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

<b>Proteomics</b>Proteins were extracted using 2.5% sodium dodecyl sulfate, 5% β-mercaptoethanol, and subjected to in-solution digest liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis at the University of Victoria Genome British Columbia Proteomics Centre, Canada. Samples were denatured, reduced, alkylated, and digested using a Preomics iST Sample Preparation kit (Preomics GmbH, Martinsried, Germany) according to the manufacturer's protocol. Samples were re-suspended in Load buffer at a concentration of 1 µg/µL.<br>Peptide mixtures (~1 µg) were separated by on-line reverse phase chromatography using a Thermo Scientific EASY-nLC 1000 system with a reversed-phase pre-column and an in-house prepared reverse phase nano-analytical column, coupled on-line with an Orbitrap Fusion Tribrid mass spectrometer (Thermo Fisher Scientific, San Jose, CA) equipped with a Nanospray Flex NG source. Solvents used were 2% acetonitrile, 0.1% formic acid (Solvent A), and 90% acetonitrile, 0.1% formic acid (Solvent B). Samples were separated by a 140-minute gradient and analyzed using the Orbitrap Fusion instrument with specified parameters for iontrap (IT-MS/MS) with HCD fragmentation. Raw data files were generated using XCalibur 4.2.28.14 (Thermo Scientific) software and analyzed with Proteome Discoverer 2.2.0.388 software suite (Thermo Scientific).