TITLE: UC Davis - Metabolomics: Lipidomics analysis
AUTHORS: Oliver Fiehn

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">Lipidomic analysis by UPLC-QTOF mass spectrometry</div></div>

[STEPS]
?. Pre-run procedures1.1 Instrument tuning (Instrument in Tune mode) a. Use “Standard Tune” before each run of 300 sample batch.  b. Use the “Tuning Solution” (see preparation of solutions below) for the instrument tuning. c. The mixture for the instrument tuning must be prepared fresh at the beginning of each 300 sample batch.d. Print the tune report from the standard tune.  - In ESI(+), check the profile of the calibrant and the intensity of ions m/z 322.0481; m/z 622.0290; and m/z 922.0098, which must be higher than 400k, 200k, and 200k, respectively.- In ESI(–), check the profile of the calibrant and the intensity of ions m/z 301.9981; m/z 601.9790; and m/z 1033.9881, which must higher then 800k, 800k, and 1100k, respectively.e. If the intensity of even one of the selected ion is below this value clean the ion source and repeat the instrument tuning.1.2 Check Reference ions (Instrument in Acquisition mode) a. Use the “Reference Ion Mass Solution” (see preparation of solutions below) for mass correction during the analyses (lock mass). b. The mixture for the reference ion solution must be prepared fresh at the beginning of each 300 sample batch.  c. The reference mass solution is pumped at a flow rate of 0.150 mL/min and split 1:10 prior entering the mass spectrometer. d. Check the following reference ions:- In ESI(+), check the intensity of ions m/z 121.0509 and m/z 922.0098, which should be between 40–60k and 8–12k, respectively.  Adjust recipe and flow rates to attain this intensity.- In ESI(–), check the intensity of ions m/z 112.9856 and m/z 966.0007, which should be between 10–20k and 10–20k, respectively.  Adjust recipe and flow rates to attain this intensity.
?. New column installationa. Purge the pumping system of any buffer-containing mobile phases and connect the inlet end of the column to the injector outlet. b. Flush column with 100% acetonitrile by setting the pump flow rate to 0.1 mL/min and increase the flow rate to 0.6 mL/min over 5 min. c. When the mobile phase is flowing freely from the column outlet, stop the flow and attach the column outlet to the ion source of the mass spectrometer. d. Gradually increase the flow rate with 100% acetonitrile by setting the pump flow rate to 0.1 mL/min and increase the flow rate to 0.6 mL/min over 5 min. e. Monitor the backpressure until a steady values is achieved.f. Stop the flow and flush column with mobile phase (A) and (B) (see preparation of solutions below) at a ratio of 50:50 by setting the pump flow rate to 0.1 mL/min and increase the flow rate to 0.6 mL/min over 5 min. g. Monitor the backpressure until a steady values is achieved.  For a new column a value of backpressure should be 500–550 bar at the beginning of the injection (elution at 40% of the mobile phase (B), see preparation of solutions below). h. Inject 5 blank (methanol).  Record the lowest and highest value of backpressure for the first and the last sample injected. f. Inject 10 citrate plasma samples.  Record the lowest and highest value of backpressure for the first and the last sample injected. NOTE: Use a new column after 300 sample injections.  The UPLC column must be coupled to a VanGuard pre-column.  The VanGuard pre-column is replaced after 150 sample injections.  The number of injections (both solvents and plasma samples) is recorded by an operator in Excel file stored at ::\\\TEDDY_Injections.XLS.
?. Preparation of solutionsa. Preparation of Tuning Solution • 88.5 mL acetonitrile • 1.5 mL H²O • 10 mL Agilent Low Concentration ESI Tuning Mix • 5 µL 322 Reference Ion (sonicate before use) • Degas by sonication for 5 min • 100 mL will typically last monthsb. Preparation of Reference Mass Solution • 95 mL acetonitrile • 5 mL H²O • 100 µL 5 mM 921 Reference Ion (sonicate before use) • 125 µL 5 mM TFA Reference Ion (sonicate before use) •125 µL 10 mM Purine Reference Ion (sonicate before use) • Degas by sonication for 5 minc. Mobile phase A (60:40 ACN:water + 10 mM Ammonium Formate + 0.1% Formic Acid) (1). Pre-rinse three times 1 L glass bottle with pure acetonitrile (2). Measure exactly 600 mL of acetonitrile in a pre-rinsed graduated cylinder and add them to the 1 L glass bottle. (3). Measure exactly 400 mL of MilliQ water in a pre-rinsed graduated cylinder and add them to the 1 L glass bottle. (4). Add 1 mL formic acid (5). Weight 0.630 g of ammonium formate and add them to the glass bottle (6). Sonicate for 10 min at room temperature until all the ammonium formate is dissolved. (7). 1 L will last for around 200 samplesd. Mobile phase B (90:10 IPA:ACN + 10 mM Ammonium Formate + 0.1% Formic Acid) (1). Measure exactly 100 mL of acetonitrile in a pre-rinsed graduated cylinder and add them to the 1 L glass bottle. (2). Add 1 mL formic acid (3). Weight 0.630 g of ammonium formate and add them to the glass bottle (4). Sonicate for 40 min at 70ºC until all the ammonium formate is dissolved. (5). 1 L will last for around 200 samples
?. Pre-run sequencea. Before starting the run inject the following: (1). 1× “No sample injection” (2). 5× Blank sample injection (methanol) (3). 2× QC-mix injection(4). 2× Citrate plasma injectionb. For the QC-mix, monitor the retention time, intensity, S/N, mass accuracy, and peak width (FWHM) of particular analytes (Table 1).  Use the MassHunter Qualitative Analysis software for data processing. The acceptable ranges of the parameters are stored at : :\\\TEDDY_QC-mix_default.XLS. c. If those criteria are not met, the following actions should be considered: (i) Replace the VanGuard pre-column and/or the UPLC column (if retention time shift >2.5% and/or peak width expressed as FWHM increased >20%); (ii) Clean the ion source (if intensity of particular analytes (iii) Re-tune the mass spectrometer (mass accuracy of particular analytes >10 ppm).Table 1  Analytes of the QC-mix solutionNOTE:  Compare the profile of citrate plasma from a previously acquired sequence to that of a pre-run sequence.  The variation within the TIC intensity must be NOTE:  The backpressure should be within the range 500–580 bar at the beginning of each run [elution at 40% of the mobile phase (B)] and should not exceed the range 850–1000 bar [elution at 99% of the mobile phase (B)]. NOTE:  If the initial backpressure is in the range of 580–725 bar replace the VanGuard pre-column.  If the initial backpressure is still high even after the replacement of the VanGuard pre-column, use the new UPLC column.
?. Lipid analysis methoda. There are four different methods for lipid analysis, under the folder ::\\\:- Positive ion mode: TEDDY_CSHC18_100mm_POS_MS_mode  - Negative ion mode: TEDDY_CSHC18_100mm_NEG_MS_mode  - Positive ion MSMS mode: TEDDY_CSHC18_100mm_POS_MSMS _mode  - Negative ion MSMS mode: TEDDY_CSHC18_100mm_NEG_MSMS_modeb. The autosampler, separation and column parameters for the lipid analysis method are as shown below: - Autosampler- Binary pump- Column manager No timetable gradientThe MS conditions are the following: 5.1 Positive ion mode - General parameters- Source parameters- Acquisition parameters:- Ref Mass parameters- Chromatogram parameters:5.2 Negative ion mode The parameters that vary from the positive mode are the following: - General parameters- Reference Mass parameters
?. Column storageUse this procedure to avoid precipitation mobile-phase buffers on the column and in the system. a. Flush column with 50% acetonitrile by setting the pump flow rate to 0.1 mL/min and increase the flow rate to 0.6 mL/min over 5 min; keep the column at this flow rate for 10 min. b. Flush column with 100% acetonitrile by setting the pump flow rate to 0.1 mL/min and increase the flow rate to 0.6 mL/min over 5 min; keep he column at this flow rate for 10 min. c. Remove the column from the system. d. Store the column in the box until the next batch analysis. Add the story usage of the column.