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40 protocols using splash lipidomix

1

Lipidomic Analysis by LC-MS

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LC/MS (Merck KGaA, Darmstadt, Germany) grade Water (LiChrosolv), Acetonitrile (ACN), Methanol (MeOH), and Isopropanol (IPA) all (Carlo Erba, Milan, Italy), ammonium fluoride, ammonium acetate, methyl-t-butyl ether (MTBE), and chloroform (Chlo) were purchased from Sigma-Aldrich (Sigma-Aldrich GmbH, Hamburg, Germany). Internal standard (IS) was Splash Lipidomix (Avanti Polar, Alabaster, AL, USA): mixture with known concentration of the following lipids [nmol/mL]: PC 15:0_18:1(d7) [212.6]; PE 15:0_18:1(d7) [7.0]; PS 15:0_18:1(d7) [6.6]; PG 15:0_18:1(d7) [40.5]; PI 15:0_18:1(d7) [12.1]; PA 15:0_18:1(d7) [10.5]; LPC 18:1(d7) [47.3]; LPE 18:1(d7) [10.3]; CE 18:1(d7) [532.2]; MG 18:1(d7) [5.5]; DG 15:0_18:1(d7) [17.0]; TG 15:0_18:1(d7)_15:0 [67.8]; SM 18:1;2O/18:1(d9) [40.7]; Cholesterol(d7)[254.2].
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2

Lipidomic Analysis of Liver Extracts

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Pooled quality control samples were prepared by aliquoting 5 µL of each liver extract into a single vial. This sample was spiked with 10 µL internal standard (Splash Lipidomix, Avanti Polar, Birmingham, AL). This analytical grade standard contains odd-chain, deuterated lipids in lipid classes and ratios present in human plasma. Pooled QC samples were run after every 10 samples as well as at the beginning and end of the analytical run. Quality control samples were used to ensure the stability of the instrument during analysis. The coefficient of variation for each identified lipid within the pooled QC was then calculated using a cutoff of <40%. The internal standard was used to optimize instrumental parameters, such as electrospray voltage, collision energy, and others; these parameters were held consistent over the course of analysis. Lipids in the internal standard were also used to monitor injection consistency from sample to sample and additionally for signal correction/batch correction. For signal correction, the analytical signal of each identified lipid was normalized by the signal of internal standard, LPC 18:1d7.
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3

High-Throughput Plasma Lipid Extraction

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Lipids were extracted from plasma using a high throughput, monophasic, methyl t-butyl ether (MtBE) based method. Using an automated pipetting and sample preparation system (Biotage Extrahera, Uppsala, Sweden), 50 µL of patient plasma was loaded into preconditioned wells containing 10 µL methanol and 10 µL of internal standard, Splash Lipidomix (Avanti Polar, Birmingham, AL). To each well, 200 µL methanol containing 50 µg/mL BHT was then added and the sample was mixed by 3 up and down passes of the automated sample handling pipette. The samples were then centrifuged at 1750 × g for 5 minutes to pellet precipitated protein. The supernatant was recovered and transferred to a separate deep well 96-well plate for extraction. To extract lipids from the supernatant, 250 µL MtBE: methanol (3:1 v/v) was added to all wells and mixed with 3 up and down passes of the automated sample handling pipette. The sample plate was then centrifuged at 1000 × g for 3 minutes and the supernatant was filtered through a 0.25 μm polytetrafluoroethylene (PFTE) filter plate (Biotage, ISOLUTE® FILTER+, Uppsala, Sweden) The recovered extract was then dried under nitrogen gas and subsequently reconstituted to 200 μl in acetonitrile: isopropanol (1:1 v/v) methanol for LC/MS analysis.
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4

Automated High-Throughput Liver Lipid Extraction

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Lipids were extracted from livers using a high-throughput, monophasic, methyl t-butyl ether (MtBE)-based method. Using an automated pipetting and sample preparation system (Biotage Extrahera, Uppsala, Sweden), 50 µL of liver extract loaded into preconditioned wells containing 10 µL methanol and 10 µL of internal standard, Splash Lipidomix (Avanti Polar, Birmingham, AL). To each well, 200 µL methanol containing 50 µg/mL BHT was then added, and the sample was mixed by 3 up and down passes of the automated sample handling pipette. The samples were then centrifuged at 4000 rpm for 5 min to pellet precipitated protein. The supernatant was recovered and transferred to a separate deep well 96-well plate for extraction. To extract lipids from the supernatant, 250 µL MtBE:methanol (3:1 v/v) was added to all wells and mixed with 3 up and down passes of the automated sample handling pipette. The sample plate was then centrifuged at 1000 × g for 3 min and the supernatant filtered through a 0.25 mm polytetrafluoroethylene (PFTE) filter plate (Biotage, ISOLUTE® FILTER + , Uppsala, Sweden) The recovered extract was then dried under nitrogen gas and subsequently reconstituted to 200 microliters in acetonitrile:isopropanol (1:1 v/v) methanol for LC/MS analysis.
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5

Lipid Extraction from Plasma Samples

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Plasma samples were divided into four batches in such a way that there were no differences among the batches in terms of the number of samples from each study group or other variables such as age, sex, and presence of comorbidities. Each sample batch was prepared simultaneously and run sequentially in order to stabilize the quality control of the experiment with regard to the instrumental setup and pH of chromatographic buffers. The plasma sample (25 μL) was transferred into a borosilicate glass tube followed by addition of internal standards (Splash Lipidomix, Avanti Polar, Alabaster, AL) at a 1:1 ratio of internal standard (IS):plasma. The complete list of IS and their corresponding concentrations has been described previously.1 (link) Water, methanol, and chloroform at a 1:2:0.9 ratio was added to the glass tube. The mixture was vortexed and left to sit at room temperature for 30 min. Next, water and chloroform were added at a 1:0.9 ratio and the sample tube was inverted several times. The tubes were centrifuged at 3500 rpm for 30 min. The bottom organic layer containing the lipids was carefully collected, and 2 mL of chloroform was added to the aqueous phase (upper layer) to re-extract the lipids. Tubes were vortexed and centrifuged again. The subsequent bottom layer was combined with the previously collected lipids and dried down using a nitrogen stream.
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6

Plasma Lipidome Quality Control

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Pooled quality control samples were prepared by aliquoting 5 μl of each patient plasma into a single vial. This sample was spiked with 10 μl internal standard (Splash Lipidomix, Avanti Polar, Birmingham, AL) and extracted in the same manner as patient samples. This analytical grade standard contains odd-chain, deuterated lipids in lipid classes and ratios present in human plasma. Pooled QC samples were run after every 10 patient samples as well as at the beginning and end of the analytical run. Quality control samples were used to ensure the stability of the instrument during the course of analysis. The coefficient of variation for each identified lipid within the pooled QC was then calculated using a cutoff of <40%. The internal standard was used to optimize instrumental parameters, such as electrospray voltage, collision energy, and others; these parameters were held consistent over the course of analysis. Lipids in the internal standard were also used to monitor injection consistency from sample to sample.
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7

Targeted Lipid Profiling by UHPLC-MS/MS

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Lipid analysis was performed by ultra-high-performance liquid chromatography–tandem mass spectrometry (UHPLC–MS/MS) using a targeted approach using predefined MRM transitions (Sciex sMRM Pro Builder, Framingham, MA, USA) and in-house chromatographic retention time windows. Plasma and serum samples (10 μL) were placed in a 96-well plate, to which 90 μL extraction solvent (propanol-2-ol) containing stable-isotope-labelled internal standards (LipidyzerTM Internal Standards Kit from Sciex (Framingham, MA, USA), SPLASH LipidoMIXTM, Lyso PI 17:1, Lyso PG 17:1, and Lyso PS 17:1 (Avanti Polar Lipids, Alabaster, AL, USA)) was added. Samples were shaken for 10 min and stored at −20 °C for 20 min before being centrifuged at 3900× g for 15 min. Supernatant was then transferred to a 96-well plate for analysis. For quality control (QC), an independent pooled sample underwent repeat extractions and was injected onto the system at frequent intervals throughout the run. The analytical platform is described in detail in the Supplementary Materials.
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8

Plasma Lipidomics Analysis Pipeline

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Lipidomic analysis was completed using an established method previously described [49 (link)], resulting in the quantification of 856 lipid species from 10 μL of rat plasma. Sample extraction was completed using a Biomek i5 sample automation system (Beckman Coulter, Mount Waverley, VIC Australia). To each 10 μL plasma sample, 90 μL of isopropanol (Fisher Scientific, Malaga, Western Australia) containing stable isotope-labelled internal standards (LipidyzerTM Internal Standards Kit from Sciex, Framingham, MA, USA, and SPLASH LipidoMIXTM, Lyso PI 17:1, Lyso PG 17:1, and Lyso PS 17:1, Avanti Polar Lipids, Alabaster, AL, USA) was added, and then mixed for 20 min. Samples were then centrifuged (3500× g for 10 min at 4 °C). Supernatant aliquots of 70 μL were then transferred into an Eppendorf 350 μL 96-well plate for LC-MS analysis. Samples were analysed within 24 h of preparation. QC samples were prepared using a commercial pooled human plasma sample (BioIVT, New York, NY, USA) and underwent replicate extraction (n = 5) using the method described. These replicate samples were periodically analysed throughout the analytical sequence.
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9

Plasma Lipidomics Extraction Protocol

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40 μL (30 μL for founder strains, FS) of plasma and 10 μL SPLASH Lipidomix internal standard mixture (Avanti Polar Lipids, Inc.) were aliquoted into a tube. Protein was precipitated by addition of 215 μL MeOH. Control samples comprised an aliquot of mixed male and female B6 plasma (Chow diet), extracted with each batch. After the mixture was vortexed for 10 s, 750 μL methyl tert-butyl ether (MTBE) were added as extraction solvent and the mixture was vortexed for 10 s and mixed on an orbital shaker for 6 min. Phase separation was induced by adding 187.5 μL of water followed by 20 s of vortexing. All steps were performed at 4 °C on ice. Finally, the mixture was centrifuged for 4 min at 14,000 x g at 4 °C and 150 μL of the lipophilic upper layer were transferred to glass vials and dried by vacuum centrifuge for 60 min. The dried extracts were re-suspended in 100 μL MeOH/Toluene (9:1, v/v).
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10

Targeted Bile Acid Profiling of Plasma

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40 μL of DO plasma collected at sacrifice (30 μL used for founder strains) were aliquoted into a tube with 10 μL SPLASH Lipidomix internal standard mixture (Avanti Polar Lipids, Inc.). Protein was precipitated by addition of 215 μL MeOH. After the mixture was vortexed for 10 s, 750 μL methyl tert-butyl ether (MTBE) were added as extraction solvent and the mixture was vortexed for 10 s and mixed on an orbital shaker for 6 min. Phase separation was induced by adding 187.5 μL of water followed by 20 s of vortexing. All steps were performed at 4°C on ice. Finally, the mixture was centrifuged for 4 min at 14,000 x g at 4°C and stored at -80°C. For targeted bile acids analysis, samples were thawed on ice. 400 μL of ethanol were added to further precipitate protein, as well as 15 μL of isotope-labeled internal standard mix (12.5 μM d4-TαMCA, 10 μM d4-CDCA). The samples were vortexed for 20 s and centrifuged for 4 min at 14,000 g at 4°C after which the supernatant (ca. 1000 μL) was taken out and dried down. Dried supernatants were resuspended in 60 μL mobile phase (50%B), vortexed for 20 s, centrifuged for 4 min at 14,000 g and then 50 μL were transferred to vials with glass inserts for MS analysis.
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