turns virtual: LipidCreator @ISMB

With great pleasure presented Lipid Creator on the annual meeting of the international Society for Computational Biology (ISCB) at the CompMS COSI track in Montreal (June 2020). Here comes the link:

The lab also would like to thank all the people involved in the development of LIPIDCREATOR and the infrastructure around it and for their support! Also, thanks for the great questions and good suggestions during ISMB! turns virtual: Virtual Podium

Social distancing is a must, but should not block the science! Due to COVID-19, you have been impacted by the cancellation of conferences and are losing the chance to connect and to present your research. Therefore the team is embracing the opportunity to present at virtual platforms. Updates where we go and present can be found here, please join to engage and discuss. We are also hosting regularly own seminars on Thursdays, please contact us for more information. turns virtual: Winter

Proteomics of the Lysosome

The lysosome is the central lytic organelle of mammalian cells. After it has been regarded for decades as a static and unregulated “cellular waste bag”, it is becoming more and more apparent, that the lysosome is a dynamic and regulated organelle, which is playing a central role in cellular metabolism. This is further underlined by the fact, that malfunctions of lysosomal hydrolases result in a group of >70 rare inherited diseases, so-called lysosomal storage disorders, and that lysosomes can play a decisive role in more common conditions such as cancer and neurodegenerative diseases. We are investigating the composition of lysosomes as well as the lysosomal response to various disease pathologies using mass spectrometry based proteomics. In particular, we optimized strategies for lysosomal enrichment, the proteomic characterization of lysosomal and lysosome-interacting proteins, and the identification of novel lysosomal proteins. Using Quantification Concatemers (QConCats), we generated absolutely quantified stable isotope labeled internal standards for the absolute quantification of lysosomal protein copy numbers and developed a multiple reaction monitoring (MRM) assay covering ~400 peptides from 143 proteins. Analysis of cell lines, isolated lysosomes, and mouse tissues revealed a dynamic range of several orders of magnitude for individual lysosomal proteins and organ-specific abundance profiles. For a better understanding of lysosomal protein-protein interactions and structures, we performed cross linking mass spectrometry experiments with isolated lysosomes. We were able to identify ~4300 cross links from >1300 proteins including 882 interactions for lysosomal and lysosome-associated proteins. This enabled us to identify novel interaction partners, to validate known structures, and to propose novel structures for lysosomal proteins and protein complexes. Taken together, these data provide us with a better view of lysosomal composition, providing valuable information for a better understanding of lysosomal function.

New Publication: Cellular stress causes cancer cell chemoresistance

Wien (UNIWIEN) – Resistance of cancer cells against therapeutic agents is a major cause of treatment failure, especially in recurrent diseases. An international team around the biochemists Robert Ahrends from the University of Vienna and Jan Medenbach from the University of Regensburg identified a novel mechanism of chemoresistance which has now been published in “Nature Communications”. It is driven by the Unfolded Protein Response, a cellular stress response pathway that alters gene expression and cellular metabolism to promote adaption and cell survival upon accumulation of unfolded proteins.

UPR triggers cancer resistance

There is a broad range of mechanisms associated with chemoresistance, many of which to date are only poorly understood. The so-called cellular stress response – a set of genetic programmes that enable the cells to survive under stressful conditions – plays a key role in the development of numerous diseases and in chemoresistance. A better understanding of the cellular stress response pathways is therefore urgently required to develop new therapeutic concepts to overcome chemoresistance. “In this context, we employed comprehensive analytical approaches to gain deep and molecular insight into the Unfolded Protein Response, a cellular stress reaction induced by unfolded proteins”, says Robert Ahrends, group leader at the Department of Analytical Chemistry of the Faculty of Chemistry.

Unfolded proteins cause stress and disease

The Unfolded Protein Response (UPR) contributes to cancer development and progression and plays an important role in diseases such as diabetes and neurodegenerative disorders. For their study of the UPR’s molecular biological characteristics, the researchers applied state-to-art analytical tools in the context of a multiomics approach, combining large datasets from genetics, proteomics and metabolomics. This allowed them to define the Unfolded Protein Response regulon, a comprehensive list of genes that are activated to promote cell survival under stress.

“Besides the previously known factors, we identified to our surprise numerous genes that have not previously been implicated in stress response pathways”, explain the researchers, “and many of them have key functions in cancer development and cellular metabolism.”

Changes in 1C metabolism

Changes in cellular metabolism are characteristic of many cancer types and promote a rapid tumour growth, as Nobel Prize winner Otto Warburg demonstrated already in the 1930s in his ground-breaking work. In their study, the researchers discovered stress-mediated genetic regulation of enzymes involved in one-carbon (1C) metabolism which relies on the vitamin folate as a cofactor. Concomitant to the metabolic re-wiring, the stressed cells became fully resistant against chemotherapeutic agents, which target this specific metabolic pathway. This includes Methotrexate, a drug commonly employed in the treatment of cancer and rheumatic diseases. Detailed biochemical and genetic investigations revealed that resistance is driven by a previously unrecognized mechanism. According to the study authors, its precise molecular characterisation might lead to novel therapeutic concepts aimed at overcoming chemoresistance in cancer therapy.

Publikation in “Nature Communications”:

Reich S, Nguyen CDL, Has C, Steltgens S, Soni H, Coman C, Freyberg M, Bichler A, Seifert N, Conrad D, Knobbe-Thomsen CB, Tews B, Toedt G, Ahrends R, und Medenbach J: A multi-omics analysis reveals the Unfolded Protein Response regulon and a role of eIF2-phosphorylation in resistance to folate-based anti-metabolites.

DOI: 10.1038/s41467-020-16747-y

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. 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 Thanks Michael for joining! 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!

Lipidomics needs Standardization

Great our Lipidomics Standard Initiative manuscript (LSI) is out! Thanks to all people and groups how supported this endeavor, which encourages researchers to engage with the Lipidomics Standards Initiative to take lipidomics research to the next level.

Great, our Lipidomics Standard Initiative manuscript (LSI) is out! Thanks to all people and groups how supported this endeavor, which encourages researchers to engage with the Lipidomics Standards Initiative to take lipidomics research to the next level.

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 ( 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 ( . 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.

Lipidomics Forum 2019

Registration for Lipidomics Forum 2019 in Borstel, Germany is now open. This year, LIFS partners offer two training courses on lipidomics supported by de.NBI. Student members of the German Mass Spectrometry Society are eligible for travel support .

We are also very happy to welcome the following KEYNOTE SPEAKERS:

Hülya Bayır, University of Pittsburgh (Pittsburgh, US), Lev Becker, University of Chicago (Chicago, US), Satyajit Mayor, National Centre for Biological Sciences – TIFR (Bangalore, India), Thomas Eichmann, University of Graz (Graz, Austria), Karsten Hiller, Technische Universität Braunschweig (Braunschweig, Germany), Shane R. Ellis, Maastricht University (Maastricht, Netherlands)