LipidSuite: interactive web server for lipidomics differential and enrichment analysis

Mohamed, Ahmed; Hill, Michelle M.

doi:10.1093/nar/gkab327

Cited by 18 publications

(21 citation statements)

References 17 publications

(19 reference statements)

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“…The lesson, moreover, could be adapted to work with other microorganisms and under other experimental conditions. We are now planning to design more lipidomics‐centered practical activities to be carried out on other highly flexible, user‐friendly web platforms, such as http://suite.lipidr.org and http://chenglab.cmu.edu.tw/lipidsig 11,12 …”

Section: Outcomes and Final Perspectivesmentioning

confidence: 99%

Using MetaboAnalyst to introduce undergraduates to lipidomic analysis and lipid remodeling in barley roots

Reyna

Margutti

Vilchez

et al. 2023

Biochem Molecular Bio Educ

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Lipidomics is a discipline that focuses on the identification and quantification of lipids. Although a part of the larger omics field, lipidomics requires specific approaches for the analysis and biological interpretation of datasets. This article presents a series of activities for introducing undergraduate microbiology students to lipidomic analysis through tools from the web‐based platform MetaboAnalyst. The students perform a complete lipidomic workflow, which includes experiment design, data processing, data normalization, and statistical analysis of molecular phospholipid species obtained from barley roots exposed to Fusarium macroconidia. The input data are provided by the teacher, but students also learn about the methods through which they were originally obtained (untargeted liquid chromatography coupled with mass spectrometry). The ultimate aim is for students to understand the biological significance of phosphatidylcholine acyl editing. The chosen methodology allows users who are not proficient in statistics to make a comprehensive analysis of quantitative lipidomic datasets. We strongly believe that virtual activities based on the analysis of such datasets should be incorporated more often into undergraduate courses, in order to improve students' data‐handling skills for omics sciences.

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Section: Outcomes and Final Perspectivesmentioning

confidence: 99%

Using MetaboAnalyst to introduce undergraduates to lipidomic analysis and lipid remodeling in barley roots

Reyna

Margutti

Vilchez

et al. 2023

Biochem Molecular Bio Educ

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“…The last category of tools and web applications provide statistical analysis, comparative analysis and comprehensive visualizations specialized for lipidomics. In this regard, lipidr [ 111 ] as an R library and LipidSuite [ 112 ] as a supporting R/Shiny web application provide assistance for interactive analysis and visualization. Specifically for the statistical analysis of fatty acid compositions from complex lipids, the liputils [ 113 ] package is available in Python, using the RefMet nomenclature as input.…”

Section: Data Post-processing Statistical Analysis Visualization and ...mentioning

confidence: 99%

A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics

et al. 2022

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Mass spectrometry is a widely used technology to identify and quantify biomolecules such as lipids, metabolites and proteins necessary for biomedical research. In this study, we catalogued freely available software tools, libraries, databases, repositories and resources that support lipidomics data analysis and determined the scope of currently used analytical technologies. Because of the tremendous importance of data interoperability, we assessed the support of standardized data formats in mass spectrometric (MS)-based lipidomics workflows. We included tools in our comparison that support targeted as well as untargeted analysis using direct infusion/shotgun (DI-MS), liquid chromatography−mass spectrometry, ion mobility or MS imaging approaches on MS1 and potentially higher MS levels. As a result, we determined that the Human Proteome Organization-Proteomics Standards Initiative standard data formats, mzML and mzTab-M, are already supported by a substantial number of recent software tools. We further discuss how mzTab-M can serve as a bridge between data acquisition and lipid bioinformatics tools for interpretation, capturing their output and transmitting rich annotated data for downstream processing. However, we identified several challenges of currently available tools and standards. Potential areas for improvement were: adaptation of common nomenclature and standardized reporting to enable high throughput lipidomics and improve its data handling. Finally, we suggest specific areas where tools and repositories need to improve to become FAIRer.

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“…Goslin is already well accepted in the community and utilized in different tools such as LipidSuite, Lux Score 2.0, or lipidomics workflows. − To allow quick adaptation of the computational field and to keep the framework up to date and usable, we released the new version Goslin 2.0 with new features and full support of the latest shorthand nomenclature.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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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.

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LipidSuite: interactive web server for lipidomics differential and enrichment analysis

Cited by 18 publications

References 17 publications

Using MetaboAnalyst to introduce undergraduates to lipidomic analysis and lipid remodeling in barley roots

Using MetaboAnalyst to introduce undergraduates to lipidomic analysis and lipid remodeling in barley roots

A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics

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

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