination of Amino Acids in Foods by Reversed-Phase High-Performance Liquid Chromatography with New Precolumn Derivatives, Butylthiocarbamyl, and Benzylthiocarbamyl Derivatives Compared to the Phenylthiocarbamyl Derivative and Ion Exchange Chromatography, Kang-Lyung Woo. Amino Acid Measurement in Body Fluids Using PITC Derivatives, Roy A. Sherwood. Determination of Proteins, Phosphatidylethanolamine, and Phosphatidylserine in Lipid-Rich Materials by Analysis. of Phenylthiocarbamyl Derivatives, Margareta Stark and Jan Johansson. Analysis of O-Phosphoamino Acids in Biological Samples by Gas Chromatography with Flame Photometric Detection, Hiroyuki Kataoka, Norihisa Sakiyama, Yukizo Ueno, Kiyohiko Nakai, and Masami Makita. Determination of Sulfur Amino Acids, Glutathione, and Related Aminothiols in Biological Samples by Gas Chromatography with Flame Photometric Detection, Hiroyuki Kataoka, Kiyomi Takagi, Hirofumi Tanaka, and Masami Makita. Capillary Electrophoretic Determination of 4-Hydroxyproline, Qingyi Chu and Michael Zeece. Total Plasma Homocysteine Analysis by HPLC with SBD-F Precolumn Derivatization, Isabella Fermo and Rita Paroni. Determination of Early Glycation Products by Mass Spectrometry and Quantification of Glycation Mediated Protein Crosslinks by the Incorporation of [14C]lysine into Proteins, Malladi Prabhakaram, Beryl J. Ortwerth, and Jean B. Smith. Index.

The elimination ofO-linked glycans from glycoproteins under non-reducing conditions

A simple procedure is described for the elimination ofO-linked glycans from bovine submaxillary mucin under non-reducing conditions, using triethylamine in aqueous hydrazine. The glycans were isolated as the hydrazones, which were converted to the reducing glycans by exchange with acetone in neutral aqueous solution. The glycan alditols obtained after reduction corresponded to those obtained by the reductive β-elimination ofO-glycans.

BOLD — A biological O-linked glycan database

Glycans can be O‐linked to proteins via the hydroxyl group of serine, threonine, tyrosine, hydroxylysine or hydroxyproline. Sometimes the glycan is O‐linked to the hydroxyl group via a phosphodiester bond. The core monosaccharide residue may be N‐acetylgalactosamine, N‐acetylglucosamine, galactose, glucose, fucose, mannose, xylose or arabinose. These O‐linked glycans can remain as a monosaccharide, but often a complex structure is built up by stepwise addition of monosaccharides. Monosaccharides known to be added include galactose, N‐acetylglucosamine, fucose, N‐acetylneuraminic acid, N‐glycolylneuraminic acid and 2‐keto‐3‐deoxynonulosonic acid. O‐linked glycans can also contain sulfate and phosphate residues. This leads to the possibility of the existence of numerous O‐glycan structures. The biological O‐linked database (BOLD) is a relational database that contains information on O‐linked glycan structures, their biological sources (with a link to the SWISS‐PROT protein database), the references in which the glycan was described (with a link to MEDLINE), and the methods used to determine the glycan structure. The database provides a valuable resource for glycobiology researchers interested in O‐linked oligosaccharide structures that have been previously described on proteins from different species and tissues.

Data standardisation in GlycoSuiteDB.

GlycoSuiteDB, a database of glycan structures, has been constructed with an emphasis on quality, consistency and data integrity. Importance has been placed on making the database a reliable and useful resource for all researchers. This database can help researchers to identify what glycan structures are known to be attached to certain glycoproteins, as well as more generally identifying what types of glycan structures are associated with different states, for example, different species, tissues and diseases. To achieve this, a major effort has gone into data standardisation. Many rules and standards have been adopted, especially for representing glycan structure and biological source information. This paper describes some of the challenges faced during the continuous development of GlycoSuiteDB.

Predicting glycan composition from experiment mass using GlycoMod

GlycoMod (http://www.expasy.org/tools/glycomod/)(1) is a computational tool that finds all possible compositions of a glycan structure from its experimentally determined mass. It may be used to calculate the possible compositions of free or derivatized glycan structures, or compositions of glycans attached to glycoproteins and glycopeptides.