Recent Publications

mzTab-M: a data standard for sharing quantitative results in mass spectrometry metabolomics

Abstract

Mass spectrometry (MS) is one of the primary techniques used for large scale analysis of small molecules in metabolomics studies. To date, there has been little data format standardization in this field, as different software packages export results in different formats represented in XML or plain text, making data sharing, database deposition and re-analysis highly challenging. Working within the consortia of the Metabolomics Standards Initiative, Proteomics Standards Initiative and the Metabolomics Society, we have created mzTab-M to act as common output format from analytical approaches using MS on small molecules. The format has been developed over several years, with input from a wide range of stakeholders. mzTab-M is a simple tab-separated text format, but, importantly, the structure is highly standardized through the design of a detailed specification document, tightly coupled to validation software, and a mandatory controlled vocabulary of terms to populate it. The format is able to represent final quantification values from analyses, as well as the evidence trail in terms of features measured directly from MS (e.g. LC-MS, GC-MS, DIMS, etc), as well as different types of approaches used to identify molecules. mzTab-M allows for ambiguity in the identification of molecules to be communicated clearly to readers of the files (both people and software). There are several implementations of the format available, and we anticipate widespread adoption in the field.

Hoffmann, N. et al. mzTab-M: a data standard for sharing quantitative results in mass spectrometry metabolomics. Analytical Chemistry (2019)
doi:10.1021/acs.analchem.8b04310

Identification of key lipids critical for platelet activation by comprehensive analysis of the platelet lipidome

Abstract

Platelet integrity and function critically depend on lipid composition. However, the lipid inventory in platelets was hitherto not quantified. Here, we examined the lipidome of murine platelets using lipid-category tailored protocols on a quantitative lipidomics platform. We could show that the platelet lipidome comprises almost 400 lipid species and covers a concentration range of seven orders of magnitude. A systematic comparison of the lipidomics network in resting and activated murine platelets, validated in human platelets, revealed that less than 20% of the platelet lipidome is changed upon activation, involving mainly lipids containing arachidonic acid. Sphingomyelin phosphodiesterase-1 (Smpd1) deficiency resulted in a very specific modulation of the platelet lipidome with an order of magnitude up-regulation of lyso-sphingomyelin (SPC), and subsequent modification of platelet activation and thrombus formation. In conclusion, this first comprehensive quantitative lipidomic analysis of platelets sheds light on novel mechanisms important for platelet function, and has therefore the potential to open novel diagnostic and therapeutic opportunities.

Peng, B. et al. Identification of key lipids critical for platelet activation by comprehensive analysis of the platelet lipidome. Blood (2018)
doi:10.1182/blood-2017-12-822890

Supplementary Material: Bioinformatics Scripts for Visualization and Network Analysis

Software-aided quality control of parallel reaction monitoring based quantitation of lipid mediators

Abstract

We characterized the performance of a micro-flow LC-ESI-MS2 approach to analyze lipid mediators (LMs) and polyunsaturated fatty acids (PUFA) that was optimized for SPE free lipid extraction. Tandem mass spectrometry was exclusively performed in parallel reaction monitoring (PRM) mode using TOF and Orbitrap analyzers. This acquisition strategy allowed in addition to quantitation by specific quantifier ions to perform spectrum comparisons using full MS2 spectra information of the analyte. Consequently, we developed a dedicated software SpeCS that allows to 1) process raw peak lists, 2) generate customized spectral libraries, 3) test specificity of quantifier ions and 4) perform spectrum comparisons. The dedicated scoring algorithm is based on signal matching and Spearman's rank correlation of intensities of matched signal. The algorithm was evaluated in respect of its specificity to distinguish structural related LMs on both instrument platforms. We show how high resolution mass spectrometry is beneficial to distinguish co-eluted LM isomers and provide a generalized quality control procedure for PRM. The applicability of the approach was evaluated analyzing the lipid mediator response during M. tuberculosis infection in the mouse lung.

Wutkowski, A. et al. Software-aided quality control of parallel reaction monitoring based quantitation of lipid mediators. Analytica Chimica Acta (2018). doi:10.1016/j.aca.2018.01.044

Shotgun Lipidomics Approach for Clinical Samples

Abstract

Shotgun lipidomics offers fast and reproducible identification and quantification of lipids in clinical samples. Lipid extraction procedures based on the methyl tert-butyl protocol are well established for performing shotgun lipidomics in biomedical research. Here, we describe a shotgun lipidomics workflow that is well suited for the analysis of clinical samples such as tissue samples, blood plasma, and peripheral blood mononuclear cells.

Eggers, L. F. & Schwudke, D. Shotgun Lipidomics Approach for Clinical Samples. in Clinical Metabolomics: Methods and Protocols (ed. Giera, M.) 163–174 (Springer New York, 2018). doi:10.1007/978-1-4939-7592-1_12