Limits...
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.

Show MeSH

Related in: MedlinePlus

Screenshot of the output of an “MS1 search engine”.Results are split into each input search mass and their corresponding lipid “Species” identifications. The columns are filterable and sortable so that results may be organised prior to exporting them in a number of available file formats. In addition, whole lipid “Categories”, “Main Classes” and “Sub Classes” may be filtered out for the purpose of simplifying the results or replicating any step in the experimental protocol that may have isolated specific sets of lipids prior to the MS analysis.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3646891&req=5

pone-0061951-g004: Screenshot of the output of an “MS1 search engine”.Results are split into each input search mass and their corresponding lipid “Species” identifications. The columns are filterable and sortable so that results may be organised prior to exporting them in a number of available file formats. In addition, whole lipid “Categories”, “Main Classes” and “Sub Classes” may be filtered out for the purpose of simplifying the results or replicating any step in the experimental protocol that may have isolated specific sets of lipids prior to the MS analysis.

Mentions: As an example of the extensibility of LipidHome, an MS1 precursor ion search engine was implemented on top of the web services and embedded into the LipidHome web application. The search engine takes as inputs a “newline” separated list of precursor ion masses, mass tolerance and a set of adduct ions to pre-process the precursor ions with (Figure S6 in File S1). The processed masses are searched against “Species” in the database with the tolerance provided and hits returned in the output panel (Figure 4). Multiple adduct ions may be selected in a single search. However, increasing the search space will inevitably increase the number of acceptable isobaric lipid hits. Results can be filtered to exclude whole lipid “Categories”, “Main Classes” or “Sub Classes” in order to utilise any a priori knowledge of detected lipid species from e.g. solid phase extraction of single lipid “Main Classes”. Finally, results may be exported to a number of file formats for offline inspection and reporting. From a single precursor ion mass value only, it is not possible to distinguish the true identity of a search mass that hits multiple isobaric lipid species. It is the user’s responsibility to accurately and reproducibly report their results.


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)

Screenshot of the output of an “MS1 search engine”.Results are split into each input search mass and their corresponding lipid “Species” identifications. The columns are filterable and sortable so that results may be organised prior to exporting them in a number of available file formats. In addition, whole lipid “Categories”, “Main Classes” and “Sub Classes” may be filtered out for the purpose of simplifying the results or replicating any step in the experimental protocol that may have isolated specific sets of lipids prior to the MS analysis.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0061951-g004: Screenshot of the output of an “MS1 search engine”.Results are split into each input search mass and their corresponding lipid “Species” identifications. The columns are filterable and sortable so that results may be organised prior to exporting them in a number of available file formats. In addition, whole lipid “Categories”, “Main Classes” and “Sub Classes” may be filtered out for the purpose of simplifying the results or replicating any step in the experimental protocol that may have isolated specific sets of lipids prior to the MS analysis.
Mentions: As an example of the extensibility of LipidHome, an MS1 precursor ion search engine was implemented on top of the web services and embedded into the LipidHome web application. The search engine takes as inputs a “newline” separated list of precursor ion masses, mass tolerance and a set of adduct ions to pre-process the precursor ions with (Figure S6 in File S1). The processed masses are searched against “Species” in the database with the tolerance provided and hits returned in the output panel (Figure 4). Multiple adduct ions may be selected in a single search. However, increasing the search space will inevitably increase the number of acceptable isobaric lipid hits. Results can be filtered to exclude whole lipid “Categories”, “Main Classes” or “Sub Classes” in order to utilise any a priori knowledge of detected lipid species from e.g. solid phase extraction of single lipid “Main Classes”. Finally, results may be exported to a number of file formats for offline inspection and reporting. From a single precursor ion mass value only, it is not possible to distinguish the true identity of a search mass that hits multiple isobaric lipid species. It is the user’s responsibility to accurately and reproducibly report their results.

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