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.

**傅里叶变换离子回旋共振（FT-ICR）**
本数据集FT-ICR模块的样本来源于根治性肾切除术切除的人体肾脏组织，剩余组织由范德堡大学医学中心合作人体组织网络（Cooperative Human Tissue Network, CHTN）开展科研处理。人类生物样本的采集严格遵循CHTN操作规范、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）的外科剩余科研样本采购最佳实践流程。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）中。随后将组织切成10 μm厚的冰冻切片，并解冻贴片至氧化铟锡（indium tin oxide, ITO）包被玻片（购自美国科罗拉多州拉夫兰市Delta Technologies公司）。使用TM Sprayer M3喷雾器（购自美国北卡罗来纳州教堂山市HTX Technologies公司）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，即刻使用15T基质辅助激光解吸电离傅里叶变换离子回旋共振（MALDI FT-ICR）质谱仪（Solarix，布鲁克道尔顿公司，美国马萨诸塞州贝德福德市）对样本进行成像（步距50 μm）。简要而言，实验采用负离子模式采集质荷比范围300~2000的质谱数据，单文件大小为4M。

**四极杆飞行时间（qTOF）**
本数据集qTOF模块的样本来源于C57BL/6J小鼠：经眶后感染金黄色葡萄球菌（Staphylococcus aureus, S. aureus）Newman菌株，于感染后5天人道处死小鼠。摘取肾脏后经异戊烷/干冰浴快速冷冻，并包埋于2.6%羧甲基纤维素中。使用徕卡生物系统CM3050S冰冻切片机切成5 μm厚的切片，解冻贴片至氧化铟锡包被玻片。随后将切片置于预冷的150 mM甲酸铵（ammonium formate）溶液中洗涤，每次45秒，共洗涤3次。使用自制升华装置喷涂5 mg的4-二甲氨基肉桂酸（4-(dimethylamino)cinnamic acid）基质。采用布鲁克MALDI timsTOF fleX平台，以负离子模式采集质谱成像数据，质荷比范围为400~2000，步幅5 μm，激光功率25%，每像素轰击25次。

搜集汇总

背景与挑战

背景概述

该数据集是为科学论文'Preserving Full Spectrum Information in Imaging Mass Spectrometry Data Reduction'提供支持的原始数据，主要包含来自FT-ICR和qTOF质谱仪的成像质谱数据，涉及人类肾脏组织和小鼠感染模型，专注于生物化学和细胞生物学领域。数据格式为专业文件类型，如.d和.tsf，旨在促进成像质谱数据降维方法的研究，同时强调全谱信息的保留，使用CC BY-NC-ND 4.0许可进行共享。