Systems Glycomics

Beilstein Glyco-Bioinformatics Symposium 2017

13 – 15 June 2017

Akademie Berlin-Schmöckwitz, Berlin, Germany

The Glyco-Bioinformatics Symposium 2017 brought together glycochemists and biologists with experts in bioinformatics and computer sciences.

Scientific Program:

Daniel Kolarich / Max Planck Institute of Colloids and Interfaces, Potsdam

René Ranzinger / University of Georgia, Athens, USA

Peter H. Seeberger / Max Planck Institute of Colloids and Interfaces, Potsdam

William S. York / University of Georgia, Athens, USA

Martin G. Hicks and Carsten Kettner / Beilstein-Institut


Topics 2017

  • unravelling the complexity of structures and roles of glycoconjugates,

  • cooperativity of glycoconjugates with other macromolecules in the cell

  • integration of data from glycomics, proteomics and genomics resources creating a systems wide functional network
  • strategies for mining and analysing large data sets and high-throughput data

  • adding glycoconjugates to the systems biology equation

  • software tools for data storage, analysis, mining and sharing


by Niclas Karlsson, University of Gothenburg, Sweden


Download PDF pdf icon


The 2017 5th Beilstein Glyco-Bioinformatic Symposium, entitled “Systems Glycomics” aimed at   highlighting glycomic research and unique glycomic tools, and how it interacts or potentiallycan interact with other life science areas to solve emerging global and local research problems. It was held on the 13th - 15th of June in Akademie Berlin-Schmöckwitz, Berlin, with more than 50 registered delegates representing 13 countries. The symposium was comprised of a mixture of comprehensive presentations about the subject, short poster (“flash”) presentations  (Richard Drake, Sergey Samsonov, John Hogan, Vinyaga Gnanapragassam, Issaku Yamada, Masaaki Matsubara, Oliver Grant, Kazuhiro Aoki, Sylvie Ricard-Blum, Bas Jansen, Kathirvel Alagesan, Niclas Karlsson and Tsuchiya Shinichiro)), and software presentations as well on Tuesday 13th (Markus Pioch; Issaku Yamada, Julien Mariethoz, Alessandra Gastaldello, Davide Alocci and Kiyoko Aoki-Kinoshita) and on Wednesday 14th (Oliver Grant, Yukie Akune, Miguel Rojas).

The poster session was held on Tuesday evening and the software demonstration session on Wednesday afternoon). The symposium also included an end-of-the-symposia panel discussion as well as plenty of time for unscheduled interactions and discussions during breaks for coffee and meals and at unscheduled evening and afternoons/evenings. The spirit of the Beilstein Symposium was maintained by the intimate interactions of senior and junior researchers in a confined location, not only for the conference but also for the accommodation. A limited number of participants and regulars as well as selected speakers provide continuity for the series as well as broadening the glycoscience topic that allows fruitful and interesting discussions throughout the days of the meeting.

The 2017 symposium’s presentations covered topics of clinical application for glycoscience, model systems to investigate the role of glycans, new technologies to investigate glycoscience, novel data handling systems and software, development of molecular tools and arrays.



Nathan Lewis initiated the scientific discussion by highlighting the fact that a level of the single glycan disialylacto-N-tetraose amongst all human milk oligosaccharides determines the severity of necrotising enterocolitis in new-born. He then illustrated how Markov modelling can be used to engineer and understand the N-glycosylation regulation including both the role of glycosyltransferases and metabolic pathways.

Linda Hsieh-Wilson demonstrated the use of quantitative proteomics to identify O-GlcNAcylated proteins and their interactions and to display cellular interactions to understand how the dynamic O-GlcNAcylation is involved in cellular processes (HEK293T cells, brain network, normal versus disease conditions).

Nicolle Packer a summarized the current state-of-the-art of glycomic/glycoproteomic MS and concluded that the current technologies for glycomics and proteomics are truly on its way, while there is a lack of both coherent efforts to enable the interpretation of data and informatics tools to support the integration with other life science data bases on the one hand and the modelling of carbohydrate interaction on the other hand. In addition, there is still a lack of technologies for other type of complex carbohydrates.

René Ranziger presented the GRITS toolbox for glycomic MS and how it can be used for archiving annotating and analysis of data as well as associating metadata. The modular toolbox also allows the extension of the GRITS by other researchers plugins.

Ajit Varki informed about the history behind the SNFG nomenclature, the use of the nomenclature driven by the Essentials of Glycobiology and the work with the discussion group with NCBI to update, develop and maintain SNFG.

Serge Perez discussed the topic of how to expand the current nomenclature to include 3D representation. This includes the POLY-GLYCAN to generate oligosaccharide structures and the SweetUnityMol to visualise 3D glycans, still keeping features of SNGF in order to easily visualise glycan features.

Jim Paulson described the use of MS to determine the type of glycosylation (high mannose, complex, no-glycosylation) on individual sites on the HIV gp160, with the membrane bound protein characterised from model systems resemble the infectious type.

Weston Struwe followed up on the HIV spike by describing the gp120 consisting of mostly high-mannose, while gp41 have more complex glycans. The group has also characterised mannose binding lectins (Banlec and Griffithsin) for HIV immune targeting as well as the use of IM-MS for characterisation of glycan isomers



Gordon Lauc showed that in order to make sense of glycomic data, large clinical sets are required. He indicates that 80% of the glycosylation is heritable, but only a limited number of the loci that regulates IgG glycosylation is directly linked to glycosyltransferases. The introduction of a glycome age can be used for early detection of disease pre-symptomatically.

Kiyoki Aoki-Kinoshita described the use of the Celldesigner software to generate the glycosylation pathway in the Neurospora fungi. She used data from the SABIO-RK kinetic database to in insilico create various  types and amounts of glycans for the wild-type and knockout strains of  this fungal system. She also presented the Glycosmos, an international collaboration that provides a platform for repositories of glycans and glycoconjugates with links to other life science databases

Thisbe Lindhorst addressed the area of mimicking the interaction of the glycocalyx for carbohydrate interactions using synthetic ligands, in particular the type 1 fimbria FimH lectin. She also analysed the stereochemistry of lectin binding using photoswitchable glycomimetics.

Sabine Flitsch presented her efforts in generating IM-MS fragment libraries in order to characterise alpha/beta configuration of glycans and its application of determining the specificity of desialylating enzymes as well as the characterisation of natural glycosides which have been extended from amygdalin.

Larah Mahal described a lectin platform and miRNA proxy platform for the role of core fucosylation and FUT8 that is upregulated in melanoma metastasis. This affects the cleavage of adhesion molecule L1CAM and thus shaping cell migration.

Hiren Joshi introduced the term Glycotopiary which is a simple cell technology to address the glycosylation of O-linked, N-linked and heparan sulphate. Examples included the discovery of new O-mannosyl transferases and the engineering of adhesins that selectively binds muc7 and gp1ba, but not other mucins. The software tool Glycodomainviewer was presented as a way to capture and display sites of glycosylation on glycoproteins.

Ola Blixt presented the development and targeting of single chain antibodies to O-linked and advanced glycation end products, including the antibody scfv g2d11 that binds bis Tn antigen in gastric mucosa and scfv D1-B2 against AGE, staining atherosclerotic plaques and pancreatic cancer.

Erdmann Rapp has identified the lack of useful tools for the analysis of MS-deteced  glycopeptides and introduced glyXtoolsMS based on open ms c++. In practice, he and demonstrated its applicability on tandem data from IgG and fibrinogen.

Frédérique Lisacek introduced the glycomic tab on Expasy and associated modular software including Pepsweetener, calculator, Glynsight, Glycosite align, Glydin and Glyconnect.

Will York asked the question of how to navigate around the glyco-data and introduced a conceptual schema to visualise data based on RDF. His vision was a bioinformatics infrastructure based on the NIH R34 Grant, unifying the current resources in glyco-bioinformatics and databases.

Kerry Gilmore presented the automated glyco- assembly line, and the use of chemistry and reaction conditions to control stereochemistry to produce designed oligosaccharides.

Ten Feizi showed the development of an O-glycan array and demonstrated its usability to Rotavirus p(10) and p(19) interaction with porcine gastric mucin oligosaccharides and in particular the linear H type 1 structure.

Manfred Wuhrer discussed how to increase throughput for glycomics for and clinical relevance (colorectal cancer and MALDI imaging) and compared his findings applying  different platforms (MALDI-MS, HILIC-HPLC and xCGE-LIF).

Gerald Hart updated us about the O-GlcNacylation and its involvement in nutrient regulation and transcriptional regulation, including O-GlcNAcylation of the tata binding protein (tbp), where the glycosylation of T114 impairs metabolic gene expression.

Matthew Campbell presented the development a repository, called Glycostore that stores analysis data from HLIC, PGC and CE analysis including retention times for N-glycans, O-glycans, glycolipids. In addition, he shows interconnections with other glycoresources using GlycoRDF ontology.

The talks were concluded by the presentation by Will York about the MIRAGE project , what it is, and how we should endorse the use of the guidelines. Finally, a panel talked about the term “Systems Glycomics”. The panelists discussed both in terms how it can specifically identify the glycosylation as part of a systems biology approach as well as providing a “buzz word” that will help in providing attention to glycosylation for decision makers and funding agencies.

Scientific Program

Towards a Systems-level Understanding of Glycosylation to Guide Drug Development and Biological Diversity
Nathan E. Lewis, University of California San Diego, La Jolla, CA

A Systems-level Approach to Identifying Key Functions for Glycosylation
Linda C. Hsieh-Wilson, California Institute of Technology, Pasadena, CA

Poster Flash Presentation #1
(Posters 1 - 4)

Technology Shapes Glycoinformatics
Nicolle H. Packer, Macquarie University Sydney

GRITS Toolbox – A Platform for the Development of Integrated Glycomics Data Processing and Data Analysis Tools
René Ranzinger, CCRC, University of Georgia, Athens, GA

Software Elevator Talks #1
(Software 1 - 5)

SNFG: Symbol Nomenclature for Glycans
Ajit Varki, University of California San Diego, La Jolla, CA

Toolboxes for Standardized Investigations, Constructions and Representations of Glycans
Serge Perez, CNRS - University Grenoble Alpes

Poster Flash Presentation #2
(Posters 5 - 8)

HIV Glycosylation
James C. Paulson, The Scripps Research Institute, La Jolla, CA

Emerging Glycomics Information from Ion Mobility and Intact Mass Spectrometry in the Study of HIV Viral Spikes
Weston Struwe, University of Oxford

Poster Flash Presentation #3
(Posters 9 - 12)

Poster Session


Adding Glycomics to the Big Data Revolution: What Did We Learn from the First 50,000 Analyses
Gordan Lauc, University of Zagreb

Revealing and Imaging Disease Glycosignatures from 2000 Cells
Daniel Kolarich, Griffith University, Southport

Simulation Analysis of N-glycan Biosynthesis in Neurospora
Kiyoko Aoki-Kinoshita, Soka University, Tokyo

Photoswitchable Glycomimetics to Probe Carbohydrate Recognition in Bacterial Adhesion
Thisbe K. Lindhorst, Christian-Albrechts Universität Kiel

Hyphenated IM-MS Methods as High-resolution Sequencing Tools for Carbohydrates
Sabine L. Flitsch, The University of Manchester

Software Elevator Talks #2
(Software 7 - 10)

Systematically Cracking the Glycocode
Lara K. Mahal, New York University

In-silico Techniques to Understand the Deconstructed Glycome
Hiren J. Joshi, University of Copenhagen

Software Demonstrations

Epitope-First Approach – An Efficient Strategy for Production of scFv Monoclonal Antibodies Targeting Post-translational modified Proteins
Ola Blixt, University of Copenhagen

glyXtoolsMS – Towards Automated Analysis of Glycopeptide Mass Spectrometry Data
Erdmann Rapp, MPI for Dynamics of Complex Technical Systems, Magdeburg

Frédérique Lisacek, Swiss Institute of Bioinformatics, Geneva

Requirements for a Unified BioInformatics Infrastructure to Increase Understandability and Accessibility of Glycoanalysis
William S. York, CCRC, University of Georgia, Athens, GA

Towards Predicting the Stereoselectivity and Mechanism of Glycosylation Reactions Using a Database Populated by Automated Flow Chemistry
Peter H. Seeberger, MPI for Colloids and Interfaces, Potsdam

Progress and Prospects for O-glycome Arrays
Ten Feizi, Imperial College London

Mass Spectrometric Glycomics – Increasing Throughput and Clinical Relevance
Manfred Wuhrer

Nutrient Regulation of Transcription and Signalling by O-GlcNAcylation
Gerald W. Hart, Johns Hopkins University, Baltimore, MD

GlycoStore: A Behind the Scenes Look
Matthew P. Campbell, Griffith University, Southport

MIRAGE Presentation and Panel Discussion
Panelists: Nicolle Packer, Niclas Karlsson, Manfred Wuhrer, ...

Poster Presentations

The Human Tumor N-glycome: Two Dimensional Mapping and Structural Class Comparisons Across 20 Tumor Types
Richard Drake

Evaluation of Computational Approaches for the Analysis of FGF1-heparin Interactions
Sergey Samsonov

Current Advances in Automated Analysis of Glycosaminoglycan Tandem Mass Spectrometry
John D. Hogan

Methylglyoxal as a Modulator of Neuroblastoma Metastasis
Vinayaga S. Gnanapragassam

GlycoNAVI: GlycoBio Database Utilizing Semantic Web Technologies
Issaku Yamada

Implementation of an Annotation System for Glycosphingolipid MS Data
Masaaki Matsubara

Predicting N-glycan Processing Based on Enzyme-glycan Accessiblity
Oliver C. Grant

Comprehensive Functional and Structural Glycosphingolipidomics in a-galactosidase A-deficient Rats
Kazuhiro Aoki

Translating Glycosaminoglycans into the GlycoCT Format: Application for the Curation of Protein-glycosaminoglycan Interactions in MatrixDB
Sylvie Ricard-Blum

High-throughput Pre-processing of Glycan and Glycopeptide Data
Bas Jansen

Developing Glycoproteomics Toolkit Using Synthetic N-glycopeptides
Kathirvel Alagesan

UniCarb-DB – A Glycomics MS Spectral Library
Niclas Karlsson

A New Version of GlycanBuilder to Draw a Wide Variety of Ambiguous Glycans
Tsuchiya Shinichiro

Software Demonstrations

Semi-automated Analysis of Glycopeptide Mass Spectrometry Data with glyXtoolMS
Markus Pioch

GlycoNAVI: GlycoBio Database Utilizing Semantic Web Technologies
Issaku Yamada

GlyConnect, an Interactive Tool to Query and Navigate across Glycoproteomics Data
Julien Mariethoz, Alessandra Gastaldello

PepSweetener and Glynsight – Two Interactive Tools Supporitng Glycoproteomics Studies
Davide Alocci

The International Glycan Structure Repository GlyTouCan
Kiyoko Aoki-Kinoshita

GRITS Toolbox – A Freely Available Software System for Processing and Storing of Glycomics MS Data and Metadata
René Ranzinger

The New Glycan-web User Interface and Webtool Suite
Oliver C. Grant

Software for Management, Storage and Presentation of Glycan Array Data
Yukie Akune

Miguel Rojas-Macias


Photos taken by Julien Mariethoz

The conference venue
Opening the conference
The audience
Nathan Lewis
Linda Hsieh-Wilson
Nicki Packer giving her talk
Rene Ranzinger talking
Software talk: Julien Mariethoz
Coffee Break: Thisbe Lindhorst, Sabine Flitsch and Frédérique Lisacek
Coffee Break: Jim Paulson, Sergey Samsonov and Serge Perez
Ajit Varki's statement
Jim Paulson
Poster Session (2)
Poster Session
Daniel Kolarich and Niclas Karlsson
Jerry Hart and Will York
Gordan Lauc answering questions
Kiyoko Aoki-Kinoshita giving her talk
Software presentation (1)
Software presentation (2)
Coffee Break: Erdmann Rapp and Gordan Lauc
Coffee Break: Nicki Packer and Carsten Kettner
Coffee Break: Kathir Alagesan and Frédérique Lisacek
Erdmann Rapp talking
Thisbe Lindhorst being introduced by Frédérique Lisacek
Lara Mahal giving her talk
Ten Feizi interacting with the audience
Coffee Break: Vinayaga Gnanapragassam and Oliver Grant
Evening light
Conference photo