Raw lipidomics data files for Multi-Omics Analysis Reveals Diapause-Associated Lipid Remodeling in the Fat Body of Colorado Potato Beetle

Raw lipidomics data files for Multi-Omics Analysis Reveals Diapause-Associated Lipid Remodeling in the Fat Body of Colorado Potato Beetle. The lipidomics service was provided by the Mass Spectrometry Core Facility (University of Wisconsin–Madison). Lipidomic analysis was performed using an integrated LC-MS system comprising an Agilent InfinityLab Poroshell 120 EC-C18 1.9 µm (2.1 x 50 mm) column maintained at 50°C. This system was connected to an Agilent HiP 1290 Multisampler, Agilent 1290 Infinity II binary pump, and column compartment, which in turn were linked to an Agilent 6546 Accurate Mass Q-TOF dual ESI mass spectrometer. Chromatographic separation was achieved using a mobile phase of ACN (60:40 v/v) containing 10 mM ammonium formate and 0.1% formic acid (Phase A) and IPA:ACN (90:9:1 v/v) with the same additives (Phase B). The gradient commenced at 15% Phase B, increasing to 99% over 13.8 minutes before returning to initial conditions, with a consistent flow rate of 0.5 mL/min. Injection volumes were 1 µL for the positive ion mode and 5 µL for the negative ion mode. Mass spectrometric detection employed both positive and negative ionization settings, adjusting parameters such as source gas temperature, flow, and various voltages to optimize the detection of lipid species. Reference masses were introduced for calibration and quality control.Data from the LC-MS runs were captured using the Agilent Mass Hunter Workstation for data acquisition. Quality control (QC) samples and process blanks were injected systematically to validate the consistency of the data. Post-acquisition data analysis was conducted using Profinder software for retention time alignment and peak area extraction against a lipid library created with Lipid Annotator. This library included detailed lipid identities with mass-to-charge (m/z) ratios and retention times. The results, including integration discrepancies and annotations for multiple occurrences of identical m/z values representing structural isomers, were compiled into .csv files for both ionization modes. Negative ionization results were used for downstream data analysis. MetaboAnalyst v6.0 was used to perform one-way ANOVA followed by Fisher's LSD tests after default filtering of the lipidomics data. False Discovery Rate (FDR) correction was applied to the results to control for multiple comparisons. R v4.3 was used to Z-normalize the normalized peak intensity values.