Analysis of lipid experiments (ALEX): A software framework for analysis of high-resolution shotgun lipidomics data

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  Husen, Peter ^a   Tarasov, Kirill ^b   Katafiasz, Maciej ^a   Sokol, Elena ^a   Vogt, Johannes ^c   Baumgart, Jan ^c   Nitsch, Robert ^c   Ekroos, Kim ^b   Ejsing, Christer S ^a  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^b Zora Biosciences Oy   (Finland)

^c JOHANNES GUTENBERG UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

LIPID PHOSPHATE PHOSPHATASE; PHOSPHATASE; UNCLASSIFIED DRUG; LIPID;

ANIMAL TISSUE; ARTICLE; AUTOMATION; CEREBELLUM; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS; DATA BASE; DATA PROCESSING; GENE; HIPPOCAMPUS; INFORMATION PROCESSING; LIPID ANALYSIS; LIPIDOMICS; MALE; MASS SPECTROMETRY; MOUSE; NEUROLIPIDOMICS; NONHUMAN; PLASTICITY RELATED GENE 1; SOMATOSENSORY CORTEX; ANIMAL; BRAIN; CHEMISTRY; COMPUTER INTERFACE; FACTUAL DATABASE; INTERNET; METABOLISM;

ANIMALS; BRAIN; DATABASES, FACTUAL; INTERNET; LIPIDS; MICE; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 84892416577     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0079736     Document Type: Article

References (38)

1. Yetukuri L, Ekroos K, Vidal-Puig A, Oresic M (2008) Informatics and computational strategies for the study of lipids. Mol Biosyst 4: 121-127. doi:10.1039/b715468b. PubMed: 18213405.
2. Shevchenko A, Simons K (2010) Lipidomics: coming to grips with lipid diversity. Nat Rev Mol Cell Biol 11: 593-598. doi:10.1038/nrg2850. PubMed: 20606693.
3. van Meer G (2005) Cellular lipidomics. EMBO J 24: 3159-3165. doi: 10.1038/sj.emboj.7600798. PubMed: 16138081.
4. Ejsing CS, Sampaio JL, Surendranath V, Duchoslav E, Ekroos K et al. (2009) Global analysis of the yeast lipidome by quantitative shotgun mass spectrometry. Proc Natl Acad Sci U S A 106: 2136-2141. doi:10.1073/pnas. 0811700106. PubMed: 19174513.
5. Klose C, Surma MA, Gerl MJ, Meyenhofer F, Shevchenko A et al. (2012) Flexibility of a eukaryotic lipidome - insights from yeast lipidomics. PLOS ONE 7: e35063. doi:10.1371/journal.pone.0035063. PubMed: 22529973.
6. Carvalho M, Sampaio JL, Palm W, Brankatschk M, Eaton S et al. (2012) Effects of diet and development on the Drosophila lipidome. Mol Syst Biol 8: 600. PubMed: 22864382.
7. Sampaio JL, Gerl MJ, Klose C, Ejsing CS, Beug H et al. (2011) Membrane lipidome of an epithelial cell line. Proc Natl Acad Sci U S A 108: 1903-1907. doi:10.1073/pnas.1019267108. PubMed: 21245337.
8. Dennis EA, Deems RA, Harkewicz R, Quehenberger O, Brown HA et al. (2010) A mouse macrophage lipidome. J Biol Chem 285: 39976-39985. doi:10.1074/jbc.M110. 182915. PubMed: 20923771.
9. Breslow DK, Collins SR, Bodenmiller B, Aebersold R, Simons K et al. (2010) Orm family proteins mediate sphingolipid homeostasis. Nature 463: 1048-1053. doi:10.1038/nature08787. PubMed: 20182505.
10. Klemm RW, Ejsing CS, Surma MA, Kaiser HJ, Gerl MJ et al. (2009) Segregation of sphingolipids and sterols during formation of secretory vesicles at the trans-Golgi network. J Cell Biol 185: 601-612. doi:10.1083/jcb.200901145. PubMed: 19433450.
11. Brügger B, Glass B, Haberkant P, Leibrecht I, Wieland FT et al. (2006) The HIV lipidome: a raft with an unusual composition. Proc Natl Acad Sci U S A 103: 2641-2646. doi:10.1073/pnas.0511136103. PubMed: 16481622.
12. Takamori S, Holt M, Stenius K, Lemke EA, Grønborg M et al. (2006) Molecular anatomy of a trafficking organelle. Cell 127: 831-846. doi:10.1016/j.cell.2006.10.030. PubMed: 17110340.
13. Zech T, Ejsing CS, Gaus K, de Wet B, Shevchenko A et al. (2009) Accumulation of raft lipids in T-cell plasma membrane domains engaged in TCR signalling. EMBO J 28: 466-476. doi:10.1038/emboj.2009.6. PubMed: 19177148.
14. Han X, Yang K, Gross RW (2012) Multi-dimensional mass spectrometry-based shotgun lipidomics and novel strategies for lipidomic analyses. Mass Spectrom Rev 31: 134-178. doi:10.1002/mas.20342. PubMed: 21755525.
15. Song H, Hsu FF, Ladenson J, Turk J (2007) Algorithm for processing raw mass spectrometric data to identify and quantitate complex lipid molecular species in mixtures by data-dependent scanning and fragment ion database searching. J Am Soc Mass Spectrom 18: 1848-1858. doi:10.1016/j.jasms.2007.07. 023. PubMed: 17720531.
16. Haimi P, Uphoff A, Hermansson M, Somerharju P (2006) Software tools for analysis of mass spectrometric lipidome data. Anal Chem 78: 8324-8331. doi:10.1021/ac061390w. PubMed: 17165823.
17. Leavell MD, Leary JA (2006) Fatty acid analysis tool (FAAT): An FT-ICR MS lipid analysis algorithm. Anal Chem 78: 5497-5503. doi:10.1021/ac0604179. PubMed: 16878888.
18. Hübner G, Crone C, Lindner B (2009) lipID - a software tool for automated assignment of lipids in mass spectra. J Mass Spectrom 44: 1676-1683. PubMed: 19816875.
19. Houjou T, Yamatani K, Imagawa M, Shimizu T, Taguchi R (2005) A shotgun tandem mass spectrometric analysis of phospholipids with normal-phase and/or reverse-phase liquid chromatography/electrospray ionization mass spectrometry. Rapid Commun Mass Spectrom 19: 654-666. doi:10.1002/rcm.1836. PubMed: 15700236.
20. Ejsing CS, Duchoslav E, Sampaio J, Simons K, Bonner R et al. (2006) Automated identification and quantification of glycerophospholipid molecular species by multiple precursor ion scanning. Anal Chem 78: 6202-6214. doi:10.1021/ac060545x. PubMed: 16944903.
21. Schwudke D, Oegema J, Burton L, Entchev E, Hannich JT et al. (2006) Lipid profiling by multiple precursor and neutral loss scanning driven by the data-dependent acquisition. Anal Chem 78: 585-595. doi:10.1021/ac051605m. PubMed: 16408944.
22. Herzog R, Schwudke D, Schuhmann K, Sampaio JL, Bornstein SR et al. (2011) A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language. Genome Biol 12: R8. doi:10.1186/gb-2011-12-1-r8. PubMed: 21247462.
23. Ejsing CS, Husen P, Tarasov K (2012) In: K Ekroos. Lipidomics: technologies and applications. Weinheim: Wiley-VCH. pp. 147-174.
24. Liebisch G, Vizcaíno JA, Köfeler H, Trötzmüller M, Griffiths WJ et al. (2013) Shorthand notation for lipid structures derived from mass spectrometry. J Lipid Res 54: 1523-1530. doi:10.1194/jlr.M033506. PubMed: 23549332.
25. Ekroos K, Ejsing CS, Bahr U, Karas M, Simons K et al. (2003) Charting molecular composition of phosphatidylcholines by fatty acid scanning and ion trap MS3 fragmentation. J Lipid Res 44: 2181-2192. doi:10.1194/jlr.D300020- JLR200. PubMed: 12923235.
26. Fahy E, Subramaniam S, Brown HA, Glass CK, Merrill AH Jr. et al. (2005) A comprehensive classification system for lipids. J Lipid Res 46: 839-861. doi:10.1194/jlr.E400004-JLR200. PubMed: 15722563.
27. Fahy E, Subramaniam S, Murphy RC, Nishijima M, Raetz CR et al. (2009) Update of the LIPID MAPS comprehensive classification system for lipids. J Lipid Res 50 Suppl: S9-14. PubMed: 19098281.
28. Curk T, Demsar J, Xu Q, Leban G, Petrovic U et al. (2005) Microarray data mining with visual programming. Bioinformatics 21: 396-398. doi:10.1093/bioinformatics/bth474. PubMed: 15308546.
29. Trimbuch T, Beed P, Vogt J, Schuchmann S, Maier N et al. (2009) Synaptic PRG-1 modulates excitatory transmission via lipid phosphate-mediated signaling. Cell 138: 1222-1235. doi:10.1016/j.cell.2009.06.050. PubMed: 19766573.
30. Schwudke D, Hannich JT, Surendranath V, Grimard V, Moehring T et al. (2007) Top-down lipidomic screens by multivariate analysis of high-resolution survey mass spectra. Anal Chem 79: 4083-4093. doi:10.1021/ac062455y. PubMed: 17474710.
31. Liebisch G, Binder M, Schifferer R, Langmann T, Schulz B et al. (2006) High throughput quantification of cholesterol and cholesteryl ester by electrospray ionization tandem mass spectrometry (ESI-MS/MS). Biochim Biophys Acta 1761: 121-128. doi:10.1016/j.bbalip.2005.12.007. PubMed: 16458590.
32. Sandhoff R, Brügger B, Jeckel D, Lehmann WD, Wieland FT (1999) Determination of cholesterol at the low picomole level by nanoelectrospray ionization tandem mass spectrometry. J Lipid Res 40: 126-132. PubMed: 9869658.
33. Bilgin M, Markgraf DF, Duchoslav E, Knudsen J, Jensen ON et al. (2011) Quantitative profiling of PE, MMPE, DMPE, and PC lipid species by multiple precursor ion scanning: a tool for monitoring PE metabolism. Biochim Biophys Acta 1811: 1081-1089. doi:10.1016/j.bbalip.2011.09.018. PubMed: 22001639.
34. Southam AD, Payne TG, Cooper HJ, Arvanitis TN, Viant MR (2007) Dynamic range and mass accuracy of wide-scan direct infusion nanoelectrospray fourier transform ion cyclotron resonance mass spectrometry-based metabolomics increased by the spectral stitching method. Anal Chem 79: 4595-4602. doi:10.1021/ ac062446p. PubMed: 17511421.
35. Schuhmann K, Almeida R, Baumert M, Herzog R, Bornstein SR et al. (2012) Shotgun lipidomics on a LTQ Orbitrap mass spectrometer by successive switching between acquisition polarity modes. J Mass Spectrom 47: 96-104. doi:10.1002/jms.2031. PubMed: 22282095.
36. Chan RB, Oliveira TG, Cortes EP, Honig LS, Duff KE et al. (2012) Comparative lipidomic analysis of mouse and human brain with Alzheimer disease. J Biol Chem 287: 2678-2688. doi:10.1074/jbc.M111.274142. PubMed: 22134919.
37. Rappley I, Myers DS, Milne SB, Ivanova PT, Lavoie MJ et al. (2009) Lipidomic profiling in mouse brain reveals differences between ages and genders, with smaller changes associated with alpha-synuclein genotype. J Neurochem 111: 15-25. doi:10.1111/j.1471-4159.2009.06290.x. PubMed: 19627450.
38. O'Brien JS, Sampson EL (1965) Lipid composition of the normal human brain: gray matter, white matter, and myelin. J Lipid Res 6: 537-544. PubMed: 5865382.