LipidMiner: a software for automated identification and quantification of lipids from multiple liquid chromatography/mass spectrometry data files

Meng, Da; Zhang, Qibin; Gao, Xiaoli; Wu, Si; Lin, Guang Jie

doi:10.1002/rcm.6865

Cited by 7 publications

(4 citation statements)

References 16 publications

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“…In general, these tools use the fragment information generated by CID to identify and quantify lipid species and chain lengths. Typical representatives of these tools are LipidFinder [132,133], LipidQA (data-dependent tools) [134], LipidMiner (for LC-MS data) [135], and LipidSearch (a commercial software). LipidFinder is a recently developed online tool that facilitates the automated search for LIPID MAPS for lipid identification and statistics.…”

Section: Lipid Databases and Identification Toolsmentioning

confidence: 99%

Tutorial on lipidomics

Wang

Han

2019

Analytica Chimica Acta

111

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The main stream of lipidomics involves mass spectrometry-based, systematic, and large-scale studies of the structure, composition, and quantity of lipids in biological systems such as organs, cells, and body fluids. As increasingly more researchers in broad fields are beginning to pay attention to and actively learn about the lipidomic technology, some introduction on the topic is needed to help the newcomers to better understand the field. This tutorial seeks to introduce the basic knowledge about lipidomics and to provide readers with some core ideas and the most important approaches for studying the field.

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Section: Lipid Databases and Identification Toolsmentioning

confidence: 99%

Tutorial on lipidomics

Wang

Han

2019

Analytica Chimica Acta

111

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“…To minimize the possibility of errors, these programs are usually equipped with various filters to eliminate unwanted matches; some of them allow the use of rule-based identification. Below, are the most popular commercial and free available ones used for these purposes: Lipid View [186], Lipid Search [177], SimLipid [187], LipidXplorer [188], LipiDex [189], LIMSA [190], Lipidyzer [191], Lipid Data Analyzer [192], LipidQA [193], CEU Mass Mediator [194], LipidLama [195], LipidMatch [196], LipidMiner [197], dGOT-MS [198], ALEX [199], The Lipid Annotation Service (LAS) [200], and LOBSTAHS [201]. Thus, the data accumulated over many years make the non-targeted approach simpler, and therefore more popular among researchers.…”

Section: Programs and Toolsmentioning

confidence: 99%

Methods of the Analysis of Oxylipins in Biological Samples

et al. 2020

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Oxylipins are derivatives of polyunsaturated fatty acids and due to their important and diverse functions in the body, they have become a popular subject of studies. The main challenge for researchers is their low stability and often very low concentration in samples. Therefore, in recent years there have been developments in the extraction and analysis methods of oxylipins. New approaches in extraction methods were described in our previous review. In turn, the old analysis methods have been replaced by new approaches based on mass spectrometry (MS) coupled with liquid chromatography (LC) and gas chromatography (GC), and the best of these methods allow hundreds of oxylipins to be quantitatively identified. This review presents comparative and comprehensive information on the progress of various methods used by various authors to achieve the best results in the analysis of oxylipins in biological samples.

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“…LipidMiner [ 65 ] supports LC-MS/MS DDA data and uses the LIPID MAPS structure database as its library for lipid identification using a rule-based approach. It is implemented in Python and C# and provides input from Thermo raw files.…”

Section: Software For Lipid Identification From Mass Spectrometrymentioning

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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LipidMiner: a software for automated identification and quantification of lipids from multiple liquid chromatography/mass spectrometry data files

Cited by 7 publications

References 16 publications

Tutorial on lipidomics

Tutorial on lipidomics

Methods of the Analysis of Oxylipins in Biological Samples

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

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