GlycoCT—a unifying sequence format for carbohydrates

Herget, Stephan; Ranzinger, René; Maaß, Kai; Lieth, C.W. von der

doi:10.1016/j.carres.2008.03.011

Cited by 172 publications

(141 citation statements)

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“…Another initiative arising from the EUROCarbDB project (http://www.eurocarbdb.org) is the development of a unifying encoding sequence format for carbohydrates (Herget et al, 2008a). The encoding capabilities of all existing carbohydrate sequence formats and the content of publically available structure databases were examined but none were found that were capable of coping with the full complexity to be expected for experimentally derived structural carbohydrate sequence data across all taxonomic sources.…”

Section: A Software For Interpreting Spectramentioning

confidence: 99%

Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for 2007–2008

Harvey

2011

Mass Spectrometry Reviews

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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.

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Section: A Software For Interpreting Spectramentioning

confidence: 99%

Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for 2007–2008

Harvey

2011

Mass Spectrometry Reviews

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“…Glycan objects can be created by reading glycan structures in the GlycoCT format [40] using the GlycoCTReader class. The GlycanFragmenter class can be used to generate theoretical glycan spectra [21].…”

Section: Accepted Manuscriptmentioning

confidence: 99%

MzJava: An open source library for mass spectrometry data processing

Horlacher

Nikitin

Alocci

et al. 2015

Journal of Proteomics

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Mass spectrometry (MS) is a widely used and evolving technique for the high-throughput identification of molecules in biological samples. The need for sharing and reuse of code among bioinformaticians working with MS data prompted the design and implementation of MzJava, an open-source Java Application Programming Interface (API) for MS related data processing. MzJava provides data structures and algorithms for representing and processing mass spectra and their associated biological molecules, such as metabolites, glycans and peptides. MzJava includes functionality to perform mass calculation, peak processing (e.g. centroiding, filtering, transforming), spectrum alignment and clustering, protein digestion, fragmentation of peptides and glycans as well as scoring functions for spectrum-spectrum and peptide/glycan-spectrum matches. For data import and export MzJava implements readers and writers for commonly used data formats. For many classes support for the Hadoop MapReduce (hadoop.apache.org) and Apache Spark (spark.apache.org) frameworks for cluster computing was implemented. The library has been developed applying best practices of software engineering. To ensure that MzJava contains code that is correct and easy to use the library's API was carefully designed and thoroughly tested. MzJava is an open-source project distributed under the AGPL v3.0 licence. MzJava requires Java 1.7 or higher. Binaries, source code and documentation can be downloaded from http://mzjava.expasy.org and https://bitbucket.org/sib-pig/mzjava. This article is part of a Special Issue entitled: Computational Proteomics.

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“…Recently Herget et al, (2008) There are three major databases for the complex carbohydrates, KEGG GLYCAN, and the database developed by the consortium for functional glycomics. All three databases are based on the carb bank database developed in 1990s.…”

Section: Introductionmentioning

confidence: 99%

Glycomics Data Mining

Rao¹,

Das²,

Umari³

2009

J Comput Sci Syst Biol

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The amount of glycomics data being generated is rapidly increasing as a result of improvements in analytical and computational methods. Correlation and analysis of this large, distributed data set requires an extensible and flexible representational standard that is also 'understood' by a wide range of software applications. An XML-based data representation standard that faithfully captures essential structural details of a glycan moiety along with additional information (such as data provenance) to aid the interpretation and usage of glycan data, will facilitate the exchange of glycomics data across the scientific community. We reviewed importance of data warehouse, showing a method of applying data mining techniques using XML, and some of the data issues, analysis problems, and results.

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GlycoCT—a unifying sequence format for carbohydrates

Cited by 172 publications

References 14 publications

Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for 2007–2008

Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for 2007–2008

MzJava: An open source library for mass spectrometry data processing

Glycomics Data Mining

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