LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.

Protein sequence databases are the pillar upon which modern proteomics is supported, representing a stable reference space of predicted and validated proteins. One example of such resources is UniProt, enriched with both expertly curated and automatic annotations. Taken largely for granted, similar...

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Autores principales:	Joseph M Foster, Pablo Moreno, Antonio Fabregat, Henning Hermjakob, Christoph Steinbeck, Rolf Apweiler, Michael J O Wakelam, Juan Antonio Vizcaíno
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/a5640c7b21884d42a2cb032a878483ec
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id	oai:doaj.org-article:a5640c7b21884d42a2cb032a878483ec
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spelling	oai:doaj.org-article:a5640c7b21884d42a2cb032a878483ec2021-11-18T07:46:44ZLipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.1932-620310.1371/journal.pone.0061951https://doaj.org/article/a5640c7b21884d42a2cb032a878483ec2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23667450/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Protein sequence databases are the pillar upon which modern proteomics is supported, representing a stable reference space of predicted and validated proteins. One example of such resources is UniProt, enriched with both expertly curated and automatic annotations. Taken largely for granted, similar mature resources such as UniProt are not available yet in some other "omics" fields, lipidomics being one of them. While having a seasoned community of wet lab scientists, lipidomics lies significantly behind proteomics in the adoption of data standards and other core bioinformatics concepts. This work aims to reduce the gap by developing an equivalent resource to UniProt called 'LipidHome', providing theoretically generated lipid molecules and useful metadata. Using the 'FASTLipid' Java library, a database was populated with theoretical lipids, generated from a set of community agreed upon chemical bounds. In parallel, a web application was developed to present the information and provide computational access via a web service. Designed specifically to accommodate high throughput mass spectrometry based approaches, lipids are organised into a hierarchy that reflects the variety in the structural resolution of lipid identifications. Additionally, cross-references to other lipid related resources and papers that cite specific lipids were used to annotate lipid records. The web application encompasses a browser for viewing lipid records and a 'tools' section where an MS1 search engine is currently implemented. LipidHome can be accessed at http://www.ebi.ac.uk/apweiler-srv/lipidhome.Joseph M FosterPablo MorenoAntonio FabregatHenning HermjakobChristoph SteinbeckRolf ApweilerMichael J O WakelamJuan Antonio VizcaínoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 5, p e61951 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Joseph M Foster Pablo Moreno Antonio Fabregat Henning Hermjakob Christoph Steinbeck Rolf Apweiler Michael J O Wakelam Juan Antonio Vizcaíno LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.
description	Protein sequence databases are the pillar upon which modern proteomics is supported, representing a stable reference space of predicted and validated proteins. One example of such resources is UniProt, enriched with both expertly curated and automatic annotations. Taken largely for granted, similar mature resources such as UniProt are not available yet in some other "omics" fields, lipidomics being one of them. While having a seasoned community of wet lab scientists, lipidomics lies significantly behind proteomics in the adoption of data standards and other core bioinformatics concepts. This work aims to reduce the gap by developing an equivalent resource to UniProt called 'LipidHome', providing theoretically generated lipid molecules and useful metadata. Using the 'FASTLipid' Java library, a database was populated with theoretical lipids, generated from a set of community agreed upon chemical bounds. In parallel, a web application was developed to present the information and provide computational access via a web service. Designed specifically to accommodate high throughput mass spectrometry based approaches, lipids are organised into a hierarchy that reflects the variety in the structural resolution of lipid identifications. Additionally, cross-references to other lipid related resources and papers that cite specific lipids were used to annotate lipid records. The web application encompasses a browser for viewing lipid records and a 'tools' section where an MS1 search engine is currently implemented. LipidHome can be accessed at http://www.ebi.ac.uk/apweiler-srv/lipidhome.
format	article
author	Joseph M Foster Pablo Moreno Antonio Fabregat Henning Hermjakob Christoph Steinbeck Rolf Apweiler Michael J O Wakelam Juan Antonio Vizcaíno
author_facet	Joseph M Foster Pablo Moreno Antonio Fabregat Henning Hermjakob Christoph Steinbeck Rolf Apweiler Michael J O Wakelam Juan Antonio Vizcaíno
author_sort	Joseph M Foster
title	LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.
title_short	LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.
title_full	LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.
title_fullStr	LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.
title_full_unstemmed	LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.
title_sort	lipidhome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/a5640c7b21884d42a2cb032a878483ec
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LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.

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