LipidHome: A Database of Theoretical Lipids Optimized for High Throughput Mass Spectrometry Lipidomics

被引：45

作者：

Foster, Joseph M. ^{[1
]}

Moreno, Pablo ^{[1
]}

Fabregat, Antonio ^{[1
]}

Hermjakob, Henning ^{[1
]}

Steinbeck, Christoph ^{[1
]}

Apweiler, Rolf ^{[1
]}

Wakelam, Michael J. O. ^{[2
]}

Vizcaino, Juan Antonio ^{[1
]}

机构：

[1] European Bioinformat Inst, EMBL Outstn, Cambridge, England

[2] Babraham Inst, Cambridge, England

来源：

PLOS ONE | 2013年 / 8卷 / 05期

基金：

英国生物技术与生命科学研究理事会; 英国惠康基金;

关键词：

ELECTROSPRAY-IONIZATION; PHOSPHOLIPIDS;

D O I：

10.1371/journal.pone.0061951

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

070301 [无机化学]; 070403 [天体物理学]; 070507 [自然资源与国土空间规划学]; 090105 [作物生产系统与生态工程];

摘要：

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.

引用

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