LipidBlast in silico tandem mass spectrometry database for lipid identification

被引：735

作者：

Kind, Tobias ^{[1
]}

Liu, Kwang-Hyeon ^{[1
,2
]}

Lee, Do Yup ^{[1
,3
]}

DeFelice, Brian ^{[1
]}

Meissen, John K. ^{[1
]}

Fiehn, Oliver ^{[1
]}

机构：

[1] Univ Calif Davis, UC Davis Genome Ctr, Metabol Core, Davis, CA 95616 USA

[2] Kyungpook Natl Univ, Coll Pharm, Pharmaceut Sci Res Inst, Taegu, South Korea

[3] Kookmin Univ, Dept Adv Fermentat Fus Sci & Technol, Seoul, South Korea

来源：

NATURE METHODS | 2013年 / 10卷 / 08期

基金：

新加坡国家研究基金会; 美国国家科学基金会; 美国国家卫生研究院;

关键词：

BIOINFORMATICS; LIBRARIES; PLATFORM; TOOL;

D O I：

10.1038/nmeth.2551

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Current tandem mass spectral libraries for lipid annotations in metabolomics are limited in size and diversity. We provide a freely available computer-generated tandem mass spectral library of 212,516 spectra covering 119,200 compounds from 26 lipid compound classes, including phospholipids, glycerolipids, bacterial lipoglycans and plant glycolipids. We show platform independence by using tandem mass spectra from 40 different mass spectrometer types including low-resolution and high-resolution instruments.

引用

页码：755 / +

页数：9

共 27 条

[1] A cross-platform toolkit for mass spectrometry and proteomics [J].

Chambers, Matthew C. ;

Maclean, Brendan ;

Burke, Robert ;

Amodei, Dario ;

Ruderman, Daniel L. ;

Neumann, Steffen ;

Gatto, Laurent ;

Fischer, Bernd ;

Pratt, Brian ;

Egertson, Jarrett ;

Hoff, Katherine ;

Kessner, Darren ;

Tasman, Natalie ;

Shulman, Nicholas ;

Frewen, Barbara ;

Baker, Tahmina A. ;

Brusniak, Mi-Youn ;

Paulse, Christopher ;

Creasy, David ;

Flashner, Lisa ;

Kani, Kian ;

Moulding, Chris ;

Seymour, Sean L. ;

Nuwaysir, Lydia M. ;

Lefebvre, Brent ;

Kuhlmann, Frank ;

Roark, Joe ;

Rainer, Paape ;

Detlev, Suckau ;

Hemenway, Tina ;

Huhmer, Andreas ;

Langridge, James ;

Connolly, Brian ;

Chadick, Trey ;

Holly, Krisztina ;

Eckels, Josh ;

Deutsch, Eric W. ;

Moritz, Robert L. ;

Katz, Jonathan E. ;

Agus, David B. ;

MacCoss, Michael ;

Tabb, David L. ;

Mallick, Parag .

NATURE BIOTECHNOLOGY, 2012, 30 (10) :918-920

[2] LIPID MAPS online tools for lipid research [J].

Fahy, Eoin ;

Sud, Manish ;

Cotter, Dawn ;

Subramaniam, Shankar .

NUCLEIC ACIDS RESEARCH, 2007, 35 :W606-W612

[3] Computational lipidomics: A multiplexed analysis of dynamic changes in membrane lipid composition during signal transduction [J].

Forrester, JS ;

Milne, SB ;

Ivanova, PT ;

Brown, HA .

MOLECULAR PHARMACOLOGY, 2004, 65 (04) :813-821

[4] Clustering millions of tandem mass spectra [J].

Frank, Ari M. ;

Bandeira, Nuno ;

Shen, Zhouxin ;

Tanner, Stephen ;

Briggs, Steven P. ;

Smith, Richard D. ;

Pevzner, Pavel A. .

JOURNAL OF PROTEOME RESEARCH, 2008, 7 (01) :113-122

[5] A reversed-phase capillary ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) method for comprehensive top-down/bottom-up lipid profiling [J].

Gao, Xiaoli ;

Zhang, Qibin ;

Meng, Da ;

Isaac, Giorgis ;

Zhao, Rui ;

Fillmore, Thomas L. ;

Chu, Rosey K. ;

Zhou, Jianying ;

Tang, Keqi ;

Hu, Zeping ;

Moore, Ronald J. ;

Smith, Richard D. ;

Katze, Michael G. ;

Metz, Thomas O. .

ANALYTICAL AND BIOANALYTICAL CHEMISTRY, 2012, 402 (09) :2923-2933

[6] In silico identification software (ISIS): a machine learning approach to tandem mass spectral identification of lipids [J].

Kangas, Lars J. ;

Metz, Thomas O. ;

Isaac, Giorgis ;

Schrom, Brian T. ;

Ginovska-Pangovska, Bojana ;

Wang, Luning ;

Tan, Li ;

Lewis, Robert R. ;

Miller, John H. .

BIOINFORMATICS, 2012, 28 (13) :1705-1713

[7] LIPIDOMICS ERA: ACCOMPLISHMENTS AND CHALLENGES [J].

Khalil, Maroun Bou ;

Hou, Weimin ;

Zhou, Hu ;

Elisma, Fred ;

Swayne, Leigh Anne ;

Blanchard, Alexandre P. ;

Yao, Zemin ;

Bennett, Steffany A. L. ;

Figeys, Daniel .

MASS SPECTROMETRY REVIEWS, 2010, 29 (06) :877-929

[8]

Kind Tobias, 2010, Bioanal Rev, V2, P23, DOI 10.1007/s12566-010-0015-9

[9] A Comparative Lipidomics Platform for Chemotaxonomic Analysis of Mycobacterium tuberculosis [J].

Layre, Emilie ;

Sweet, Lindsay ;

Hong, Sunhee ;

Madigan, Cressida A. ;

Desjardins, Danielle ;

Young, David C. ;

Cheng, Tan-Yun ;

Armand, John W. ;

Kim, Keunpyo ;

Shamputa, Isdore C. ;

McConnell, Matthew J. ;

Debono, C. Anthony ;

Behar, Samuel M. ;

Minnaard, Adriaan J. ;

Murray, Megan ;

Barry, Clifton E., III ;

Matsunaga, Isamu ;

Moody, D. Branch .

CHEMISTRY & BIOLOGY, 2011, 18 (12) :1537-1549

[10] Lipid extraction by methyl-tert-butyl ether for high-throughput lipidomics [J].

Matyash, Vitali ;

Liebisch, Gerhard ;

Kurzchalia, Teymuras V. ;

Shevchenko, Andrej ;

Schwudke, Dominik .

JOURNAL OF LIPID RESEARCH, 2008, 49 (05) :1137-1146

← 1 2 3 →