A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language.
Shotgun lipidome profiling relies on direct mass spectrometric analysis of total lipid extracts from cells, tissues or organisms and is a powerful tool to elucidate the molecular composition of lipidomes. We present a novel informatics concept of the molecular fragmentation query language implemented within the LipidXplorer open source software kit that supports accurate quantification of individual species of any ionizable lipid class in shotgun spectra acquired on any mass spectrometry platform.
Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.
Ronny
R
Herzog
Dominik
D
Schwudke
Kai
K
Schuhmann
Julio L
JL
Sampaio
Stefan R
SR
Bornstein
Michael
M
Schroeder
Andrej
A
Shevchenko
D000465:Algorithms; D019295:Computational Biology; D016208:Databases, Factual; D008055:Lipids / Q000032:analysis* / Q000737:chemistry*; D013058:Mass Spectrometry; D011381:Programming Languages; D015203:Reproducibility of Results; D012984:Software
D008055:Lipids
PLoS One. 2009 Jul 15;4(7):e6261
19603071
J Lipid Res. 2006 Apr;47(4):804-14
16443931
Angew Chem Int Ed Engl. 2010 Dec 3;49(49):9430-5
21053225
Mol Biosyst. 2008 Feb;4(2):121-7
18213405
J Lipid Res. 2003 Jun;44(6):1071-9
12671038
J Am Soc Mass Spectrom. 2006 Jul;17(7):977-982
16750636
J Proteome Res. 2008 Jan;7(1):113-22
18067247
J Am Soc Mass Spectrom. 2007 Oct;18(10):1848-58
17720531
EMBO J. 2005 Sep 21;24(18):3159-65
16138081
Proc Natl Acad Sci U S A. 2009 Feb 17;106(7):2136-41
19174513
Anal Chem. 2006 Sep 1;78(17):6202-14
16944903
Anal Chem. 2007 Jun 1;79(11):4083-93
17474710
Proc Natl Acad Sci U S A. 2009 Feb 17;106(7):2089-90
19211786
Development. 2010 Nov;137(21):3675-85
20940226
Nat Rev Drug Discov. 2005 Jul;4(7):594-610
16052242
Bioinformatics. 2005 Jul 15;21(14):3066-73
15879456
Anal Biochem. 2001 Aug 1;295(1):88-100
11476549
Methods Enzymol. 2007;433:175-91
17954235
Nat Rev Mol Cell Biol. 2010 Aug;11(8):593-8
20606693
Anal Chem. 2002 Mar 1;74(5):941-9
11924996
Rapid Commun Mass Spectrom. 2007;21(20):3229-33
17828792
Rapid Commun Mass Spectrom. 2005;19(5):654-66
15700236
J Am Soc Mass Spectrom. 2006 Feb;17(2):264-74
16413201
J Mass Spectrom. 2009 Dec;44(12):1676-83
19816875
Biochim Biophys Acta. 2006 Jan;1761(1):121-8
16458590
Nat Biotechnol. 2004 Nov;22(11):1459-66
15529173
Anal Chem. 2006 Dec 15;78(24):8324-31
17165823
Traffic. 2009 Jul;10(7):868-82
19453975
J Bacteriol. 2000 Jan;182(2):371-6
10629182
Prog Lipid Res. 2010 Jan;49(1):46-60
19703488
J Lipid Res. 2003 Nov;44(11):2181-92
12923235
Exp Dermatol. 2010 Aug;19(8):e103-10
19845761
J Am Soc Mass Spectrom. 2008 Feb;19(2):161-72
18187337
Proteome Sci. 2007 Jan 16;5:3
17227583
Mass Spectrom Rev. 2005 May-Jun;24(3):367-412
15389848
Biochim Biophys Acta. 2004 Nov 8;1686(1-2):108-17
15522827
Trends Biotechnol. 2008 Dec;26(12):647-52
18951641
Rapid Commun Mass Spectrom. 2007;21(11):1721-8
17477452
Anal Chem. 2006 Jan 15;78(2):585-95
16408944
Mol Pharmacol. 2004 Apr;65(4):813-21
15044609
BMC Bioinformatics. 2007 Mar 26;8:102
17386090
Proc Natl Acad Sci U S A. 2009 May 19;106(20):8350-5
19416849
Anal Chem. 2006 Aug 1;78(15):5497-503
16878888