The next version of GOSLIN is there! Goslin is the first grammar-based computational library for the recognition/parsing and normalization of lipid names following the hierarchical lipid shorthand nomenclature. The new version Goslin 2.0 implements the latest nomenclature and adds an additional grammar to recognize systematic IUPAC-IUB fatty acyl names as stored, e.g., in the LIPID MAPS database and is perfectly suited to update lipid names in LIPID MAPS or HMDB databases to the latest nomenclature. Goslin 2.0 is available as a standalone web application with a REST API as well as C++, C#, Java, Python 3, and R libraries. Importantly, it can be easily included in lipidomics tools and scripts providing direct access to translation functions. All implementations are open source. https://pubs.acs.org/doi/10.1021/acs.analchem.1c05430

HFSP Award goes to our lab!

With great pleasure, I announce that we were awarded through the Human Frontier Science Program. We are eager to start the chapter of synaptoneurolipidomics, and we are thrilled to start this great project with labs around the globe:

We Love Lipids

We are delighted to contribute to the “We Love Lipids” Tutorial in 2022, introducing lipidomics and lipid sciences. Please save the dates and meet us again soon!

100 min with ILS

It is with great pleasure to announce the 2022 100 min with ILS podcast again. Stay tuned!  https://lipidomicssociety.org/2021/05/17/100-minutes-with-ils-podcast/

Signaling Lipidomics

Prof. Schebb

Prof. Dr. Nils Helge Schebb (Food Chemist and European Registered Toxicologist) is full professor for food chemistry at the University of Wuppertal, Germany. His group is developing instrumental analytical methods to investigate the biological activity of food ingredients.

The major focus of his research group in the last decade is set on targeted lipidomics of oxylipins. His lab developed one the most comprehensive internationally validated platforms for the analysis of oxylipins. Using this approach, the effect how n3-PUFA as well as polyphenols elicit their beneficial effects on human health, are analyzed. Dr. Schebb has published >100 peer reviewed publications of those > 50 about the analysis, formation and biology of oxylipins. Prof. Schebb gave a fantastic talk at the lipidomics seminar (24th of June 2021) on:

“Investigating the formation of eicosanoids and other oxylipins by means of LC-MS/MS (QqQ)”

We very much would like to thanks Prof. Schebb for his great and inspiring talk!

Prof. Thorsten Hornemann
Prof. Hornemann

It is for us a great pleasure to have Prof. Thorsten Hornemann as a guest speaker in our Department at the 24th of June 2021 on the topic of sphingolipid signaling. Th. Hornemann is professor for clinical chemistry and head of the lipidomics research facility at the Institute for Clinical Chemistry, University Zurich. His primary interest is the sphingolipid metabolism where he pioneered by identifying several new lipid metabolic pathways. He and his team developed several unique analytical methods and metabolic labelling techniques to investigate the structure, function and metabolism of sphingolipids with a particular focus on rare and atypical sphingolipid metabolites. He also established several lipid metabolites and lipid based metabolic signatures as diagnostic and prospective biomarkers for cardio-metabolic diseases including NAFLD, CVD, MetS and T2DM.

Thorsten many thanks for joining us it is always fantastic to listens to such great science!

Lipidomics.at turns virtual: ELM 2020 Bioinformatics for Lipidomics Symposium

Thanks to all attendees who helped to make this a great event! The ILS Applied Bioinformatics Interest Group invited to join the Bioinformatics for Lipidomics Symposium on October 2nd, 2020, as part of this year’s joint virtual European Lipidomics Meeting & Lipidomics Forum. With over 150 attendees discussing the challenges and future of lipidomics bioinformatics the event was a great success! We were very happy that this conference was supported by the ILS and the University of Vienna.

The schedule is available at ILS https://bit.ly/2IdlyJl

The symposium was divided into four major sessions:

Databases, Ontologies and Online Resources, Visualization and Exploration, Data Integration and Applications, Identification and Quantification Tools

The presentations of this symposium will be available soon via the ILS homepage!!

New Publication: LipidCreator

Mass spectrometry (MS)-based targeted lipidomics enables the robust quantification of selected lipids under various biological conditions but comprehensive software tools to support such analyses are lacking. Here we present LipidCreator (LC), a software that fully supports targeted lipidomics assay development. LC offers a comprehensive framework to compute MS/MS fragment masses for over 60 lipid classes. LC provides all functionalities needed to define fragments, manage stable isotope labeling, optimize collision energy and generate in silico spectral libraries. We validate LC assays computationally and analytically and prove that it is capable to generate large targeted experiments to analyze blood and to dissect lipid-signaling pathways such as in human platelets.


Lipidomics.at turns virtual: Witting

This week we are looking forward to a presentation from Michael Witting from the Helmholtz Zentrum München. Michael is especially interested in lipidomics and metabolomics of C. elegans and we are anticipating his talk about LC-MS based strategies for the study of this popular model organism. The talk will take place on Thursday, 10 a.m. via Zoom. Registration is still possible, just write an e-mail to robert.ahrends@univie.ac.at. Thanks Michael for joining!

Lipidomics.at turns virtual: Scwudke

Dominik Schwudke, Forschungszentrum Borstel

While scientists around the world are facing restrictions due to the current COVID-19 pandemic, the challenging situation also offers new possibilities: the international exchange among the scientific community has never been higher, and never was it easier to get colleagues from abroad to share their exciting projects in our Analytical Chemistry Seminar series (now turned webinar series). Last week we had the pleasure of hosting Dominik Schwudke from the Research Center Borstel at our institute webinar. He gave a very insightful talk about the potential of lipidomics for the therapy monitoring of lung diseases in context of Mycobacterium tuberculosis. Dominik is an integral part of the clinical lipidomics community and we are glad that he took the time to share his expertise with us and engaged in the lively discussion that followed his talk. Thanks again Dominik for joining!

LipoSysMed 2019

Turning hay into needles: the road to integration of large-scale analytical lipidomics data into biomedical research

Lipidomics studies networks, pathways and interactions of cellular lipids within the biological system.

As a newly emerging discipline and highly interdisciplinary field based on the application of mass spectrometry, analytical chemistry and computational biology, lipidomics is evolving into a promising stepping stone for systems biology research with recent applications in human health and disease.

A rapid increase in the number of measurements, as well as increasing amounts of data per measurement due to higher sensitivity, generate massive data sets that pose a challenge to traditional data analysis and integration.

Similar to other “omics” disciplines, lipidomics is thus facing the “big data trap”, challenging the ways we store and process large amounts of data acquired over time, extracting useful information from it, and moreover, interpreting the data from a systems medicine research perspective.

The bioinformatics team of our lab works on projects (https://lifs.isas.de/) to overcome these challenges and develops computational tools and programs covering the requirements of life science researchers. These tools are first tested internally by our team members who generate the data, and are subsequently optimized and released for general use to the scientific community. Moreover, we also organize and arrange workshops, where our team teaches how to use and implement our programs and tools, helping the user to achieve scientifically meaningful data from their research.

To advertise the newest generation of lipid analysis tools and programs, we hosted the LipoSysMed summer school 2019 in alliance with the research groups of Dr. Maria Fedorova (Institute of Bioanalytical Chemistry) and Dr. Robert Ahrends (Institut für Analytische Wissenschaften – ISAS) in Leipzig / Germany (https://home.uni-leipzig.de/liposysmed/) . For one week, the participants got in touch with the newest computational technologies and attended workshops and tutorials. The rationale for the summer school was to bring practitioners with diverse clinical research backgrounds together to network with the bioinformatics tool developers and their colleagues. At LipoSysMed, we had the opportunity for mutual exchange and to troubleshoot scientific challenges with the tool developers directly, giving us fresh ideas on application-oriented targets and providing us with even more input on user-friendly software development. Overall, we especially set a high value on the constant bilateral communication with clinical staff scientists and tool developers, to increase the usability and functionality of our analysis programs, in order to reduce analysis time and getting most out of very costly clinical samples.

Our message is that just collecting “big data” is meaningless without proper analytics. We are convinced that only with consecutive and routine teaching and support of our fellow researchers, an increasing number of laboratories will introduce and extend their bioinformatics pipelines  for the benefit of more insightful, reproducible research.

We design next-generation lipid analysis tools for tailored analytics, enhancing and bringing forward research on topics such as the development of Obesity, Alzheimer disease or insufficiency in blood clotting, which are all highly lipid-dependent.