Difference between revisions of "MFQL library"

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(MFQL used in [4] For identification of lipids in caveolae induced in E. coli)
 
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===MFQL used in '''[1]''' for lipid identification in E.coli===
 
===MFQL used in '''[1]''' for lipid identification in E.coli===
  
* Phosphatidylethanolamine in negative mode: [[File:PE_negative_FAS.mfql]]
+
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). MS/MS experiments were performed using Pulsed Q Collision Induced Dissociation(PQD).
* Lyso-Phosphatidylethanolamine in negative mode: [[File:LPE_negative_FAS.mfql]]
+
 
* Phosphatidylglycerol in negative mode: [[File:PG_negative_FAS.mfql]]
+
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.[[media:lpdX_benchmark.txt]] ('''IMPORTANT:''' for usage in LipidXplorer please rename file to lpdX_benchmark.ini)
* Phosphatidylinositol in negative mode: [[File:PI_negative_FAS.mfql]]
+
 
* Phosphatidylserine in negative mode: [[File:PS_negative_FAS.mfql]]
+
* Phosphatidylethanolamine in negative mode: [[media:PE_negative_FAS.mfql|PE_negative_FAS.mfql]]
* Phosphatic acid in negative mode: [[File:PA_negative_FAS.mfql]]
+
* Lyso-Phosphatidylethanolamine in negative mode: [[media:LPE_negative_FAS.mfql|LPE_negative_FAS.mfql]]
 +
* Phosphatidylglycerol in negative mode: [[media:PG_negative_FAS.mfql|PG_negative_FAS.mfql]]
 +
* Phosphatidylinositol in negative mode: [[media:PI_negative_FAS.mfql|PI_negative_FAS.mfql]]
 +
* Phosphatidylserine in negative mode: [[media:PS_negative_FAS.mfql|PS_negative_FAS.mfql]]
 +
* Phosphatic acid in negative mode: [[media:PA_negative_FAS.mfql|PA_negative_FAS.mfql]]
  
 
===MFQL used in '''[1]''' for lipid identification in bovine heart===
 
===MFQL used in '''[1]''' for lipid identification in bovine heart===
  
* Phosphatidylethanolamine in negative mode: [[File:neg_bovine_heart_PE.mfql]]
+
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.
* Lyso-Phosphatidylethanolamine in negative mode: [[File:neg_bovine_heart_LPE.mfql]]
+
 
* Phosphatidylethanolamine ether in negative mode: [[File:neg_bovine_heart_PEO.mfql]]
+
* Phosphatidylethanolamine in negative mode: [[media:neg_bovine_heart_PE.mfql|neg_bovine_heart_PE.mfql]]
* Phosphatidylcholine in negative mode: [[File:neg_bovine_heart_PC.mfql]]
+
* Lyso-Phosphatidylethanolamine in negative mode: [[media:neg_bovine_heart_LPE.mfql|neg_bovine_heart_LPE.mfql]]
* Lyso-Phosphatidylcholine in negative mode: [[File:neg_bovine_heart_LPC.mfql]]
+
* Phosphatidylethanolamine ether in negative mode: [[media:neg_bovine_heart_PEO.mfql|neg_bovine_heart_PEO.mfql]]
* Phosphatidylcholine ether in negative mode: [[File:neg_bovine_heart_PCO.mfql]]
+
* Phosphatidylcholine in negative mode: [[media:neg_bovine_heart_PC.mfql|neg_bovine_heart_PC.mfql]]
* Phosphatic acid in negative mode: [[File:neg_bovine_heart_PA.mfql]]
+
* Lyso-Phosphatidylcholine in negative mode: [[media:neg_bovine_heart_LPC.mfql|neg_bovine_heart_LPC.mfql]]
* Lyso-Phosphatic acid in negative mode: [[File:neg_bovine_heart_LPA.mfql]]
+
* Phosphatidylcholine ether in negative mode: [[media:neg_bovine_heart_PCO.mfql|neg_bovine_heart_PCO.mfql]]
* Phosphatidylglycerol in negative mode: [[File:neg_bovine_heart_PG.mfql]]
+
* Phosphatic acid in negative mode: [[media:neg_bovine_heart_PA.mfql|neg_bovine_heart_PA.mfql]]
* Lyso-Phosphatidylglycerol in negative mode: [[File:neg_bovine_heart_LPG.mfql]]
+
* Lyso-Phosphatic acid in negative mode: [[media:neg_bovine_heart_LPA.mfql|neg_bovine_heart_LPA.mfql]]
* Phosphatidylinositol in negative mode: [[File:neg_bovine_heart_PI.mfql]]
+
* Phosphatidylglycerol in negative mode: [[media:neg_bovine_heart_PG.mfql|neg_bovine_heart_PG.mfql]]
* Lyso-Phosphatidylinositol in negative mode: [[File:neg_bovine_heart_LPI.mfql]]
+
* Lyso-Phosphatidylglycerol in negative mode: [[media:neg_bovine_heart_LPG.mfql|neg_bovine_heart_LPG.mfql]]
* Sphingomylien in negative mode: [[File:neg_bovine_heart_LPI.mfql]]
+
* Phosphatidylinositol in negative mode: [[media:neg_bovine_heart_PI.mfql|neg_bovine_heart_PI.mfql]]
* Ceramide in negative mode: [[File:neg_bovine_heart_DAG.mfql]]
+
* Lyso-Phosphatidylinositol in negative mode: [[media:neg_bovine_heart_LPI.mfql|neg_bovine_heart_LPI.mfql]]
* Diacylglycerol in negative mode: [[File:neg_bovine_heart_DAG.mfql]]
+
* Sphingomylien in negative mode: [[media:neg_bovine_heart_LPI.mfql|neg_bovine_heart_LPI.mfql]]
* Triacylglycerol in negative mode: [[File:neg_bovine_heart_TAG.mfql]]
+
* Ceramide in negative mode: [[media:neg_bovine_heart_DAG.mfql|]neg_bovine_heart_DAG.mfql]
* Cardiolipin in negative mode: [[File:neg_bovine_heart_CL.mfql]]
+
* Diacylglycerol in negative mode: [[media:neg_bovine_heart_DAG.mfql|neg_bovine_heart_DAG.mfql]]
 +
* Triacylglycerol in negative mode: [[media:neg_bovine_heart_TAG.mfql|neg_bovine_heart_TAG.mfql]]
 +
* Cardiolipin in negative mode: [[media:neg_bovine_heart_CL.mfql|neg_bovine_heart_CL.mfql]]
  
 
===MFQL used in '''[2]''' for identification of Maradolipids in Dauer Larva in Caenorhabditis elegans===
 
===MFQL used in '''[2]''' for identification of Maradolipids in Dauer Larva in Caenorhabditis elegans===
  
* Maradolipids in negative ion mode: [[File:Maradolipid.mfql]]
+
* Maradolipids in negative ion mode: [[media:Maradolipid.mfql|Maradolipid.mfql]]
  
 
===MFQL used in '''[3]''' for identification of Lipids in human blood plasma===
 
===MFQL used in '''[3]''' for identification of Lipids in human blood plasma===
  
In this zip file: [[File:Mfql_screens_MS-only_positive.zip‎|Positive MS only screens]] the following queries can be found which were used in '''[3]''':
+
Mass spectrometric analysis was performed on a hybrid LTQ Orbitrap mass spectrometer (Thermo Fisher Scientific, Bremen, Germany) equipped with a robotic nanoflow ion source TriVersa (Advion BioSciences Ltd, Ithaca NY) using chips with 4.1 µm nozzle diameter. The ion source was controlled by Chipsoft 6.4. software (Advion BioSciences) and operated at the ionization voltage of 0.95 kV and gas pressure 1.25 psi. Plates with lipid extracts were chilled down to 12°C.
 +
MS survey scans were acquired in positive ion mode using the Orbitrap analyzer operated under the target mass resolution of 100,000 (Full Width at Half Maximum, FWHM), defined at m/z 400 under automatic gain control set to 1.0×106 as the target value.
 +
Spectra acquired within 28 s to 120 s from the start of sample infusion (timing required to stabilize the analyte flow and electrospray, as was judged by total ion current (TIC) trace) were averaged and recalibrated using m/z of synthetic standards SM 35:1 and PC –O 20:0/-O 20:0 as references. Only peaks detected at the signal-to-noise ratio above the factor of 5 and recognized in more than 20% of all spectra were further considered. Identification of lipid species relied on accurately determined masses considering a mass accuracy of better than 4 ppm and a retrieval rate of 90% for all plasma samples.
 +
 
 +
In this zip file: [[media:Mfql_screens_MS-only_positive.zip|Positive MS only screens]] the following queries can be found which were used in '''[3]''':
 
* Ceramide
 
* Ceramide
 
* Cholesterylester
 
* Cholesterylester
Line 50: Line 60:
 
* Sphingomyline (SM)
 
* Sphingomyline (SM)
 
* Triacylglycerols (TAG)
 
* Triacylglycerols (TAG)
 +
 +
===MFQL used in '''[4]''' For identification of lipids in caveolae induced in ''E. coli'' ===
 +
 +
In this zip file [[media:Walser_Schwudke_2012_MFQLs.zip|Walser_Schwudke_2012_MFQLs.zip]] following scripts are included.
 +
 +
* Lysophosphatic acid (LPA)
 +
* Lysophosphatidylethanolamine (LPE)
 +
* Lysophosphatidylglycerol (LPG)
 +
* Cardiolipin (CL)
 +
* Diacylglycerol (DAG)
 +
* Phosphatic acid (PA)
 +
* Phosphatidylglycerol (PG)
 +
* Phosphatidylethanolamine (PE)
 +
* Phosphatidylethanolamine ether (PE-O)
 +
* determination of fatty acid composition of PE
 +
* determination of fatty acid composition of PG
 +
 +
===MFQL for identification of lipids in positive mode using MS/MS ===
 +
 +
In this zip file [https://wiki.mpi-cbg.de/lipidxscr/images/8/8e/MFQL_MS-MS_positive.zip.zip MFQL_MS-MS_positive.zip] the following scripts are included:
 +
 +
* Ceramide (Cer-PIS.mfql)
 +
* Diacyglycerol (DAG-NLS.mfql)
 +
* Hexosyl Ceramide (HexCer-PIS.mfql)
 +
* Lactosyl Ceramide (LacCer-PIS.mfql)
 +
* Lysophosphatedylcholine (LPC-PIS.mfql)
 +
* Lysophosphatedylethanolamine (LPE-PIS.mfql)
 +
* Phosphatedylcholine Ether (PCO-PIS.mfql)
 +
* Phosphatedylcholine (PC-PIS.mfql)
 +
* Phosphatedylethanolamine (PE-PIS.mfql)
 +
* Phosphatedylethanolamine Plasmalogen (PEplasmalogens.mfql)
 +
* Sphingomyelin (SM-PIS.mfql)
 +
* Triacylglycerol (TAG-NLS.mfql)
 +
  
 
-----
 
-----
Line 61: Line 105:
 
lipidomics reveals ether lipid deficiency in blood plasma of hypertensive patients. PLoS One
 
lipidomics reveals ether lipid deficiency in blood plasma of hypertensive patients. PLoS One
 
2009, 4:e6261.
 
2009, 4:e6261.
 +
 +
'''[4]''' [[LX Reference Walser 2012 | Walser PJ, Ariotti N, Howes M, Ferguson C, Webb R, Schwudke D, Leneva N, Cho KJ, Cooper L, Rae J, Floetenmeyer M, Oorschot VM, Skoglund U, Simons K, Hancock JF, Parton RG.
 +
'''Constitutive formation of caveolae in a bacterium.'''
 +
''Cell. 2012 Aug 17;150(4):752-63.'']]

Latest revision as of 11:23, 25 June 2015

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). MS/MS experiments were performed using Pulsed Q Collision Induced Dissociation(PQD).

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.media: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

Mass spectrometric analysis was performed on a hybrid LTQ Orbitrap mass spectrometer (Thermo Fisher Scientific, Bremen, Germany) equipped with a robotic nanoflow ion source TriVersa (Advion BioSciences Ltd, Ithaca NY) using chips with 4.1 µm nozzle diameter. The ion source was controlled by Chipsoft 6.4. software (Advion BioSciences) and operated at the ionization voltage of 0.95 kV and gas pressure 1.25 psi. Plates with lipid extracts were chilled down to 12°C. MS survey scans were acquired in positive ion mode using the Orbitrap analyzer operated under the target mass resolution of 100,000 (Full Width at Half Maximum, FWHM), defined at m/z 400 under automatic gain control set to 1.0×106 as the target value. Spectra acquired within 28 s to 120 s from the start of sample infusion (timing required to stabilize the analyte flow and electrospray, as was judged by total ion current (TIC) trace) were averaged and recalibrated using m/z of synthetic standards SM 35:1 and PC –O 20:0/-O 20:0 as references. Only peaks detected at the signal-to-noise ratio above the factor of 5 and recognized in more than 20% of all spectra were further considered. Identification of lipid species relied on accurately determined masses considering a mass accuracy of better than 4 ppm and a retrieval rate of 90% for all plasma samples.

In this zip file: Positive MS only screens 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)

MFQL used in [4] For identification of lipids in caveolae induced in E. coli

In this zip file Walser_Schwudke_2012_MFQLs.zip following scripts are included.

  • Lysophosphatic acid (LPA)
  • Lysophosphatidylethanolamine (LPE)
  • Lysophosphatidylglycerol (LPG)
  • Cardiolipin (CL)
  • Diacylglycerol (DAG)
  • Phosphatic acid (PA)
  • Phosphatidylglycerol (PG)
  • Phosphatidylethanolamine (PE)
  • Phosphatidylethanolamine ether (PE-O)
  • determination of fatty acid composition of PE
  • determination of fatty acid composition of PG

MFQL for identification of lipids in positive mode using MS/MS

In this zip file MFQL_MS-MS_positive.zip the following scripts are included:

  • Ceramide (Cer-PIS.mfql)
  • Diacyglycerol (DAG-NLS.mfql)
  • Hexosyl Ceramide (HexCer-PIS.mfql)
  • Lactosyl Ceramide (LacCer-PIS.mfql)
  • Lysophosphatedylcholine (LPC-PIS.mfql)
  • Lysophosphatedylethanolamine (LPE-PIS.mfql)
  • Phosphatedylcholine Ether (PCO-PIS.mfql)
  • Phosphatedylcholine (PC-PIS.mfql)
  • Phosphatedylethanolamine (PE-PIS.mfql)
  • Phosphatedylethanolamine Plasmalogen (PEplasmalogens.mfql)
  • Sphingomyelin (SM-PIS.mfql)
  • Triacylglycerol (TAG-NLS.mfql)



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.

[4] Walser PJ, Ariotti N, Howes M, Ferguson C, Webb R, Schwudke D, Leneva N, Cho KJ, Cooper L, Rae J, Floetenmeyer M, Oorschot VM, Skoglund U, Simons K, Hancock JF, Parton RG. Constitutive formation of caveolae in a bacterium. Cell. 2012 Aug 17;150(4):752-63.