Data underlying the publication: Preserving Full Spectrum Information in Imaging Mass Spectrometry Data Reduction

<strong>FT-ICR</strong>Human kidney tissue was surgically removed during a fullnephrectomy, and remnant tissue was processed for researchpurposes by the Cooperative Human Tissue Network (CHTN)at Vanderbilt University Medical Center. Human biospecimenswere collected in compliance with the CHTN protocols,institutional IRB policies, and the National Cancer Institute’sbest practices for procurement of remnant surgical researchmaterial. The tissue was flash-frozen over an isopentane-dryice slurry and embedded in carboxymethylcellulose. Tissuesections were cryosectioned with a thickness of 10 μm andthaw-mounted onto indium tin-oxide-coated glass slides (DeltaTechnologies, Loveland, CO, USA). 1,5-Diaminonaphthalene(DAN) was applied to the tissue surface using a TM Sprayer M3(HTX Technologies, Chapel Hill, NC, USA). The sample wasimaged (50 μm pitch) directly after matrix application witha 15T MALDI Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer (Solarix, Bruker Daltonics, Billerica,MD, USA). Briefly, data were generated from m/z 300-2000with a 4M file size in negative ion mode.<br><strong>qTOF</strong>C57BL6/J mice were retro-orbitally infected with <em>S. aureus</em> Newman and sacrificed humanely five days post-infection. Kidneys were flash frozen on an isopentane/dry ice slurry and embedded in 2.6\% carboxymethylcellulose. 5 μm thick sections were collected using a Leica Biosystems CM3050S cryostat and thaw-mounted onto indium tin oxide coated glass slides. Sections were washed with cold 150 mM ammonium formate for 45 seconds for three total washes. 5 mg of 4-(dimethylamino)cinnamic acid matrix was applied using an in-house sublimation device. MALDI IMS data were collected in negative ion mode from m/z 400-2000 using a Bruker MALDI timsTOF fleX platform with a 5 μm step size, 25% laser power, and 25 shots per pixel.

<strong>傅里叶变换离子回旋共振（FT-ICR）</strong>：本数据集的FT-ICR子部分样本来源于根治性肾切除术术中切除的人体肾脏组织，剩余组织由范德堡大学医学中心的合作人体组织网络（Cooperative Human Tissue Network, CHTN）开展研究用途的前处理。人体生物样本的采集严格遵循合作人体组织网络（CHTN）采集方案、机构伦理审查委员会（Institutional Review Board, IRB）政策以及美国国家癌症研究所（National Cancer Institute, NCI）关于剩余手术研究材料获取的最佳实践规范。组织样本经异戊烷-干冰浴快速冷冻后，包埋于羧甲基纤维素（Carboxymethylcellulose, CMC）中。将组织以10 μm厚度进行冰冻切片，解冻裱贴于氧化铟锡（Indium Tin Oxide, ITO）涂层载玻片上（Delta Technologies，美国科罗拉多州拉夫兰市）。使用TM Sprayer M3喷雾仪（HTX Technologies，美国北卡罗来纳州教堂山市）将1,5-二氨基萘（1,5-Diaminonaphthalene, DAN）基质喷涂于组织表面。基质喷涂完成后，即刻采用15T基质辅助激光解吸电离（Matrix-Assisted Laser Desorption/Ionization, MALDI）傅里叶变换离子回旋共振（FT-ICR）质谱仪（Solarix，布鲁克道尔顿公司，美国马萨诸塞州比勒里卡市）以50 μm的像素间距进行成像。简要而言，数据采集范围为m/z 300~2000，采用负离子模式，单文件大小为4M。<br><strong>四极杆-飞行时间（qTOF）</strong>：本数据集的qTOF子部分样本来源于C57BL6/J品系小鼠，通过眶后静脉注射感染金黄色葡萄球菌（*S. aureus*）Newman菌株，于感染后5天实施人道处死。小鼠肾脏经异戊烷/干冰浴快速冷冻后，包埋于2.6%羧甲基纤维素（CMC）中。使用Leica Biosystems CM3050S冰冻切片机制备5 μm厚度的组织切片，并解冻裱贴于氧化铟锡（ITO）涂层载玻片上。将切片置于预冷的150 mM甲酸铵溶液中洗涤，每次45秒，共洗涤3次。使用自研升华装置喷涂4-二甲氨基肉桂酸基质，用量为5 mg。采用布鲁克MALDI timsTOF fleX平台，以5 μm的步长、25%的激光功率、每个像素采集25次激光脉冲，在负离子模式下采集m/z 400~2000范围的MALDI成像质谱（Imaging Mass Spectrometry, IMS）数据。