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

Foster JM, Moreno P, Fabregat A, Hermjakob H, Steinbeck C, Apweiler R, Wakelam MJ, Vizcaíno JA - PLoS ONE (2013)

Bottom Line: 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.The web application encompasses a browser for viewing lipid records and a 'tools' section where an MS1 search engine is currently implemented.

View Article: PubMed Central - PubMed

Affiliation: EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom. jfoster@ebi.ac.uk

ABSTRACT
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.

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Related in: MedlinePlus

A diagram of in silico construction of theoretical diradyl lipid “Sub Species”.Steps: 1. All viable potential fatty acids are generated from a set of starting parameters; 2. They are combined all against all; 3. The head groups with alpha-carbons and linkages are generated; 4. The head groups are crossed with the fatty acid pairs to produce all viable lipid structures within the predefined chemical space.
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pone-0061951-g002: A diagram of in silico construction of theoretical diradyl lipid “Sub Species”.Steps: 1. All viable potential fatty acids are generated from a set of starting parameters; 2. They are combined all against all; 3. The head groups with alpha-carbons and linkages are generated; 4. The head groups are crossed with the fatty acid pairs to produce all viable lipid structures within the predefined chemical space.

Mentions: The complete lipid generation process (Figure 2), was provided by the open source ‘FASTLipid’ Java library (https://github.com/pcm32/FASTLipid), which relies on the computational chemistry framework ‘Chemical Development Kit’ (CDK) [23]. ‘FASTLipid’ can be used as a standalone Java application for the generation of theoretical lipids, but also for local mass searches of ‘on-the-fly’ generated structures. ‘FASTLipid’ differs significantly in its approach to the generation of theoretical lipids, in comparison to the recently published ‘LipidMapsTools’ [24]. Whole lipids are not enumerated from a restricted set of “Fatty Acid Isomers” but from a set of flexible rules. The ‘FASTLipid’ library enumerates not just chains onto the phosphoglycerol body but also all possible double bond positions within the fatty acids, producing considerably more possible lipid “Isomers”. For example, ‘FASTLipid’ is capable of generating the “Isomer” PC 18∶1 [3]/16∶0 by defining the appropriate fatty acid structural components (chain 1∶18 carbons, 1 double bond at position 3, chain 2∶16 carbons, no double bonds). Attempting the generation of the same with ‘LipidMapsTools’ will fail because it has no predefined fatty acid 18∶1 [3].


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

Foster JM, Moreno P, Fabregat A, Hermjakob H, Steinbeck C, Apweiler R, Wakelam MJ, Vizcaíno JA - PLoS ONE (2013)

A diagram of in silico construction of theoretical diradyl lipid “Sub Species”.Steps: 1. All viable potential fatty acids are generated from a set of starting parameters; 2. They are combined all against all; 3. The head groups with alpha-carbons and linkages are generated; 4. The head groups are crossed with the fatty acid pairs to produce all viable lipid structures within the predefined chemical space.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3646891&req=5

pone-0061951-g002: A diagram of in silico construction of theoretical diradyl lipid “Sub Species”.Steps: 1. All viable potential fatty acids are generated from a set of starting parameters; 2. They are combined all against all; 3. The head groups with alpha-carbons and linkages are generated; 4. The head groups are crossed with the fatty acid pairs to produce all viable lipid structures within the predefined chemical space.
Mentions: The complete lipid generation process (Figure 2), was provided by the open source ‘FASTLipid’ Java library (https://github.com/pcm32/FASTLipid), which relies on the computational chemistry framework ‘Chemical Development Kit’ (CDK) [23]. ‘FASTLipid’ can be used as a standalone Java application for the generation of theoretical lipids, but also for local mass searches of ‘on-the-fly’ generated structures. ‘FASTLipid’ differs significantly in its approach to the generation of theoretical lipids, in comparison to the recently published ‘LipidMapsTools’ [24]. Whole lipids are not enumerated from a restricted set of “Fatty Acid Isomers” but from a set of flexible rules. The ‘FASTLipid’ library enumerates not just chains onto the phosphoglycerol body but also all possible double bond positions within the fatty acids, producing considerably more possible lipid “Isomers”. For example, ‘FASTLipid’ is capable of generating the “Isomer” PC 18∶1 [3]/16∶0 by defining the appropriate fatty acid structural components (chain 1∶18 carbons, 1 double bond at position 3, chain 2∶16 carbons, no double bonds). Attempting the generation of the same with ‘LipidMapsTools’ will fail because it has no predefined fatty acid 18∶1 [3].

Bottom Line: 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.The web application encompasses a browser for viewing lipid records and a 'tools' section where an MS1 search engine is currently implemented.

View Article: PubMed Central - PubMed

Affiliation: EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom. jfoster@ebi.ac.uk

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus