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Guiding the choice of informatics software and tools for lipidomics research applications

Guiding the choice of informatics software and tools for lipidomics research applications

February 2023.

Zhixu Ni , Michele Wölk, Geoff Jukes, Karla Mendivelso Espinosa, Robert Ahrends, Lucila Aimo, Jorge Alvarez-Jarreta, Simon Andrews, Robert Andrews, Alan Bridge, Geremy C Clair, Matthew J Conroy, Eoin Fahy, Caroline Gaud, Laura Goracci, Jürgen Hartler, Nils Hoffmann, Dominik Kopczyinki, Ansgar Korf, Andrea F Lopez-Clavijo, Adnan Malik, Jacobo Miranda Ackerman, Martijn R Molenaar, Claire O’Donovan, Tomáš Pluskal, Andrej Shevchenko, Denise Slenter, Gary Siuzdak, Martina Kutmon, Hiroshi Tsugawa, Egon L Willighagen, Jianguo Xia, Valerie B O’Donnell, Maria Fedorova

 

Abstract

Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researchers, deciding which approach best suits their application relies on ad hoc testing, which is inefficient and time consuming. Here we first review the data processing pipeline, summarizing the scope of available tools. Next, to support researchers, LIPID MAPS provides an interactive online portal listing open-access tools with a graphical user interface. This guides users towards appropriate solutions within major areas in data processing, including (1) lipid-oriented databases, (2) mass spectrometry data repositories, (3) analysis of targeted lipidomics datasets, (4) lipid identification and (5) quantification from untargeted lipidomics datasets, (6) statistical analysis and visualization, and (7) data integration solutions. Detailed descriptions of functions and requirements are provided to guide customized data analysis workflows.

 

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A platelet lipidomics signature in patients with COVID-19

A platelet lipidomics signature in patients with COVID-19

December 2023.

Laura Goracci, Eleonora Petito, Alessandra Di Veroli, Emanuela Falcinelli, Caterina Bencivenga, Elisa Giglio, Cecilia Becattini, Edoardo De Robertis, Gaetano Vaudo, Paolo Gresele

Abstract

Ischemic cardiovascular and venous thromboembolic events are a frequent cause of death in severe COVID-19 patients. Platelet activation plays a key role in these complications, however platelet lipidomics have not been studied yet. The aim of our pilot investigation was to perform a preliminary study of platelet lipidomics in COVID-19 patients compared to healthy subjects. Lipid extraction and identification of ultrapurified platelets from eight hospitalized COVID-19 patients and eight age- and sex-matched healthy controls showed a lipidomic pattern almost completely separating COVID-19 patients from healthy controls. In particular, a significant decrease of ether phospholipids and increased levels of ganglioside GM3 were observed in platelets from COVID-19 patients. In conclusion, our study shows for the first time that platelets from COVID-19 patients display a different lipidomics signature distinguishing them from healthy controls, and suggests that altered platelet lipid metabolism may play a role in viral spreading and in the thrombotic complications of COVID-19.

Keywords: COVID-19; Platelet lipidomics.

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Analysis of Phosphatidylinositol Modifications by Reactive Nitrogen Species Using LC-MS: Coming to Grips with Their Nitroxidative Susceptibility

Analysis of Phosphatidylinositol Modifications by Reactive Nitrogen Species Using LC-MS: Coming to Grips with Their Nitroxidative Susceptibility

July 2023.

Stefano Bonciarelli, Bruna Neves, Pedro Domingues, Tânia Melo, Laura Goracci, Maria Rosário Domingues

Abstract

Phosphatidylinositols (PIs) are complex lipids that play a key role in cell signaling. Like other phospholipids, they are esterified with unsaturated fatty acyl residues (FAs), making them susceptible to modification by reactive oxygen and nitrogen species (RNS). Recent studies using mass spectrometry (MS)-based lipidomics approaches have revealed that lipid nitration results in a plethora of structurally and chemically modified lipids (epilipids), including nitrated and nitroxidized derivatives of phosphatidylcholines, phosphatidylethanolamines, phosphatidylserines, and cardiolipins. However, there is a notable lack of knowledge regarding the characterization of RNS-modified PI derivatives. In this study, we used C18 high-resolution liquid chromatography-tandem MS approaches to describe the fragmentation signature of nitrated and nitroxidized PIs, bearing different fatty acyl chains. Using this approach and accurate mass measurements, we were able to identify nitro- PI derivatives, dinitro- and nitrohydroxy- derivatives for a few PI species. The data showed the typical neutral loss of nitrous acid (HNO2) as well as the fragmentation patterns corresponding to modified fatty acyl chains (such as NOx-RCOO–, [M – NOx-RCOOH – H]– and [M – NOx-RCOOH – C6H10O5 – H]–), making it possible to identify these epilipids. The susceptibility of PIs to nitration was also investigated, revealing that it depends exclusively on the chains of unsaturated FAs esterified in PI, showing a higher conversion rate for those with C18:1. Overall, the knowledge gathered in this study will contribute to the precise characterization of these epilipids in complex biological samples, offering new opportunities to unveil the pathophysiological roles of nitrated and nitroxidized PI derivatives at the cellular and tissue levels.

Keywords: LC-MS; lipidomics; nitration; nitrative stress; nitroxidative stress.

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User Meeting Agenda

Wednesday 12th October

15.00h General presentation about Mass Analytica.
Gabriele Cruciani & Ismael Zamora. Molecular Discovery & Lead Molecular Design.

15.30h ONIRO: an efficient tool for Biotransformation studies.
Christophe Bouillod. Servier

16.00h How we use MassMetaSite and ONIRO in metabolite identification work at AstraZeneca, Gothenburg
Anja Ekdahl – AstraZeneca

16.30h Use of ONIRO
Virginie Gosselin – Sanofi

17.00h Roche/Biotransformation group
Bernd Steinhuber. F.Hoffmann La-Roche

17.30h Strategy for elucidation of VHH constructs (NANOBODY®)
Sabrina Schmeier – Sanofi

18.00h Harmonizing Discovery Workflows between Waters and Molecular Discovery
Russell Mortishire-Smith and David Heywood – Waters

Thursday 13th October

09.00h HRMS based Quantitation enabled through Automated Data Processing
Kevin Bateman – Merck

09.30h Quantification studies in ADME
Ismael Zamora. Lead Molecular Design

10.30h Macromolecule degradation studies
Fabien Fontaine / Luca Morettoni. Lead Molecular Design / Molecular Discovery

11.30h EAD vs CID Fragmentation for Small Molecule and their Metabolites
Christopher Kochansky – Exelisis

12.00h Benefits & challenges of software aided MetID
Christine Maurer – Merck Group

14.30h Lipostar 2 (the present) & MARS (on the way)
Laura Goracci. Molecular Discovery

15.00h In-depth and high throughput lipidomics solutions with Lipostar
Michele Wölk. Technische Universität Dresden

15.30h Add spatial dimension to your omics and metID: LipostarMSI and Pyxis for mass spec imaging data analysis”
Sara Tortorella. Molecular Horizon

16.00h Towards multimodal mass spectrometry analysis for cancer pathology assessment: current progress and unmet need.
Arash Zarrine. University of Toronto

16.30h How we use LipostarMSI and Pyxis at M4i and where to go from here
Tim Hendriks – Maastricht MultiModal Molecular Imaging Institute (M4i), The Netherlands

Friday 14th October

09.00h Compound Library: Model building
Ismael Zamora

9:30h Fase 2: Metabolism prediction
Gabriele Cruciani

10,30h Roundtable discussion

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