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LipidFrag: Improving reliability of in silico fragmentation of lipids and application to the Caenorhabditis elegans lipidome

ABSTRACT: Lipid identification is a major bottleneck in high-throughput lipidomics studies. We combined the in silico fragmentation tool MetFrag with LipidMaps lipid-class specific classifiers which calculate probabilities for lipid class assignments. The LipidFrag approach was then applied to MS/MS spectra of lipid extracts of the nematode Caenorhabditis elegans.

OTHER RELATED OMICS DATASETS IN: PXD009709

INSTRUMENT(S): maXis (Bruker)

SUBMITTER: Michael Witting Christoph Ruttkies Steffen Neumann

PROVIDER: MTBLS291 | MetaboLights | 2017-03-09

REPOSITORIES: MetaboLights

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			Action	DRS
	MTBLS291	Other
	FILES	Other
	a_MTBLS291_NEG_mass_spectrometry.txt	Txt
	a_MTBLS291_POS_mass_spectrometry.txt	Txt
	i_Investigation.txt	Txt

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Publications

Metabolomic Profiling of Submaximal Exercise at a Standardised Relative Intensity in Healthy Adults.

Muhsen Ali Ali A Burleigh Mia M Daskalaki Evangelia E Zhang Tong T Easton Chris C Watson David G DG

Metabolites 20160226 1

Ten physically active subjects underwent two cycling exercise trials. In the first, aerobic capacity (VO2max) was determined and the second was a 45 min submaximal exercise test. Urine samples were collected separately the day before (day 1) , the day of (day 2), and the day after (day 3) the submaximal exercise test (12 samples per subject). Metabolomic profiling of the samples was carried out using hydrophilic interaction chromatography (HILIC) coupled to an Orbitrap Exactive mass spectrometer ...[more]

PMID: 26927198

Similar Datasets

LipidFrag: Improving reliability of in silico fragmentation of lipids and application to the Caenorhabditis elegans lipidome.

Project description:Lipid identification is a major bottleneck in high-throughput lipidomics studies. However, tools for the analysis of lipid tandem MS spectra are rather limited. While the comparison against spectra in reference libraries is one of the preferred methods, these libraries are far from being complete. In order to improve identification rates, the in silico fragmentation tool MetFrag was combined with Lipid Maps and lipid-class specific classifiers which calculate probabilities for lipid class assignments. The resulting LipidFrag workflow was trained and evaluated on different commercially available lipid standard materials, measured with data dependent UPLC-Q-ToF-MS/MS acquisition. The automatic analysis was compared against manual MS/MS spectra interpretation. With the lipid class specific models, identification of the true positives was improved especially for cases where candidate lipids from different lipid classes had similar MetFrag scores by removing up to 56% of false positive results. This LipidFrag approach was then applied to MS/MS spectra of lipid extracts of the nematode Caenorhabditis elegans. Fragments explained by LipidFrag match known fragmentation pathways, e.g., neutral losses of lipid headgroups and fatty acid side chain fragments. Based on prediction models trained on standard lipid materials, high probabilities for correct annotations were achieved, which makes LipidFrag a good choice for automated lipid data analysis and reliability testing of lipid identifications.

| S-EPMC5344313 | biostudies-literature

Modulation of atherogenic lipidome

Project description:Objective: Although relationships between smoking and cardiovascular diseases (CVD), and CVD and lipids are established, direct impact of cigarette smoke (CS) on lipidomes remains elusive. We investigated the effect of 6 month smoke exposure on a well-established mouse model for human atherogenesis, Apoe mouse plasma, liver, and aorta molecular lipid profiles and liver transcriptome. // Methods: Plasma, liver, and aorta samples from Apoe mice exposed to CS or fresh air for 6 months were extracted for lipids using robotic-assisted method and analyzed by mass spectrometry. Gene expression of samples from the same livers was obtained on microarrays. Development of atherosclerosis in aorta was further assessed by plaque size measurement in the aortic arch and lipoprotein measurements in plasma and in the plaque. // Results: CS increased most lipid classes and molecular lipid species in tissues evaluated. In plasma, free cholesterol, ceramides, cerebrosides, and majority of phospholipids were increased in CS-exposed mice. In liver, CS elevated several lipid species including free and esterified cholesterol, triacylglycerols, phospholipids, sphingomyelins, and ceramides. In aorta, more than 2-fold higher cholesteryl ester (CE), lysophosphatidylcholine, and glucosyl/galactosylceramide levels were recorded in mice exposed to CS compared to mice exposed to fresh air. Moreover, CS exposure induced a significant decrease in several plasma CE and phosphatidylcholine species that contained polyunsaturated fatty acids. Genes involved in amino acid and lipid metabolism showed perturbed transcription profiles in liver. // Conclusion: These data reveal molecular details accompanying the increase in plaque size, sign of atherogenesis in Apoe mice, which is accelerated by CS exposure.

2013-10-03 | E-MTAB-1195 | biostudies-arrayexpress

Global profiling of protein lactylation in Caenorhabditis elegans (label-free quantitative proteomic data)

Project description:We identified 1836 Class I (locnalization probabilities > 0.75) lactylated sites in 487 proteis,This study establish the first lactylome database in Caenorhabditis elegans and provides a basis for studying the role of lactylation. In addition, it provides a evidence for the existence of lactylation of non-histones and their possible involvement in biological processes.

2023-03-30 | PXD041277 |

Widespread roles for piRNAs and WAGO-class siRNAs in shaping the germline transcriptome of Caenorhabditis elegans

Project description:To explore the roles of piRNAs and WAGO-class 22G-RNAs in regulating gene expression and transposon silencing in Caenorhabditis elegans, we used RNA-seq to assess changes in small RNA and mRNA levels in prg-1 and mut-16 mutants, which disable the piRNA and WAGO-class 22G-RNA pathways respectively. We identified numerous roles for piRNAs and WAGO-class 22G-RNAs in regulating germline genes, including transposons, histones, and spermatogenic and oogenic transcripts.

2019-12-03 | GSE141243 | GEO

Caenorhabditis elegans

Project description:mut-16 and other mutator-class genes modulate 22G and 26G siRNA pathways in Caenorhabditis elegans

| PRJNA135287 | ENA

Caenorhabditis elegans

Project description:The roles of Class I HDACs, HDA-1, HDA-2, and HDA-3 in Caenorhabditis elegans during embryogenesis

| PRJDB14540 | ENA

C. elegans LPIN-1 moderates lifespan-shortening effects of dietary glucose via maintaining ω-6 polyunsaturated fatty acids

Project description:A glucose-rich diet shortens lifespan via altering lipid metabolism in many organisms, including Caenorhabditis elegans. However, it remains incompletely understood how glucose and lipid metabolism regulates lifespan. Here, we show that Lipin 1/LPIN-1, a phosphatidic acid phosphatase and a putative transcription co-regulator that mediates glucose-to-triacylglyceride synthesis, prevents the life-shortening effects of glucose-rich diets on C. elegans. We showed that the expression levels of many genes related to lipid metabolism were differentially regulated by lpin-1 RNAi and glucose treatment.

2020-06-02 | GSE138035 | GEO

Caenorhabditis elegans

Project description:Caenorhabditis elegans

| PRJNA265871 | ENA

Lipidome- and Genome-Wide Study to Understand Sex Differences in Circulatory Lipids.

Project description:Background Despite well-recognized differences in the atherosclerotic cardiovascular disease risk between men and women, sex differences in risk factors and sex-specific mechanisms in the pathophysiology of atherosclerotic cardiovascular disease remain poorly understood. Lipid metabolism plays a central role in the development of atherosclerotic cardiovascular disease. Understanding sex differences in lipids and their genetic determinants could provide mechanistic insights into sex differences in atherosclerotic cardiovascular disease and aid in precise risk assessment. Herein, we examined sex differences in plasma lipidome and heterogeneity in genetic influences on lipidome in men and women through sex-stratified genome-wide association analyses. Methods and Results We used data consisting of 179 lipid species measured by shotgun lipidomics in 7266 individuals from the Finnish GeneRISK cohort and sought for replication using independent data from 2045 participants. Significant sex differences in the levels of 141 lipid species were observed (P<7.0×10-4). Interestingly, 121 lipid species showed significant age-sex interactions, with opposite age-related changes in 39 lipid species. In general, most of the cholesteryl esters, ceramides, lysophospholipids, and glycerides were higher in 45- to 50-year-old men compared with women of same age, but the sex differences narrowed down or reversed with age. We did not observe any major differences in genetic effect in the sex-stratified genome-wide association analyses, which suggests that common genetic variants do not have a major role in sex differences in lipidome. Conclusions Our study provides a comprehensive view of sex differences in circulatory lipids pointing to potential sex differences in lipid metabolism and highlights the need for sex- and age-specific prevention strategies.

| S-EPMC9673737 | biostudies-literature

Lipids in the development and treatment of human intestinal diseases - Lipids in intestinal diseases

Project description:Interventions: Group 1: Colon tissue (tumor, control tissue and tissue from diverticulitis patients) which is optained within a surgical intervention at the Asklepios Paulinen Clinic in Wiesbaden is directly transferred to the Clinic of Pathology of the Helios Dr.-Horst-Schmidt-Clinic Wiesbaden, where it is categorized. Within 24 h the tissue is collected from a staff of the Insitute of clinical Pharamcology University of Frankfurt. At the Institute of clinical Pharmacology of the University hospital Frankfurt the tissue is prepared for immunohistochemistry, for detection of lipids by liquid-chromatography-tandem mass spectrometry, for single cell isolation, FACS analysis, and in vitro culture experiments. Primary outcome(s): Lipid level after stimulation and anti-inflammatory therapy Study Design: Allocation: ; Masking: ; Control: ; Assignment: ; Study design purpose: basic science

| 2434471 | ecrin-mdr-crc

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