LipidXplorer: Software for Quantitative Shotgun Lipidomics Compatible with Multiple Mass Spectrometry Platforms

Herzog, Ronny; Schwudke, Dominik; Shevchenko, Andrej

doi:10.1002/0471250953.bi1412s43

Cited by 50 publications

(56 citation statements)

References 26 publications

(43 reference statements)

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“…Automated processing of acquired mass spectra and identification and quantification of detected molecular lipid species were performed with the Lipid Profiler software (MDS Sciex) [25] and the LipidXplorer software (in-house software, Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)) [26].…”

Section: Lipid Analysis Of Virus Particlesmentioning

confidence: 99%

Influence of the production system on the surface properties of influenza A virus particles

Hämmerling

Hennig

Serve

et al. 2017

Engineering in Life Sciences

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In this study, influenza A/Puerto Rico/8/34 H1N1 virus particles (VP) produced in adherent and suspension Madin Darby canine kidney cells were investigated with a broad analytical toolbox to obtain more information on the VP's surface properties potentially affecting their aggregation behavior. First, differences in aggregation behavior were revealed by VP size distributions obtained via differential centrifugal sedimentation and confirmed by dynamic light scattering. The VP produced in adherent cells showed increased levels of aggregation in a 20 mM NaCl 10 mM Tris‐HCl pH 7.4 low‐salt buffer. This included the formation of multimers (dimers up to pentamers), whereas VP produced in suspension cells displayed no tendency toward aggregate formation. To investigate the cause of these differences in aggregation behavior, the VP samples were compared based on their zeta potential, their surface hydrophobicity, their lipid composition, and the N‐glycosylation of their major VP surface protein hemagglutinin. The zeta potential and the hydrophobicity of the VP produced in the adherent cells was significantly decreased compared to the VP produced in the suspension cells. The lipid composition of both VP systems was approximately identical. The hemagglutinin of the VP produced in adherent cells included more of the larger N‐glycans, whereas the VP produced in suspension cells included more of the smaller N‐glycans. These results indicate that differences in the glycosylation of viral surface proteins should be monitored to characterize VP hydrophobicity and aggregation behavior, and to avoid aggregate formation and product losses in virus purification processes for vaccines and gene therapy.

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Section: Lipid Analysis Of Virus Particlesmentioning

confidence: 99%

Influence of the production system on the surface properties of influenza A virus particles

Hämmerling

Hennig

Serve

et al. 2017

Engineering in Life Sciences

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“…The acyl chain/head group composition of intact lipids can be determined from MS/MS spectra using various commercial (LipidView [www.absciex.com] and LipidSearch [www.thermo.com]) or open-source software tools (http://www.lipidmaps.org/tools/ms/ and LipidXplorer; Herzog et al, 2002), because the rules of fragmentation are well understood for the most relevant lipids (LipidBlast; Kind et al, 2013). But the availability of and knowledge regarding MS/MS spectra of oxidized lipids are quite scarce and restricted to single lipid species like TAGs (Zeb, 2012) and PLs (Spickett and Pitt, 2015) or to particular acyl residues like oxidized C18 and C16 FA esters (Vu et al, 2012).…”

mentioning

confidence: 99%

Structure Annotation and Quantification of Wheat Seed Oxidized Lipids by High-Resolution LC-MS/MS

2017

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Lipid oxidation is a process ubiquitous in life, but the direct and comprehensive analysis of oxidized lipids has been limited by available analytical methods. We applied high-resolution liquid chromatography-mass spectrometry (LC-MS) and tandem mass spectrometry (MS/MS) to quantify oxidized lipids (glycerides, fatty acids, phospholipids, lysophospholipids, and galactolipids) and implemented a platform-independent high-throughput-amenable analysis pipeline for the high-confidence annotation and acyl composition analysis of oxidized lipids. Lipid contents of 90 different naturally aged wheat (Triticum aestivum) seed stocks were quantified in an untargeted high-resolution LC-MS experiment, resulting in 18,556 quantitative mass-to-charge ratio features. In a posthoc liquid chromatography-tandem mass spectrometry experiment, high-resolution MS/MS spectra (5 mD accuracy) were recorded for 8,957 out of 12,080 putatively monoisotopic features of the LC-MS data set. A total of 353 nonoxidized and 559 oxidized lipids with up to four additional oxygen atoms were annotated based on the accurate mass recordings (1.5 ppm tolerance) of the LC-MS data set and filtering procedures. MS/MS spectra available for 828 of these annotations were analyzed by translating experimentally known fragmentation rules of lipids into the fragmentation of oxidized lipids. This led to the identification of 259 nonoxidized and 365 oxidized lipids by both accurate mass and MS/MS spectra and to the determination of acyl compositions for 221 nonoxidized and 295 oxidized lipids. Analysis of 15-year aged wheat seeds revealed increased lipid oxidation and hydrolysis in seeds stored in ambient versus cold conditions. Lipid oxidation is a process inevitably connected to life. Although essential for all respiring organisms, oxygen can form reactive species (ROS). The accumulation of these compounds leads to the phenomenon commonly referred to as oxidative stress in microbes and plant and animal tissues. ROS play a role in the attack against microbial pathogens by host cells (Imlay, 2013), time-dependent death of dormant seeds (Lee et al., 2010), human diseases (Coyle and Puttfarcken, 1993;Giugliano et al., 1996), in aging (Sohal and Weindruch, 1996;Sohal et al., 2002), and in signaling processes (Gilroy et al., 2016;Mignolet-Spruyt et al., 2016) Unlike oxidized fatty acids (FAs), oxidized lipids are hardly available commercially. Targeted liquid chromatography-mass spectrometry (LC-MS) analysis of oxidized lipids using authentic standards is not very common (Hui et al., 2010;Ravandi et al., 2014). Often, oxidized lipids are detected using tandem mass spectrometry (MS/MS), where the collision-induced products of precursor ions (PRs) are scanned for fragments or neutral losses (NLs) that correspond to oxidized acyl residues expected in oxidized lipids (Spickett and Pitt, 2015), and in some cases, higher resolution MS/MS spectra are provided to support the identification (Buseman et al., 2006;Vu et al., 2012).High-resolution mass spectrometry (MS) allows for ...

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“…The same filters were applied to extracts from the nematode Caenorhabditis elegans to assess the specificity of the method. Detailed information on the generation the MFQL files are found in the Supporting Information and the terminology used is based on previously published LipidXplorer papers …”

Section: Resultsmentioning

confidence: 99%

“…MS2Analyser, MzMine, and XCMS, LipidBlast, LipidProfiler are some popular examples. However, such approaches all rely on a well‐defined library and the natural product chemistry community still lacks a comprehensive open access database. Progress has recently been made to implement in silico tandem mass spectrometry (MS2) libraries to improve the process .…”

Section: Introductionmentioning

confidence: 99%

Dereplication of plant phenolics using a mass‐spectrometry database independent method

Borges

Taujale

Souza

et al. 2018

Phytochemical Analysis

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The targeted LipidXplorer method implemented using common phenolic fragmentation patterns, was found to be able to annotate more phenolics than MZMine® that is based on automated queries on the available databases. Additionally, screening for ascarosides, natural products with unrelated structures to plant phenolics collected from the nematode Caenorhabditis elegans, demonstrated the specificity of this method by cross-testing both groups of chemicals in both plants and nematodes.

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LipidXplorer: Software for Quantitative Shotgun Lipidomics Compatible with Multiple Mass Spectrometry Platforms

Cited by 50 publications

References 26 publications

Influence of the production system on the surface properties of influenza A virus particles

Influence of the production system on the surface properties of influenza A virus particles

Structure Annotation and Quantification of Wheat Seed Oxidized Lipids by High-Resolution LC-MS/MS

Dereplication of plant phenolics using a mass‐spectrometry database independent method

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