We introduce Goslin (August 2020), a polyglot grammar for common lipid shorthand nomenclatures based on the LipidMaps nomenclature and the shorthand nomenclature established by Liebisch et al. and used by LipidHome and SwissLipids. Goslin was designed to address the following pressing issues in the lipidomics field: 1) to simplify the implementation of lipid name handling for developers of mass spectrometry-based lipidomics tools; 2) to offer a tool that unifies and normalizes the main existing lipid name dialects enabling a lipidomics analysis in a high-throughput fashion. We provide implementations of Goslin in four major programming languages, namely C++, Java, Python 3, and R to kick-start adoption and integration. Further, we set up a web service for users to work with Goslin directly. All implementations are available free of charge under a permissive open source license. Here some links:

With great pleasure Lipidomics.at 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: https://www.iscb.org/cms_addon/conferences/ismb2020/tracks/compmscosi

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!

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 lipidomics.at 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.

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.