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===MFQL used for lipid identification in E.coli===

====Materials and Methods====

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)

====The MFQL's====

* Phosphatidylethanolamine in negative mode: [[media:PE_negative_FAS.mfql|PE_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]]
-> zip file: [[File:Mfql_neg_FAS_Ecoli.zip | mfql_neg_FAS_Ecoli.zip]]

===MFQL used for lipid identification in bovine heart===

====Materials and Methods====

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.

====The MFQL's====

* Phosphatidylethanolamine in negative mode: [[media:neg_bovine_heart_PE.mfql|neg_bovine_heart_PE.mfql]]
* Lyso-Phosphatidylethanolamine in negative mode: [[media:neg_bovine_heart_LPE.mfql|neg_bovine_heart_LPE.mfql]]
* Phosphatidylethanolamine ether in negative mode: [[media:neg_bovine_heart_PEO.mfql|neg_bovine_heart_PEO.mfql]]
* Phosphatidylcholine in negative mode: [[media:neg_bovine_heart_PC.mfql|neg_bovine_heart_PC.mfql]]
* Lyso-Phosphatidylcholine in negative mode: [[media:neg_bovine_heart_LPC.mfql|neg_bovine_heart_LPC.mfql]]
* Phosphatidylcholine ether in negative mode: [[media:neg_bovine_heart_PCO.mfql|neg_bovine_heart_PCO.mfql]]
* Phosphatic acid in negative mode: [[media:neg_bovine_heart_PA.mfql|neg_bovine_heart_PA.mfql]]
* Lyso-Phosphatic acid in negative mode: [[media:neg_bovine_heart_LPA.mfql|neg_bovine_heart_LPA.mfql]]
* Phosphatidylglycerol in negative mode: [[media:neg_bovine_heart_PG.mfql|neg_bovine_heart_PG.mfql]]
* Lyso-Phosphatidylglycerol in negative mode: [[media:neg_bovine_heart_LPG.mfql|neg_bovine_heart_LPG.mfql]]
* Phosphatidylinositol in negative mode: [[media:neg_bovine_heart_PI.mfql|neg_bovine_heart_PI.mfql]]
* Lyso-Phosphatidylinositol in negative mode: [[media:neg_bovine_heart_LPI.mfql|neg_bovine_heart_LPI.mfql]]
* Sphingomylien in negative mode: [[media:neg_bovine_heart_LPI.mfql|neg_bovine_heart_LPI.mfql]]
* Ceramide in negative mode: [[media:neg_bovine_heart_DAG.mfql|neg_bovine_heart_DAG.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]]

-> zip File: [[File:Neg_bovine_heart_MFQL.zip‎]]

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