A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language

[1]  Stefan R. Bornstein,et al.  Top-Down Lipidomics Reveals Ether Lipid Deficiency in Blood Plasma of Hypertensive Patients , 2009, PloS one.

[2]  A. Shevchenko,et al.  Lipidome of narrow‐band ultraviolet B irradiated keratinocytes shows apoptotic hallmarks , 2009, Experimental dermatology.

[3]  A. Shevchenko,et al.  Glycosphingolipid Requirements for Endosome‐to‐Golgi Transport of Shiga Toxin , 2009, Traffic.

[4]  Dominik Schwudke,et al.  Maradolipids: diacyltrehalose glycolipids specific to dauer larva in Caenorhabditis elegans. , 2010, Angewandte Chemie.

[5]  Chris F. Taylor,et al.  A common open representation of mass spectrometry data and its application to proteomics research , 2004, Nature Biotechnology.

[6]  Christer S. Ejsing,et al.  Charting molecular composition of phosphatidylcholines by fatty acid scanning and ion trap MS3 fragmentation Published, JLR Papers in Press, August 16, 2003. DOI 10.1194/jlr.D300020-JLR200 , 2003, Journal of Lipid Research.

[7]  Kouji Matsumoto,et al.  Viability of an Escherichia coli pgsANull Mutant Lacking Detectable Phosphatidylglycerol and Cardiolipin , 2000, Journal of bacteriology.

[8]  G. Hübner,et al.  lipID--a software tool for automated assignment of lipids in mass spectra. , 2009, Journal of mass spectrometry : JMS.

[9]  G. van Meer,et al.  Cellular lipidomics , 2005, The EMBO journal.

[10]  Alexander Makarov,et al.  Dynamic range of mass accuracy in LTQ orbitrap hybrid mass spectrometer , 2006, Journal of the American Society for Mass Spectrometry.

[11]  Edward A Dennis,et al.  Lipidomics joins the omics evolution , 2009, Proceedings of the National Academy of Sciences.

[12]  M. Wenk.  The emerging field of lipidomics , 2005, Nature Reviews Drug Discovery.

[13]  S. Chevalier,et al.  Identification and relative quantification of fatty acids in Escherichia coli membranes by gas chromatography/mass spectrometry. , 2007, Rapid communications in mass spectrometry : RCM.

[14]  Martin Hermansson,et al.  Software tools for analysis of mass spectrometric lipidome data. , 2006, Analytical chemistry.

[15]  Matej Oresic,et al.  Informatics and computational strategies for the study of lipids. , 2008, Molecular bioSystems.

[16]  A. Shevchenko,et al.  Quantitative profiling of phospholipids by multiple precursor ion scanning on a hybrid quadrupole time-of-flight mass spectrometer. , 2002, Analytical chemistry.

[17]  Xianlin Han,et al.  Global analyses of cellular lipidomes directly from crude extracts of biological samples by ESI mass spectrometry: a bridge to lipidomics. , 2003, Journal of lipid research.

[18]  Haowei Song,et al.  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 , 2007, Journal of the American Society for Mass Spectrometry.

[19]  A. Shevchenko,et al.  Top-down lipidomic screens by multivariate analysis of high-resolution survey mass spectra. , 2007, Analytical chemistry.

[20]  G. Meer.  New EMBO Member's Review Cellular lipidomics , 2005 .

[21]  Gerd Schmitz,et al.  High-throughput quantification of phosphatidylcholine and sphingomyelin by electrospray ionization tandem mass spectrometry coupled with isotope correction algorithm. , 2004, Biochimica et biophysica acta.

[22]  M. D. Leavell,et al.  Fatty acid analysis tool (FAAT): An FT-ICR MS lipid analysis algorithm. , 2006, Analytical chemistry.

[23]  Kai Simons,et al.  Automated identification and quantification of glycerophospholipid molecular species by multiple precursor ion scanning. , 2006, Analytical chemistry.

[24]  Matej Oresic,et al.  Lipidomics: a new window to biomedical frontiers. , 2008, Trends in biotechnology.

[25]  Gerd Schmitz,et al.  Shotgun lipidomics by tandem mass spectrometry under data-dependent acquisition control. , 2007, Methods in enzymology.

[26]  A. Shevchenko,et al.  Ablation of cholesterol biosynthesis in neural stem cells increases their VEGF expression and angiogenesis but causes neuron apoptosis , 2009, Proceedings of the National Academy of Sciences.

[27]  O. Sparkman.  Mass Spectrometry Desk Reference , 2006 .

[28]  O. Geiger,et al.  Amino acid-containing membrane lipids in bacteria. , 2010, Progress in lipid research.

[29]  Christer S. Ejsing,et al.  Lipid profiling by multiple precursor and neutral loss scanning driven by the data-dependent acquisition. , 2006, Analytical chemistry.

[30]  S. Chevalier,et al.  Lipid composition of membranes of Escherichia coli by liquid chromatography/tandem mass spectrometry using negative electrospray ionization. , 2007, Rapid communications in mass spectrometry : RCM.

[31]  Brian Carrillo,et al.  Methods for peptide identification by spectral comparison , 2007, Proteome Science.

[32]  U. Sommer,et al.  LC-MS based method for the qualitative and quantitative analysis of complex lipid mixtures , 2006 .

[33]  H. Brown,et al.  Computational lipidomics: a multiplexed analysis of dynamic changes in membrane lipid composition during signal transduction. , 2004, Molecular pharmacology.

[34]  Xianlin Han,et al.  Shotgun lipidomics: electrospray ionization mass spectrometric analysis and quantitation of cellular lipidomes directly from crude extracts of biological samples. , 2005, Mass spectrometry reviews.

[35]  Xianlin Han,et al.  Quantitative analysis and molecular species fingerprinting of triacylglyceride molecular species directly from lipid extracts of biological samples by electrospray ionization tandem mass spectrometry. , 2001, Analytical biochemistry.

[36]  Richard D. Smith,et al.  Clustering millions of tandem mass spectra. , 2008, Journal of proteome research.

[37]  Christer S. Ejsing,et al.  Global analysis of the yeast lipidome by quantitative shotgun mass spectrometry , 2009, Proceedings of the National Academy of Sciences.

[38]  Takao Shimizu,et al.  A shotgun tandem mass spectrometric analysis of phospholipids with normal-phase and/or reverse-phase liquid chromatography/electrospray ionization mass spectrometry. , 2005, Rapid communications in mass spectrometry : RCM.

[39]  A. Shevchenko,et al.  Lipidomics: coming to grips with lipid diversity , 2010, Nature Reviews Molecular Cell Biology.

[40]  G. Glish,et al.  Hybrid mass spectrometers for tandem mass spectrometry , 2008, Journal of the American Society for Mass Spectrometry.

[41]  A. Shevchenko,et al.  Survival strategies of a sterol auxotroph , 2010, Development.

[42]  Neal O. Jeffries,et al.  Algorithms for alignment of mass spectrometry proteomic data , 2005, Bioinform..

[43]  Andreas Wilke,et al.  SAMPI: Protein Identification with Mass Spectra Alignments , 2007, BMC Bioinformatics.

[44]  Gerd Schmitz,et al.  High throughput quantification of cholesterol and cholesteryl ester by electrospray ionization tandem mass spectrometry (ESI-MS/MS). , 2006, Biochimica et biophysica acta.

[45]  Richard W. Gross,et al.  Factors influencing the electrospray intrasource separation and selective ionization of glycerophospholipids , 2006, Journal of the American Society for Mass Spectrometry.