Recent Publications

Goslin 2.0 Implements the Recent Lipid Shorthand Nomenclature for MS-Derived Lipid Structures

Abstract

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.

DOI: 10.1021/acs.analchem.1c05430

Multiomics of synaptic junctions reveals altered lipid metabolism and signaling following environmental enrichment

Abstract

Membrane lipids and their metabolism have key functions in neurotransmission. Here we provide a quantitative lipid inventory of mouse and rat synaptic junctions. To this end, we developed a multiomics extraction and analysis workflow to probe the interplay of proteins and lipids in synaptic signal transduction from the same sample. Based on this workflow, we generate hypotheses about novel mechanisms underlying complex changes in synaptic connectivity elicited by environmental stimuli. As a proof of principle, this approach reveals that in mice exposed to an enriched environment, reduced endocannabinoid synthesis and signaling is linked to increased surface expression of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) in a subset of Cannabinoid-receptor 1 positive synapses. This mechanism regulates synaptic strength in an input-specific manner. Thus, we establish a compartment-specific multiomics workflow that is suitable to extract information from complex lipid and protein networks involved in synaptic function and plasticity.

DOI: 10.1016/j.celrep.2021.109797

Goslin: A Grammar of Succinct Lipid Nomenclature

Abstract

We introduce Goslin, a polyglot grammar for common lipid shorthand nomenclatures based on the LIPID MAPS nomenclature and the shorthand nomenclature established by Liebisch and co-authors 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 and 3) to provide a consistent mapping from lipid shorthand names to lipid building blocks and structural properties. 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.

 

Kopczynski, D., Hoffmann, N., et al. Goslin - A Grammar of Succinct Lipid Nomenclature. Analytical Chemistry, 92, 16, 10957–10960 , June 26th, (2020)
doi:10.1021/acs.analchem.0c01690

LipidCreator workbench to probe the lipidomic landscape

Abstract

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, a software that fully supports targeted lipidomics assay development. LipidCreator offers a comprehensive framework to compute MS/MS fragment masses for over 60 lipid classes. LipidCreator provides all functionalities needed to define fragments, manage stable isotope labeling, optimize collision energy and generate in silico spectral libraries. We validate LipidCreator 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.

 

Peng, B. et al. LipidCreator workbench to probe the lipidomic landscape. Nature Communications 11, 2057 (2020)
doi:10.1038/s41467-020-15960-z