Web-based resources for mass-spectrometry-based metabolomics: A user's guide

被引：99

作者：

Tohge, Takayuki ^{[1
]}

Fernie, Alisdair R. ^{[1
]}

机构：

[1] Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany

来源：

PHYTOCHEMISTRY | 2009年 / 70卷 / 04期

关键词：

Bioinformatics; Web-resource; Metabolomics; LC-MS; GC-MS; Peak identification; Peak alignment; PLANT METABOLOMICS; METABOLITE IDENTIFICATION; DIFFERENTIAL ANALYSIS; FUNCTIONAL GENOMICS; GAS-CHROMATOGRAPHY; BIOCYC COLLECTION; DATABASE; ARABIDOPSIS; INTEGRATION; SEARCH;

D O I：

10.1016/j.phytochem.2009.02.004

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

In recent years, a plethora of web-based tools aimed at supporting mass-spectrometry-based metabolite profiling and metabolomics applications have appeared. Given the huge hurdles presented by the chemical diversity and dynamic range of the metabolites present in the plant kingdom, profiling the levels of a broad range of metabolites is highly challenging. Given the scale and costs involved in defining the plant metabolome, it is imperative that data are effectively shared between laboratories pursuing this goal. However, ensuring accurate comparison of samples run on the same machine within the same laboratory, let alone cross-machine and cross-laboratory comparisons, requires both careful experimentation and data interpretation. In this review, we present an overview of currently available software that aids either in peak identification or in the related field of peak alignment as well as those with utility in defining structural information of compounds and metabolic pathways. (C) 2009 Elsevier Ltd. All rights reserved.

引用

页码：450 / 456

页数：7

共 86 条

[1]

Adams RP, 2007, IDENTIFICATION ESSEN

[2]

Aharoni Asaph, 2002, OMICS A Journal of Integrative Biology, V6, P217, DOI 10.1089/15362310260256882

[3]

ARITA M, 2008, BRIEF BIOINFORM

[4] Search extension transforms Wiki into a relational system: A case for flavonoid metabolite database [J].

Arita, Masanori ;

Suwa, Kazuhiro .

BIODATA MINING, 2008, 1 (1)

[5] The critical evaluation of a comprehensive mass spectral library [J].

Ausloos, P ;

Clifton, CL ;

Lias, SG ;

Mikaya, AI ;

Stein, SE ;

Tchekhovskoi, DV ;

Sparkman, OD ;

Zaikin, V ;

Zhu, D .

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 1999, 10 (04) :287-299

[6] XCMS2:: Processing tandem mass spectrometry data for metabolite identification and structural characterization [J].

Benton, H. P. ;

Wong, D. M. ;

Trauger, S. A. ;

Siuzdak, G. .

ANALYTICAL CHEMISTRY, 2008, 80 (16) :6382-6389

[7]

Caspi R, 2008, NUCLEIC ACIDS RES, V36, pD623, DOI [10.1093/nar/gkt1103, 10.1093/nar/gkm900]

[8] ChemDB: a public database of small molecules and related chemoinformatics resources [J].

Chen, J ;

Swamidass, SJ ;

Bruand, J ;

Baldi, P .

BIOINFORMATICS, 2005, 21 (22) :4133-4139

[9] ChemDB update - full-text search and virtual chemical space [J].

Chen, Jonathan H. ;

Linstead, Erik ;

Swamidass, S. Joshua ;

Wang, Dennis ;

Baldi, Pierre .

BIOINFORMATICS, 2007, 23 (17) :2348-2351

[10] Metabolite identification via the Madison Metabolomics Consortium Database [J].

Cui, Qiu ;

Lewis, Ian A. ;

Hegeman, Adrian D. ;

Anderson, Mark E. ;

Li, Jing ;

Schulte, Christopher F. ;

Westler, William M. ;

Eghbalnia, Hamid R. ;

Sussman, Michael R. ;

Markley, John L. .

NATURE BIOTECHNOLOGY, 2008, 26 (02) :162-164

← 1 2 3 4 5 6 7 8 9 →