Lipid database

The mentioned data management systems are only first steps toward comprehensive lipid databases and global lipid networks. An example for such a data bank is LIPIDMAPS (http //www.lipidmaps.org), which covers structures and annotations of biologically relevant lipids (43). The structures originate from the core laboratories of the LIPIDMAPS consortium and their partners. In this database, users can search the LIPID MAPS proteome database using either text-based or structure-based search options. In addition to LIPIDMAPS, other databases in Europe (http //www.lipidomics.net) and Japan (http //www.lipidbank.jp) have been initiated. 

LMSD has the following distinct features in comparison to other existing lipid databases such as LipidBank ... 

S LipidSearch LipidSearch is the commercial software (Thermo Fisher Scientific) developed jointly by Prof. Ryo Taguchi and MKI (Tokyo, Japan). It is a powerful new tool for automatic identification and relative quantification of cellular lipid species from a large amount of mass spectrometric data obtained from both LC-MS and shotgun lipidomics approaches. A lipid database containing... 

Watanabe, K., Yasugi, E., Oshima, M. (2000) How to search the glycoUpid data in LIPID-BANK for Web The newly developed lipid database. Japan Trend Glycosci. Glycotechnol. 12,175-184. 

Beyond the analysis of the primary MS data, there is a need for tools allowing one to correlate lipid compositions with other compositional and functional data. This is because the lipid profiles alone are difficult to interpret in terms of mechanisms and functions. Lipid databases are also needed, but are yet under construction [40]. 

There are no convenient databases for liposome log P values. Most measured quantities need to be ferreted from original publications [149,162,376,381-387,443], The handbook edited by Cevc [380] is a comprehensive collection of properties of phospholipids, including extensive compilations of structural data from X-ray crystallographic studies. Lipid-type distributions in various biological membranes have been reported [380,388,433]. 

Studying the sequences of farnesylated proteins indicated that all lipidated proteins bear a cysteine residue near the C-terminus revealing the CAAX-motif, where C is a cysteine, A stands for an aliphatic amino acid, and X can be any amino acid. Database searches resulted in more prenylated proteins, all bearing the CAAX-motif, in systems from lower eukaryotes to mammals. A closer look at the mature proteins revealed that prenylation was only the first step of processing of the CAAX-motif-encoded proteins. After transfer of the isoprene unit, the last three amino acids are cleaved proteolytically by an endoprotease and the C-terminal cysteine is carboxymethylated by a methyltransferase. ... 

Attanasio AF, Bates PC, Ho KK, Webb SM, Ross RJ, Strasburger CJ, Bouillon R, Crowe B, Selander K, Valle D, Lamberts SWHypoptiuitary Control and Complications Study International Advisory Board. Human growth hormone replacement in adult hypopitui-tary patients long-term effects on body composition and lipid status—3-year results from the HypoCCS Database. J Clin Endocrinol Metab 2002 87(4) 1600-6. 

The identification of the lipids is a very challenging task. The lack of comprehensive mass spectral libraries often limits the identification of compounds in LC-MS and shotgun methods. Some spectral libraries are available, such as the Human Metabolome Database (http /www.hmdb.ca), the METLIN Metabolite Database (http /metlin.scripps.edu) (24), and the MassBank (http /www. massbank.jp) (25). However, construction of universal spectral databases for API-MS is challenging due to the poor reproducibility and high interinstru-ment variability of fragmentation patterns. 

LIPID Membrane lipid structures Merck manual Monosaccharide database Mptopo Membrane protein topology PDB 3D structures of biomacromolecules RNA modification database RNA Structure database Spectral Database Systems (SDBS)... 

Finally, we will identify the structure of enriched ions by using accurate mass (obtained during our standard MS experiments) and searching metabolite databases, such as METLIN [75], PubChem [76], or the lipid MAPS [77] for... 

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