Deciphering lipid structures based on platform-independent decision rule sets

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Abstract

We developed decision rule sets for Lipid Data Analyzer (LDA; http://genome.tugraz.at/lda2), enabling automated and reliable annotation of lipid species and their molecular structures in high-throughput data from chromatography-coupled tandem mass spectrometry. Platform independence was proven in various mass spectrometric experiments, comprising low- and high-resolution instruments and several collision energies. We propose that this independence and the capability to identify novel lipid molecular species render current state-of-the-art lipid libraries now obsolete.

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HMDB: a knowledgebase for the human metabolome

David Wishart, Craig Knox, An Guo … (2009)

The Human Metabolome Database (HMDB, http://www.hmdb.ca) is a richly annotated resource that is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. Since its first release in 2007, the HMDB has been used to facilitate the research for nearly 100 published studies in metabolomics, clinical biochemistry and systems biology. The most recent release of HMDB (version 2.0) has been significantly expanded and enhanced over the previous release (version 1.0). In particular, the number of fully annotated metabolite entries has grown from 2180 to more than 6800 (a 300% increase), while the number of metabolites with biofluid or tissue concentration data has grown by a factor of five (from 883 to 4413). Similarly, the number of purified compounds with reference to NMR, LC-MS and GC-MS spectra has more than doubled (from 380 to more than 790 compounds). In addition to this significant expansion in database size, many new database searching tools and new data content has been added or enhanced. These include better algorithms for spectral searching and matching, more powerful chemical substructure searches, faster text searching software, as well as dedicated pathway searching tools and customized, clickable metabolic maps. Changes to the user-interface have also been implemented to accommodate future expansion and to make database navigation much easier. These improvements should make the HMDB much more useful to a much wider community of users.

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LMSD: LIPID MAPS structure database

Manish Sud, Eoin Fahy, Dawn Cotter … (2006)

The LIPID MAPS Structure Database (LMSD) is a relational database encompassing structures and annotations of biologically relevant lipids. Structures of lipids in the database come from four sources: (i) LIPID MAPS Consortium's core laboratories and partners; (ii) lipids identified by LIPID MAPS experiments; (iii) computationally generated structures for appropriate lipid classes; (iv) biologically relevant lipids manually curated from LIPID BANK, LIPIDAT and other public sources. All the lipid structures in LMSD are drawn in a consistent fashion. In addition to a classification-based retrieval of lipids, users can search LMSD using either text-based or structure-based search options. The text-based search implementation supports data retrieval by any combination of these data fields: LIPID MAPS ID, systematic or common name, mass, formula, category, main class, and subclass data fields. The structure-based search, in conjunction with optional data fields, provides the capability to perform a substructure search or exact match for the structure drawn by the user. Search results, in addition to structure and annotations, also include relevant links to external databases. The LMSD is publicly available at

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ChEBI: a database and ontology for chemical entities of biological interest

Kirill Degtyarenko, Paula de Matos, Marcus Ennis … (2008)

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The molecular entities in question are either natural products or synthetic products used to intervene in the processes of living organisms. Genome-encoded macromolecules (nucleic acids, proteins and peptides derived from proteins by cleavage) are not as a rule included in ChEBI. In addition to molecular entities, ChEBI contains groups (parts of molecular entities) and classes of entities. ChEBI includes an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. ChEBI is available online at http://www.ebi.ac.uk/chebi/

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Author and article information

Journal

Journal ID (nlm-journal-id): 101215604

Journal ID (pubmed-jr-id): 32338

Journal ID (nlm-ta): Nat Methods

Journal ID (iso-abbrev): Nat. Methods

Title: Nature methods

ISSN (Print): 1548-7091

ISSN (Electronic): 1548-7105

Publication date Nihms-submitted: 29 May 2018

Publication date (Electronic): 23 October 2017

Publication date (Print): December 2017

Publication date PMC-release: 05 June 2018

Volume: 14

Issue: 12

Pages: 1171-1174

Affiliations

[1 ]Institute of Computational Biotechnology, Graz University of Technology, Graz, Austria

[2 ]Center for Medical Research, Medical University of Graz, Graz, Austria

[3 ]Omics Center Graz, BioTechMed-Graz, Graz, Austria

[4 ]Department of Molecular Biosciences, University of Graz, Graz, Austria

[5 ]Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, U.S.A.

[6 ]Department of Medicine, Harvard Medical School, Boston, Massachusetts, U.S.A.

[7 ]Singapore Lipidomics Incubator, National University of Singapore, Singapore, Singapore

[8 ]Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden

[9 ]School of Medicine, University of California San Diego, La Jolla, California, U.S.A.

[10 ]The Babraham Institute, Babraham Research Campus, Cambridge, U.K.

[11 ]Department of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria

Author notes

Correspondence should be addressed to G.G.T. ( gerhard.thallinger@ 123456tugraz.at ) or H.C.K. ( harald.koefeler@ 123456medunigraz.at ).

Article

Manuscript ID: EMS74338

DOI: 10.1038/nmeth.4470

PMC ID: 5988032

PubMed ID: 29058722

SO-VID: a1dffb17-4cbb-437a-9ca8-cf6ed8bf8ebe

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Deciphering lipid structures based on platform-independent decision rule sets

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Genes & Diseases

Most cited references 19

HMDB: a knowledgebase for the human metabolome

LMSD: LIPID MAPS structure database

ChEBI: a database and ontology for chemical entities of biological interest

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