"Quick Search" Tutorial

         

Introduction

The "Quick Search" tool on the home page of the Lipidomics Gateway may conveniently be used to search the LIPID MAPS structure database (LMSD), the lipid-related gene/protein database (LMPD), the lipid standards database as well as all text pages on the website by entering a complete or partial lipid class, common name, systematic name or synonym, InChIKey, LIPID MAPS ID, gene or protein term. Results are then organized and displayed in a context-specific format.


Example: Searching by lipid class, lipid name/synonym/abbreviation or lipid-related gene/protein name

Using the term 'sphingomyelin' as a search term, the "Quick Search" tool returns a set of results including Lipid Classification terms (2), lipid structures (23), lipid standards (1), lipid-related genes/proteins (23) where a name or synonym matched the search term. In this particular example, several gene names or synonyms (e.g. sphingomyelin phosphodiesterase) match the query.In addition, several other matches are returned (Lipidomics update/Resources) from varoius text pages on the Lipidomics Gateway website. The user has various options to follow the hyperlinks from the results summary page in order to view details of the lipid structures, genes and classification hierarchy


Example: Searching by lipid abbreviation

The partial abbreviation 'PC(16:0/' will retrieve all phosphatidylcholine structures with a palmitoyl (16:0) chain at the sn1 position. Other examples of queries are 'PC(16:0/18:1(9Z))', 'Linoleic', 'HETE', '5Z,8Z,14Z-eicosatrienoic', 'MGDG', 'PAF', 'PGE', 'docosa' and 'phytosphingosine'.




Example: Searching by protein Swissprot ID

Enter a Swissprot ID (mouse/human) to search the lipid-related gene/protein database (LMPD) for that entry




Example: Searching by Gene symbol or Entrez/SwissProt annotation



In the example below a mouse/human Gene symbol ('Fabp') is used to search the lipid-related gene/protein database (LMPD). An Entrez/SwissProt annotation (e.g.glycerol kinase) may also be used as a query.




Example: Searching by formula

Enter a formula such as 'C12H24O2' to search the LMSD for structures whose formula in the neutral (uncharged) state corresponds to the query.




Example: Searching by lipid mass

Enter a lipid mass such as '352.4' to search the LMSD for structures whose exact mass in the neutral (uncharged) state is within 0.5 daltons of the query.




Example: Searching by LIPID MAPS ID (LM ID)

Enter a LIPID MAPS ID (LM ID) corresponding to an entry in the LMSD.




Example: Searching by InChIKey


Enter a full InChIKey corresponding to an entry in the LMSD (e.g 'BHQCQFFYRZLCQQ-OELDTZBJSA-N').






Alternatively, enter the 1st 14 uppercase letters of the InChIKey in order to ignore stereochemistry, isotopic substitution and bond geometry. in this case, all stereoisomers and geometrical isomers will be returned.



LIPID MAPS®
Position Announcements

Key LIPID MAPS® Resources
Publications
- publications related to projects funded through the LIPID MAPS® consortium
Lipid Classification System
- the first internationally accepted lipid classification system
Lipid Standards
- MS/MS spectra, annotations for principal product ions, and acquisition parameters
Experimental Data
- centralized studies on macrophages, lipidomics data on human plasma, and more
Structure Database (LMSD)
- over 40,000 unique structures of biologically relevant lipids
Proteome Database (LMPD)
- over 12,500 lipid-associated proteins from major research species
Pathways
- manually curated lipid metabolism and signaling pathways
LIPID MAPS® REST Service
- web-based/programmatic access to lipid structure and lipid-related gene/protein data
MS analysis tools
- tools for searching various lipid classes by precursor or product ion
Structure Drawing Tools
- draw and save lipid structures using online menus
Protocols
- LIPID MAPS® techniques for lipidomics and macrophage cell culture

LIPID MAPS® is funded by a grant from the Wellcome Trust.

logo LIPID MAPS® is funded by a grant from the Wellcome Trust.