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).

<b>蛋白质组学</b>采用2.5%十二烷基硫酸钠、5%β-巯基乙醇提取蛋白质，随后在加拿大大不列颠哥伦比亚大学维多利亚分校不列颠哥伦比亚基因组蛋白质组学中心完成溶液内酶解及液相色谱-串联质谱（liquid chromatography-tandem mass spectrometry, LC-MS/MS）分析。样品依照德国马丁斯里德Preomics GmbH公司的Preomics iST样品制备试剂盒说明书进行变性、还原、烷基化与酶解处理，并将样品重悬于上样缓冲液中，终浓度为1 µg/µL。
肽段混合物（约1 µg）采用赛默飞世尔科技EASY-nLC 1000系统进行在线反相色谱分离，该系统配备反相预柱与自制反相纳米分析柱，并与搭载Nanospray Flex NG离子源的Orbitrap Fusion Tribrid质谱仪（美国加利福尼亚州圣何塞赛默飞世尔科技公司）在线联用。所用流动相为：流动相A：2%乙腈、0.1%甲酸；流动相B：90%乙腈、0.1%甲酸。样品采用140分钟梯度洗脱程序进行分离，并通过Orbitrap Fusion质谱仪以离子阱（iontrap, IT-MS/MS）结合高能碰撞解离（high-energy collisional dissociation, HCD）碎裂的指定参数开展分析。原始数据文件通过赛默飞世尔科技XCalibur 4.2.28.14软件生成，并采用赛默飞世尔科技Proteome Discoverer 2.2.0.388软件套件完成数据分析。