Agilent 6560 im qtof ms platform

The IMS/MS studies were executed with two different drift tube IMS (DTIMS)/MS platforms. The first was an in-house home-built DTIMS/MS instrument that coupled a 1 m IMS drift tube with an Agilent 6224 TOF MS upgraded to a 1.5 m flight tube (providing MS resolution of ~25 000),^{23 (link)} and the second was the Agilent 6560 IM-QTOF MS platform (Agilent Technologies).^{24 (link)–26 (link)} The Agilent 6560 was outfitted with the commercial gas kit (Alternate Gas Kit, Agilent) and a precision flow controller (640B, MKS Instruments) to allow for real-time pressure adjustment based on absolute readings of the drift tube pressure using a capacitance manometer (CDG 500, Agilent). For the DTIMS measurements on both instruments, ions were passed through an inlet capillary, focused by a high-pressure ion funnel, and accumulated in an ion funnel trap. Ions were then pulsed into the drift tubes filled with ~3.95 Torr of nitrogen gas, where they traveled under the influence of a weak electric field (10 to 20 V/cm). Ions exiting the drift tube were refocused by a rear ion funnel prior to TOF or QTOF MS detection, and their arrival times were recorded.

The cortical lipid extracts were evaluated using an Agilent 1290 UPLC coupled to an Agilent 6560 IM-QTOF platform (Santa Clara, CA) with a commercial gas kit and MKS Instruments precision flow controller (Andover, MA). Lipids were first separated by reversed-phase LC by injecting 10 μL onto a Waters (Milford, MA) CSH column (3.0 mm x 150 mm x 1.7 μm particle size). The 34-minute gradient having a flow rate of 250 μL/min and mobile phase A of 10 mM ammonium acetate in 40:60 LC-MS grade acetonitrile/water and mobile phase B of 10 mM ammonium acetate in 90:10 LC-MS grade isopropanol/acetonitrile is detailed in (Table S3). Both positive and negative mode ESI analyses were performed on all samples. Following electrospray ionization (ESI), the ions were analyzed using the Agilent 6560 IM-QTOF MS platform (65 (link), 66 (link)). Collision cross section were collected for all features detected and collision induced dissociation (CID) was performed with high purity nitrogen by ramping collision energies based on the ion arrival times analogous to previous IMS experiments (43 (link), 67 (link), 68 (link)). Alternating scans of no fragmentation and all-ions data independent acquisition (DIA) were used to collect precursor and fragmentation information at 1 sec/spectra for a mass range of 50-1700 m/z. All lipidomic raw data for this analysis is deposited and available in MassIVE (X).