MFQL library

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MFQL used in [1] for lipid identification in E.coli

E. coli total lipid extract was purchased from Avanti Polar Lipids (Alabaster, AL, USA) and analyzed on the LTQ Orbitrap XL instrument in negative ion mode. A solution of the total lipid concentration of 2.5 μg/ml in 7.5 mM ammonium acetate in choloroform/methanol/2-propanol (1/2/4, v/v/v) was infused into the mass spectrometer by TriVersa robotic ion source using a chip with the diameter of spraying nozzles of 4.1 μm. To produce the spectra dataset, the extract was analyzed in several independent experiments: experiment I, eight acquisitions under the unit mass resolution (R) settings using ion trap (IT) to acquire both MS and MS/MS spectra; experiment II, six acquisitions with R = 7,500 for MS spectra (Orbitrap) and unit resolution for MS/MS spectra (IT); experiment III, four acquisitions with R = 30,000 for MS spectra (Orbitrap) and unit resolution for MS/MS spectra (IT); experiment IV, four acquisitions with R = 100,000 for MS spectra (Orbitrap) and unit resolution for MS/MS spectra (IT); experiment V, seven acquisitions with R = 100,000 for MS spectra (Orbitrap) and R = 15,000 for MS/MS spectra (Orbitrap).

The below listed MFQL files can be applied for all mass spectrometric settings. The mass spectrometric settings are saved in the *ini file utilized for the import of a dataset.File:LpdX benchmark.txt (IMPORTANT: for usage in LipidXplorer please rename file to lpdX_benchmark.ini)

MFQL used in [1] for lipid identification in bovine heart

Total lipid extract of bovine heart (Avanti Polar Lipids) was analyzed in six technical replicates on a LTQ-Orbitrap XL mass spectrometer using a target resolution of 100,000 for MS spectra (Orbitrap) and unit resolution for MS/MS (IT) in negative ion mode. Six replicates were acquired, each consisting of 31 MS and 310 MS/MS spectra.

MFQL used in [2] for identification of Maradolipids in Dauer Larva in Caenorhabditis elegans

MFQL used in [3] for identification of Lipids in human blood plasma

In this zip file: File:Mfql screens MS-only positive.zip the following queries can be found which were used in [3]:

  • Ceramide
  • Cholesterylester
  • Diacylglycerols
  • Glucosylceramide
  • GPL-diether
  • Lysophosphatidylcholine (LPC)
  • Lysophosphatidylethanolamine (LPE)
  • Phosphatidylcholine (PC)
  • Phosphatidylcholine ether (PC-O)
  • Phosphatidylethanolamine (PE)
  • Phosphatidylethanolamine ether (PE-O)
  • Phosphatidylinositol (PI)
  • Phosphatidylserine (PS)
  • Sphingomyline (SM)
  • Triacylglycerols (TAG)

References

[1] Herzog, R., Schwudke, D., Schuhmann, K., Sampaio, J.L., Bornstein, S.R., Schroeder, M., and Shevchenko, A. 2011. A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language. Genome Biol 12(1): R8.

[2]Penkov S, Mende F, Zagoriy V, Erkut C, Martin R, Pässler U, Schuhmann K, Schwudke D, Gruner M, Mäntler J, Reichert-Müller T, Shevchenko A, Knölker HJ, Kurzchalia TV. 2010. Maradolipids: diacyltrehalose glycolipids specific to dauer larva in Caenorhabditis elegans. Angew Chem Int Ed Engl. 49(49):9430-5.

[3] Graessler J, Schwudke D, Schwarz PE, Herzog R, Shevchenko A, Bornstein SR: Top-down lipidomics reveals ether lipid deficiency in blood plasma of hypertensive patients. PLoS One 2009, 4:e6261.