LipID - A software tool for automated assignment of lipids inmass spectra

Journal of Mass Spectrometry

Volumn 44, Issue 12, 2009, Pages 1676-1683

  Hübner, Göran ^a   Crone, Catharina ^a   Lindner, Buko ^a  

^a RESEARCH CENTER BORSTEL   (Germany)

Author keywords

Glycerophospholipids; Glycosphingolipids; LC MS; Lipidomics; Lipids

Indexed keywords

GLYCEROPHOSPHOLIPIDS; GLYCOSPHINGOLIPIDS; LC-MS; LIPID ANALYSIS; LIPIDOMICS; MASS SPECTRA; MASS-TO-CHARGE VALUE; MODE OF OPERATIONS; MS EXCEL; SOFTWARE TOOL; VISUAL BASIC FOR APPLICATIONS;

FATTY ACIDS; LIPIDS; MASS SPECTROMETRY; SPREADSHEETS;

COMPUTER SOFTWARE;

FATTY ACID; GLYCEROPHOSPHOLIPID; GLYCOSPHINGOLIPID; LIPID; OLIGOSACCHARIDE;

ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; ELECTROSPRAY MASS SPECTROMETRY; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; ION CYCLOTRON RESONANCE MASS SPECTROMETRY; LIPID ANALYSIS; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PRIORITY JOURNAL;

CHROMATOGRAPHY, HIGH PRESSURE LIQUID; EMBRYO, MAMMALIAN; ESCHERICHIA COLI; FATTY ACIDS; GLYCEROPHOSPHOLIPIDS; GLYCOSPHINGOLIPIDS; HUMANS; KIDNEY; LIPIDS; MASS SPECTROMETRY; OLIGOSACCHARIDES; SOFTWARE; TOLL-LIKE RECEPTOR 4; TRANSFECTION;

EID: 72449164424     PISSN: 10765174     EISSN: 10969888     Source Type: Journal    
DOI: 10.1002/jms.1673     Document Type: Article

References (39)

1. A. Heller, T. Koch, J. Schmeck, K. van Ackern. Lipid mediators in inflammatory disorders. Drugs 1998, 55(4), 487.
2. X. Han, R. W. Gross. Shotgun lipidomics: electrospray ionization mass spectrometric analysis and quantitation of cellular lipidomes directly fromcrudeextractsofbiological samples. Mass Spectrometry Reviews 2005, 24(3), 367.
3. B. Brügger, G. Erben, R. Sandhoff, F. T. Wieland, W. D. Lehmann. Quantitative analysis of biological membrane lipids at the low picomole level by nano-electrospray ionization tandem mass spectrometry. Proceedings of theNational Academy of Sciences of the United States of America 1997, 94(6), 2339.
4. K. Ekroos, I. V. Chernushevich, K. Simons, A. Shevchenko. Quantitative profiling of phospholipids by multiple precursor ion scanning onahybridquadrupole time-of-flight mass spectrometer. Analytical Chemistry 2002, 74(5), 941.
5. X. Han, R. W. Gross. Electrospray ionization mass spectroscopic analysis of human erythrocyte plasma membrane phospholipids. Proceedings of the National Academy of Sciences of the United States of America 1994, 91(22), 10635.
6. T. Houjou, K. Yamatani, H. Nakanishi, M. Imagawa, T. Shimizu, R. Taguchi. Rapid and selective identification of molecular species in phosphatidylcholine and sphingomyelin by conditional neutral loss scanning and MS3. Rapid Communications in Mass Spectrometry 2004, 18(24), 3123.
7. T. Houjou, K. Yamatani, M. Imagawa, T. Shimizu, R. Taguchi. A shotgun tandem mass spectrometric analysis of phospholipids with normal-phase and/or reverse-phase liquid chromatography/electrospray ionization mass spectrometry. Rapid Communications inMass Spectrometry 2005, 19(5), 654.
8. S. N. Jackson, H. Y. Wang, A. S. Woods. In situ structural characterization of glycerophospholipids and sulfatides in brain tissue using MALDI-MS/MS. Journal of the American Society for Mass Spectrometry 2007, 18(1), 17.
9. J. L. Kerwin, A. R. Tuininga, L. H. Ericsson. Identification ofmolecular species of glycerophospholipids and sphingomyelin using electrospray mass spectrometry. Journal of Lipid Research 1994, 35(6), 1102.
10. S. Milne, P. Ivanova, J. Forrester, B. H. Alex. Lipidomics: an analysis of cellular lipids by ESI-MS. Methods 2006, 39(2), 92.
11. T. W. Mitchell, K. Ekroos, S. J. Blanksby, A. J. Hulbert, P. L. Else. Differences in membrane acyl phospholipid composition between an endothermic mammal and an ectothermic reptile are not limited to any phospholipid class. The Journal of Experimental Biology 2007, 210(19), 3440.
12. J. Schiller, R. Suss, J. Arnhold, B. Fuchs, J. Lessig, M. Müller, M. Petković, H. Spalteholz, O. Zschörnig, K. Arnold. Matrix-assisted laser desorption and ionization time-of-flight (MALDI-TOF) mass spectrometry in lipid and phospholipid research. Progress in Lipid Research 2004, 43(5), 449.
13. P. B. W. Smith, A. P. Snyder, C. S. Harden. Characterization of bacterial phospholipids by electrospray ionization tandem mass spectrometry. Analytical Chemistry 1995, 67(11), 1824.
14. G. Sweetman, M. Trinei, J. Modha, J. Kusel, P. Freestone, I. Fishov, D. Joselau-Petit, C. Redman, P. Farmer, V. Norris. Electrospray ionization mass spectrometric analysis of phospholipids of Escherichia coli. Molecular Microbiology 1996, 20(1), 233.
15. S. M. Batoy, S. Borgmann, K. Flick, J. Griffith, J. J. Jones, V. Saraswathi, A. H. Hasty, P. Kaiser, C. L. Wilkins. Lipid and phospholipid profiling of biological samples using MALDI Fourier transform mass spectrometry. Lipids 2009, 44(4), 367.
16. I. Bobeldijk, M. Hekman, J. de Vries-van der Weij, L. Coulier, R. Ramaker, R. Kleemann, T. Kooistra, C. Rubingh, A. Freidig, C. Verheij. Quantitative profiling of bile acids in biofluids and tissues based on accurate mass high resolution LC-FT-MS: compound class targeting in a metabolomics workflow. Journal of Chromatography B 2008, 871(2), 306.
17. C. Hu, J. van Dommelen, R. van der Heijden, G. Spijksma, T. H. Reijmers, M. Wang, E. Slee, X. Lu, G. Xu, J. van der Greef, T. Hankemeier. RPLC-ion-trap-FTMS method for lipid profiling of plasma: method validation and application to p53 mutant mouse model. Journal of Proteome Research 2008, 7(11), 4982.
18. J. J. Jones, M. J. Stump, R. C. Fleming, J. O. Lay Jr, C. L. Wilkins. Strategies and data analysis techniques for lipid and phospholipid chemistry elucidation by intact cell MALDI-FTMS. Journal of the American Society for Mass Spectrometry 2004, 15(11), 1665.
19. J. J. Jones, S. Borgmann, C. L. Wilkins, R. M. O'Brien. Characterizing the phospholipid profiles in mammalian tissues by MALDI FTMS. Analytical Chemistry 2006, 78(9), 3062.
20. C.-M. Koppelman, T. Den Blaauwen, M. C. Duursma, R. M. A. Heeren, N. Nanninga. Escherichia coli minicell membranes are enriched in cardiolipin. Journal of Bacteriology 2001, 183(20), 6144.
21. J. A. Marto, F. M. White, S. Seldomridge, A. G. Marshall. Structural characterization of phospholipids by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry. Analytical Chemistry 1995, 67(21), 3979.
22. A. Koulman, G. Woffendin, V. K. Narayana, H. Welchman, C. Crone, D. A. Volmer. High-resolution extracted ion chromatography, a new tool for metabolomics and lipidomics using a second-generation orbitrap mass spectrometer. Rapid Communications in Mass Spectrometry 2009, 23(10), 1411.
23. J. Graessler, D. Schwudke, P. E. H. Schwarz, R. Herzog, A. Shevchenko, S. R. Bornstein. Top-down lipidomics reveals ether lipid deficiency in blood plasma of hypertensive patients. PloS One 2009, 4(7), e6261.
24. M. Sud, E. Fahy, D. Cotter, A. Brown, E. A. Dennis, C. K. Glass, A. H. Merrill Jr, R. C. Murphy, C. R. Raetz, D. W. Russell, S. Subramaniam. LMSD: LIPID MAPS structure database. Nucleic Acids Research 2007, 35, (database issue), D527.
25. K. Watanabe, E. Yasugi, M. Oshima. How to search the glycolipid data in LIPIDBANK for Web: the newly developed lipid database. Trends in Glycoscience and Glycotechnology 2000, 12(65), 175.
26. E. Fahy, M. Sud, D. Cotter, S. Subramaniam. LIPIDMAPS online tools for lipid research. Nucleic Acids Research 2007, 35, (web server issue), W606.
27. C. S. Ejsing, E. Duchoslav, J. Sampaio, K. Simons, R. Bonner, C. Thiele, K. Ekroos, A. Shevchenko. Automated identification and quantification of glycerophospholipid molecular species by multiple precursor ion scanning. Analytical Chemistry 2006, 78(17), 6202.
28. H. Song, F.-F. Hsu, J. Ladenson, J. Turk. 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. Journal of the American Society for Mass Spectrometry 2007, 18(10), 1848.
29. D. Schwudke, J. Oegema, L. Burton, E. Entchev, J. T. Hannich, C. S. Ejsing, T. Kurzchalia, A. Shevchenko. Lipid profiling by multiple precursor and neutral loss scanning driven by the data-dependent acquisition. Analytical Chemistry 2006, 78(2), 585.
30. M. D. Leavell, J. A. Leary. Fatty acid analysis tool (FAAT): an FT-ICR MS lipid analysis algorithm. Analytical Chemistry 2006, 78(15), 5497.
31. P. Haimi, A. Uphoff, M. Hermansson, P. Somerharju. Software tools for analysis of mass spectrometric lipidome data. Analytical Chemistry 2006, 78(24), 8324.
32. K. Maass, R. Ranzinger, H. Geyer, C.-W. von der Lieth, R. Geyer. "Glyco-peakfinder" - de novo composition analysis of glycoconjugates. Proteomics 2007, 7(24), 4435.
33. E. G. Bligh, W. J. Dyer. A rapid method of total lipid extraction and purification. Canadian Journal of Biochemistry and Physiology 1959, 37(8), 911.
34. E. Fahy, S. Subramaniam, H. A. Brown, C. K. Glass, A. H. Merrill Jr, R. C. Murphy, C. R. Raetz, D. W. Russell, Y. Seyama, W. Shaw, T. Shimizu, F. Spener, G. van Meer, M. S. VanNieuwenhze, S. H. White, J. L. Witztum, E. A. Dennis. A comprehensive classification system for lipids. Journal of Lipid Research 2005, 46(5), 839.
35. J. S. Forrester, S. B. Milne, P. T. Ivanova, H. A. Brown. Computational lipidomics: a multiplexed analysis of dynamic changes in membrane lipid composition during signal transduction. Molecular Pharmacology 2004, 65(4), 813.
36. L. Svennerholm. Chromatographic separation of human brain gangliosides. Journal of Neurochemistry 1963, 10(9), 613.
37. W. E. Connor, D. S. Lin, G. Thomas, F. Ey, T. DeLoughery, N. Zhu. Abnormal phospholipid molecular species of erythrocytes in sickle cell anemia. Journal of Lipid Research 1997, 38(12), 2516.
38. H. Goldfine. Bacterial membranes and lipid packing theory. Journal of Lipid Research 1984, 25(13), 1501.
39. S. Morein, A.-S. Andersson, L. Rilfors, G. Lindblom. Wild-type Escherichia coli cells regulate the membrane lipid composition in a "window" between gel and non-lamellar structures. The Journal of Biological Chemistry 1996, 271(12), 6801.