This work was supported by the Walther Cancer Foundation under the Advancing Basic Cancer Research program to the Harper Cancer Research Institute of the University of Notre Dame (DARW) and the 2011 Starter Grant from the Society for Analytical Chemists of Pittsburgh (ABH). Thanks also to the staff of the Mass Spectrometry and Proteomics Facility for useful discussions.

1. 3D细胞培养和准备成像<ol><li>培养一合适的细胞系， 即，HCT116结肠癌细胞系，在二维，单层培养。 </li><li>成长的HCT 116细胞中的T-25烧瓶中的McCoy的5A介质，在5％的CO 2培养箱直至50-70％汇合，通常需要几天的时间+ 10％胎牛血清。 </li><li>释放的细胞用0.25％胰蛋白酶-EDTA溶液，并计数使用血球细胞的一部分和台盼蓝染色以检查细胞密度和生存力。 </li><li>计数后，稀释细胞用完全培养基以达到6000细胞的一个合适的接种密度/孔，或30000个细胞/ ml。 </li></ol> 2.准备琼脂糖涂层的96孔板<ol><li>添加0.19克琼脂糖至10ml标准培养基的50ml锥形管中（在介质的1.5％琼脂糖溶液）10。确保纳入轻轻搅拌。高压灭菌琼脂糖在水浴20分钟。 </li><li>使用多道移液器，吸50微升琼脂糖+媒体混合到平底96孔板培养板的60家中央水井。作为孔在板的外周边缘具有稍高的蒸发率，添加200μl的1×磷酸盐缓冲盐水（PBS）代替琼脂糖这些边缘。 </li><li>一旦琼脂糖混合物已被添加到所述内孔中，除了设置在板冷却到37〜 °C中的加入细胞前。 </li></ol> 3.种子，往往在三维培养注：更多或更少的细胞可以取决于所涉及的文化的要求进行接种，但已经确定，这些条件后10-14天培养物导致在大约1毫米直径的三维细胞培养物的结构（数据未显示） 。 <ol><li>加入200μl适当的细胞溶液（稀释含有〜6000细胞）的琼脂糖涂层96孔板中。覆盖板并在潮湿的培养箱，用5％的CO 2设定在37℃下细胞生长。 </li><li>改变细胞的媒体至少每48小时，或者出现媒体时，会改变颜色。 <ol><li>通过仔细吸出旧媒体从周围的小三维细胞培养物（可见的肉眼由第2天），在琼脂糖的底部改变介质。加入200微升新鲜培养基轻轻在三维细胞培养物。 </li><li> （可选步骤），在这些媒体的变化，增加化疗药物或其他药物进行测试。稀的首选药物，以提供完整的媒体的终浓度并添加必要的200μl到每个孔中。 </li><li>监控三维细胞培养物的生长通过光学显微镜，直到三维细胞培养物大约1毫米的直径。 </li></ol></li></ol> 4.收获的3D细胞培养<ol><li>用2毫升血清吸管从琼脂糖床上轻轻地取下3D细胞培养。 </li> &lt;LI&gt;轻轻吹打成约1毫升PBS在等待24孔板洗净3D细胞培养与PBS。 </li><li>传输通过血清​​吸管收获3D细胞培养的离心管中的蛋白质或代谢物的提取，或将它们嵌入在切割中，以协助对切片成像应用。 </li></ol>在明胶5.嵌入的3D细胞培养<ol><li>准备〜175毫克/毫升明胶的高纯度水（18MΩ首选），22,23混合明胶大力。观察溶液变得粘稠，难以操作。将含有明胶的锥形管在水浴中在约60℃，温暖，直到溶液变得清晰和容易抽吸。 注：温暖明胶溶液变硬迅速，因为它的冷却，所以冷冻前快速地执行所有以下步骤。 </li><li>之后将其加热，立即采取明胶到细胞培养罩。保持管明胶在BEAKER用预热的水在约60 °C至避免明胶溶液硬化。 </li><li>使用2ml的血清吸液管，沉积0.6毫升暖明胶溶液成24平底板的孔中。此体积是足以覆盖一薄层的底部。轻轻沉积立即上使用不同的2毫升吸管，以避免破裂的三维结构中的明胶层的顶部的三维细胞培养物。 注意：必须注意在此阶段不放置的PBS放入明胶。如果发生这种情况，但是，使用的是200微升吸管从明胶的顶部取出PBS中。 </li><li>后的三维细胞培养物放置在明胶层的表面上，小心地吸取另一个0.6暖明胶混合物在三维细胞培养物的毫升，以便不扰乱培养物的位置。之后的第二层放置，冻结明胶包埋三维细胞培养物在-80℃下。 </li></ol> 6切片和解冻日山Ë明胶嵌入式3D细胞培养质谱成像<ol><li>除去24孔板含有从冷冻的三维细胞培养物。暖板与热的底部，从你的手，直到镊子或者手术刀会轻轻滑下井的一侧。 </li><li>顺畅滑动钳或手术刀，释放明胶没有解冻的中心。取一滴的水，低温恒温器的支持，并以此来坚持明胶盘的支持。 <ol><li>嵌入在明胶三维细胞培养物是最适合于切片在-30℃。清洁低温恒温器叶片和玻璃在使用前用70％的乙醇。使用刀片或每个三维细胞培养物，明胶盘，以防止变钝的刀片的一个新的刀片的不同部分。 </li></ol></li><li>使用低温恒温器，轻轻面临关闭多余的明胶，直到3D细胞培养变得可见。 </li><li>此时慢慢切片3D细胞培养在12-16微米的部分一个平稳的运动。 注：关键因素切片包括玻璃到叶片的距离，刀片角度，低温恒温器的温度，并在盘上的支撑件的角度，因此，所有的这些都必须进行检查，以确保结果的一致性。 </li><li>小心解冻片和它们安装于氧化铟钛（ITO）涂覆的玻璃载片适当标记，并将其存储在干燥器中。使用切片尽快为最高质量。 </li></ol>对于MALDI成像7.矩阵的应用和样品制备<ol><li>此前MALDI成像，准备切片用适当的矩阵。 <ol><li>对于小分子分析，一般不需要洗涤步骤。为完整蛋白质的检测，用冷100％丙酮的切片，卡诺液，或70％/ 95％的异丙醇，以除去小分子，例如脂类，可能掩盖信号24 - 26 </li><li>轻轻洗脸不超过30秒的时间。别惊动任何片。 </li></ol></li><li>制备基质中有机溶剂和水的溶液，用0.1％的TFA。对于小分子诸如α氰基-4-羟基肉桂酸（CHCA），使用60％的ACN：40％的H 2 O：0.1％TFA（10毫克/毫升）。用于蛋白质检测，例如芥子酸（30毫克/毫升），使用相同的溶剂溶液。用于芥子酸的最佳溶解性，在乙腈首先溶解加入TFA中之前:H 2 O溶液。其它基质可以适当地使用。 注：基质可以与几种不同的方法被应用，但应当注意的一些矩阵已经发现共crystalize与明胶，如阿魏酸，使该样品不能使用。较小的晶体产生更一致的质谱，允许更多的分子种类进行检测，并归因于生理差异，而不是基体效应。 </li><li>通过handspotting方法应用矩阵。 <ol><li>用细尖的注射器适用0.5微升的MATR的三维细胞培养物切片上IX溶液，并允许矩阵crystalize。 </li></ol></li><li>或者，使用喷枪方法。填补了商业级喷枪与基体的解决方案。 <ol><li>持喷雾器8-12英寸远离幻灯片，瞄准精细喷雾在片。在道次之间，允许基质干燥1分钟，以允许最佳晶体形成。可达10-20通行证的喷枪的要求产生矩阵22的一个最佳的层。 </li></ol></li><li>或者，使用升华法在其他地方详细说明。25,27 </li><li>干片在干燥器中至少30分钟前MALDI-MSI，不管矩阵应用的方法的。25 </li></ol> 8. MALDI-MSI使用MALDI-TOF系统分析（ 即 AUTOFLEX III） 注：本部分包含的说明和建议的设置参数的MALDI-TOF成像实验。取决于插件trument制造商，所使用的软件，该方法可能会发生变化。 <ol><li>适合于制成以牢固地保持75毫米×25毫米幻灯片将图像附加到ITO涂覆的载玻片的三维细胞培养物的切片的适配器的幻灯片。加载幻灯片适配器插入仪器。 </li><li>选择的质量范围问题的适当校准标准准备仪器MALDI-MSI。对于小分子的询问，对应于所使用的基质，α-CHCA检测到的信号，是校准物的一个共同的基团。对于蛋白质分析，已知蛋白质标准（ 即，泛素，胰蛋白酶）的质量范围的兴趣被选择和斑点邻近于三维细胞培养物作为校准物。在进行方法开发之前校准仪器。 </li><li>在成像之前，开发的数据采集方法的选择，用由仪器制造商提供的软件的质量范围。参见图1和2为小分子和蛋白质成像。为小分子成像，使用反射模式的最高质量分辨率。 <ol><li>调整质量范围为小分子的数据采集与100-1,000 米/ z和对之间8,000-25000米/ Z蛋白质。调整质量范围以涵盖所选择的区域，同时提供与仪器的最高质量分辨率成为可能。 </li><li>调整激光功率，频率，激光射击和光斑尺寸使用校准溶液和附近的“牺牲”三维细胞培养物切片的数量。观察主要仪器控制软件这些设置。使用以下设置为推荐的出发点：60％的功率，400激光枪，超小尺寸光斑。这些设置将整个仪器和方法各不相同，因此优化仪器参数，从而为每个特定仪器的最高质量的光谱。可以调整其它参数包括检测器的增益，采样率，和电子增益。 SAVE这种方法在成像软件的使用（ 即 ，自动执行方法FlexImaging将借鉴）。 注意：下面的质量范围的兴趣抑制离子（在仪器控制再次发现），以便不干扰检测。 </li><li>开发蛋白质数据采集方法选择的质量范围。按照上面概述的相同的步骤，但对于中到高的质量范围，高于约3 kDa的，采用线性模式。 注：设置将不同于那些用于小分子的方法。 </li></ol></li><li>使用由仪器制造商，如FlexImaging对于布鲁克MALDI-TOF系统所提供的成像软件设置特定MS仪器参数。 <ol><li>创建一个新的影像文件和文件夹，使用前制定并保存方法。选择仪器参数，如光栅光斑尺寸（从默认的变化约200微米至50微米），设置仪器控制方法（设置步骤8.3.2或8.3.3），和POSI灰其中扫描整个三维细胞培养物。 </li><li>在样本选择三个合适的教点，激光移动到每个反过来。获得使用“打印屏幕”的MALDI-TOF激光控制软件的光学照片。 注：许多成像软件程序所需要的样本为&#39;教&#39;，可以用扫描仪或常仪器相机来获得软件的激光的位置，的光学照片。 </li></ol></li><li>然后开始从成像软件（未仪器控制）在成像过程并从每个切片获得质谱。观察最群众横跨三维细胞培养物和其他本地化到特定的区域。 </li></ol> 9.可选数据分析方法<ol><li>进行有针对性的分析，通过单击平均频谱群众进行光谱的人工分析，或允许成像软件自动选择以上特定阈值群众（ 如 ，AB峰奥雅纳前20％的阈值）。对于质量控制，检验的基质峰分布或平均频谱。 </li><li>执行统计分析，在数学软件提取的数据集，例如R或Matlab。 <ol><li>以ASCII格式，可读的文本文件，加载到所选择的软件出口单光谱。 </li><li>各个光谱转换为ASCII的mzML格式，mzXML，对于由几个不同的软件程序读取，28 - 31或数据导出为分析（.IMG）格式的文件中，用于其它成像应用例如MRI共同格式32分析两个开源选项MSiReader和BioMap 32,33。 </li><li>一旦文件被导出到一个可读的格式，通过软件，通过在各自的软件指令加载数据集。装载之后，执行采集后处理，诸如基线去除和正常化。 </li><li>有了这个数据集，执行为staticstical治疗，如使用任何自定义脚本或内置算法软件如Matlab 18聚类的主成分分析。 </li></ol></li></ol>

<ol>
	<li>Schober, Y., Guenther, S., Spengler, B., R&#246;mpp, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single+cell+matrix-assisted+laser+desorption/ionization+mass+spectrometry+imaging.">Single cell matrix-assisted laser desorption/ionization mass spectrometry imaging.</a> Anal Chem. 84 (15), 6293-6297 (2012).</li><li>Cornett, D., Frappier, S., Caprioli, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MALDI-FTICR+imaging+mass+spectrometry+of+drugs+and+metabolites+in+tissue.">MALDI-FTICR imaging mass spectrometry of drugs and metabolites in tissue.</a> Anal Chem. 80 (14), 5648-5653 (2008).</li><li>Reyzer, M. L., Hsieh, Y., Ng, K., Korfmacher, W. a., Caprioli, R. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Direct+analysis+of+drug+candidates+in+tissue+by+matrix-assisted+laser+desorption/ionization+mass+spectrometry.">Direct analysis of drug candidates in tissue by matrix-assisted laser desorption/ionization mass spectrometry.</a> J Mass Spectrom. 38 (10), 1081-1092 (2003).</li><li>Reyzer, M. L., Chaurand, P., Angel, P. M., Caprioli, R. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Direct+molecular+analysis+of+whole-body+animal+tissue+sections+by+MALDI+imaging+mass+spectrometry.">Direct molecular analysis of whole-body animal tissue sections by MALDI imaging mass spectrometry.</a> Methods Mol Biol. 656 (18), 285-301 (2010).</li><li>Cornett, D., Reyzer, M., Chaurand, P., Caprioli, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MALDI+imaging+mass+spectrometry:+molecular+snapshots+of+biochemical+systems.">MALDI imaging mass spectrometry: molecular snapshots of biochemical systems.</a> Nat Methods. 4 (10), 828-833 (2007).</li><li>Guenther, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Histology+by+mass+spectrometry:+label-free+tissue+characterization+obtained+from+high-accuracy+bioanalytical+imaging.">Histology by mass spectrometry: label-free tissue characterization obtained from high-accuracy bioanalytical imaging.</a> Angew Chem Int Ed Engl. 49 (22), 3834-3838 (2010).</li><li>Schwamborn, K., Caprioli, R. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+imaging+by+mass+spectrometry--looking+beyond+classical+histology.">Molecular imaging by mass spectrometry--looking beyond classical histology.</a> Nat Rev Cancer. 10 (9), 639-646 (2010).</li><li>Kunz-Schughart, L. a., Kreutz, M., Knuechel, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multicellular+spheroids:+a+three-dimensional+in+vitro+culture+system+to+study+tumour+biology.">Multicellular spheroids: a three-dimensional in vitro culture system to study tumour biology.</a> Int J Exp Pathol. 79 (1), 1-23 (1998).</li><li>Hirschhaeuser, F., Menne, H., Dittfeld, C., West, J., Mueller-Klieser, W., Kunz-Schughart, L. a. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multicellular+tumor+spheroids:+an+underestimated+tool+is+catching+up+again.">Multicellular tumor spheroids: an underestimated tool is catching up again.</a> J Biotechnol. 148 (1), 3-15 (2010).</li><li>Friedrich, J., Seidel, C., Ebner, R., Kunz-Schughart, L. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spheroid-based+drug+screen:+considerations+and+practical+approach.">Spheroid-based drug screen: considerations and practical approach.</a> Nat Protoc. 4 (3), 309-324 (2009).</li><li>Lee, G. Y., Kenny, P. A., Lee, E. H., Bissell, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Three-dimensional+culture+models+of+normal+and+malignant+breast+epithelial+cells.">Three-dimensional culture models of normal and malignant breast epithelial cells.</a> Nat Methods. 4 (4), 359-365 (2007).</li><li>Yamada, K. M., Cukierman, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modeling+tissue+morphogenesis+and+cancer+in+3D.">Modeling tissue morphogenesis and cancer in 3D.</a> Cell. 130 (4), 601-610 (2007).</li><li>Fernandes, T. G., Kwon, S. -. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Three-dimensional+cell+culture+microarray+for+high-throughput+studies+of+stem+cell+fate.">Three-dimensional cell culture microarray for high-throughput studies of stem cell fate.</a> Biotechnol Bioeng. 106 (1), 106-118 (2010).</li><li>Meli, L., Jordan, E. T., Clark, D. S., Linhardt, R. J., Dordick, J. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Influence+of+a+three-dimensional,+microarray+environment+on+human+cell+culture+in+drug+screening+systems.">Influence of a three-dimensional, microarray environment on human cell culture in drug screening systems.</a> Biomaterials. 33 (35), 9087-9096 (2012).</li><li>Weaver, E. M., Hummon, A. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Imaging+mass+spectrometry:+From+tissue+sections+to+cell+cultures.">Imaging mass spectrometry: From tissue sections to cell cultures.</a> Adv Drug Deliv Rev. 65 (8), 1039-1055 (2013).</li><li>Li, H., Hummon, A. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Imaging+mass+spectrometry+of+three-dimensional+cell+culture+systems.">Imaging mass spectrometry of three-dimensional cell culture systems.</a> Anal Chem. 83 (22), 8794-8801 (2011).</li><li>Liu, X., Weaver, E. M., Hummon, A. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evaluation+of+Therapeutics+in+Three-Dimensional+Cell+Culture+Systems+by+MALDI+Imaging+Mass+Spectrometry.">Evaluation of Therapeutics in Three-Dimensional Cell Culture Systems by MALDI Imaging Mass Spectrometry.</a> Anal Chem. 85 (13), 6295-6302 (2013).</li><li>Ahlf, D. R., Masyuko, R. N., Hummon, A. B., Bohn, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Correlated+Mass+Spectrometry+Imaging+and+Confocal+Raman+Microscopy+for+Studies+of+Three-Dimensional+Cell+Culture+Sections.">Correlated Mass Spectrometry Imaging and Confocal Raman Microscopy for Studies of Three-Dimensional Cell Culture Sections.</a> Analyst. 139 (18), 4578-4585 (2014).</li><li>Derda, R., Tang, S. K. Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multizone+paper+platform+for+3D+cell+cultures.">Multizone paper platform for 3D cell cultures.</a> PloS one. 6 (5), 18940 (2011).</li><li>Imbeault, S., Valenzuela, N., Fai, S., Bennett, S. a. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Localizing+protein+in+3D+neural+stem+cell+culture:+a+hybrid+visualization+methodology.">Localizing protein in 3D neural stem cell culture: a hybrid visualization methodology.</a> J Vis Exp. 2 (46), 2-7 (2010).</li><li>He, W., Kuang, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Proteomic+Comparison+of+3D+and+2D+Glioma+Models+Reveals+Increased+HLA-E+Expression+in+3D+Models+is+Associated+with+Resistance+to+NK+Cell-Mediated+Cytotoxicity.">Proteomic Comparison of 3D and 2D Glioma Models Reveals Increased HLA-E Expression in 3D Models is Associated with Resistance to NK Cell-Mediated Cytotoxicity.</a> J Proteome Res. 13 (5), 2272-2281 (2014).</li><li>Chen, R., Cape, S. S., Sturm, R. M., Li, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mass+Spectrometric+Imaging+of+Neuropeptides+in+Decapod+Crustacean+Neuronal+Tissues.">Mass Spectrometric Imaging of Neuropeptides in Decapod Crustacean Neuronal Tissues.</a> Methods Mol Biol. 656, 451-463 (2010).</li><li>DeKeyser, S. S., Kutz-Naber, K. K., Schmidt, J. J., Barrett-Wilt, G. A., Li, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Imaging+Mass+Spectrometry+of+Neuropeptides+in+Decapod+Crustacean+Neuronal+Tissues.">Imaging Mass Spectrometry of Neuropeptides in Decapod Crustacean Neuronal Tissues.</a> J Proteome Res. 6 (5), 1782-1791 (2007).</li><li>Van Hove, E. R. A., Smith, D. F., Fornai, L., Glunde, K., Heeren, R. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+alternative+paper+based+tissue+washing+method+for+mass+spectrometry+imaging:+localized+washing+and+fragile+tissue+analysis.">An alternative paper based tissue washing method for mass spectrometry imaging: localized washing and fragile tissue analysis.</a> J Am Soc Mass Spectrom. 22 (10), 1885-1890 (2011).</li><li>Yang, J., Caprioli, R. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Matrix+Sublimation/Recrystalization+for+Imaging+Proteins+by+Mass+Spectrometry+at+High+Spatial+Resolution.">Matrix Sublimation/Recrystalization for Imaging Proteins by Mass Spectrometry at High Spatial Resolution.</a> Anal Chem. 83 (14), 5728-5734 (2012).</li><li>Seeley, E. H., Oppenheimer, S. R., Mi, D., Chaurand, P., Caprioli, R. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enhancement+of+protein+sensitivity+for+MALDI+imaging+mass+spectrometry+after+chemical+treatment+of+tissue+sections.">Enhancement of protein sensitivity for MALDI imaging mass spectrometry after chemical treatment of tissue sections.</a> J Am Soc Mass Spectrom. 19 (8), 1069-1077 (2008).</li><li>Gemperline, E., Li, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MALDI-mass+spectrometric+imaging+for+the+investigation+of+metabolites+in+Medicago+truncatula+root+nodules.">MALDI-mass spectrometric imaging for the investigation of metabolites in Medicago truncatula root nodules.</a> J Vis Exp. 1 (85), 1-11 (2014).</li><li>Deutsch, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=mzML:+a+single,+unifying+data+format+for+mass+spectrometer+output).">mzML: a single, unifying data format for mass spectrometer output).</a> Proteomics. 8 (14), 2776-2777 (2008).</li><li>Pedrioli, P. G. a., Eng, J. K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+common+open+representation+of+mass+spectrometry+data+and+its+application+to+proteomics+research.">A common open representation of mass spectrometry data and its application to proteomics research.</a> Nat Biotechnol. 22 (11), 1459-1466 (2004).</li><li>Lin, S., Zhu, L., Winter, A., Sasinowski, M., Kibbe, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=What+is+mzXML+good+for.">What is mzXML good for.</a> Expert Rev Proteomics. 2 (6), 839-845 (2005).</li><li>Orchard, S., Hoogland, C., Bairoch, A., Eisenacher, M., Kraus, H. -. J., Binz, P. -. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Managing+the+data+explosion.+A+report+on+the+HUPO-PSI+Workshop.+August+2008,+Amsterdam,+The+Netherlands.">Managing the data explosion. A report on the HUPO-PSI Workshop. August 2008, Amsterdam, The Netherlands.</a> Proteomics. 9 (3), 499-501 (2009).</li><li>Robichaud, G., Garrard, K. P., Barry, J. a., Muddiman, D. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MSiReader:+an+open-source+interface+to+view+and+analyze+high+resolving+power+MS+imaging+files+on+Matlab+platform.">MSiReader: an open-source interface to view and analyze high resolving power MS imaging files on Matlab platform.</a> J Am Soc Mass Spectrom. 24 (5), 718-721 (2013).</li><li>Andersson, M., Groseclose, M. R., Deutch, A. Y., Caprioli, R. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Imaging+mass+spectrometry+of+proteins+and+peptides+3D+volume+reconstruction.">Imaging mass spectrometry of proteins and peptides 3D volume reconstruction.</a> Nat Methods. 5 (1), 101-108 (2008).</li></ol>

This article is part of a special issue on Multimodal Pre-Clinical Imaging, sponsored by Bruker Biospin. The MALDI-TOF system used to obtain the representative results is a Bruker AutoFlex III.

使用以上概述的方法中，三维细胞培养物可以生长并用MALDI-MSI进行分析。许多永生化细胞系将形成三维结构的培养适当9,10应注意培养，但没有通过次数过多，即，具有低传代数的细胞时。在一般情况下，细胞10和下部的通路数是最佳生长的三维细胞培养物。越来越多的3D细胞培养在传统的琼脂糖支持提供了具有成本效益的方式为有志于3D细胞培养来尝试这个制度的研究小组。此方法利用少数部件尚未在大多数哺乳动物细胞培养实验室。仔细必须注意的琼脂糖板成长的准备，这样的三维细胞培养物的大小和形状相一致;一些方面中，需要小心注意包括检查没有气泡被截留到该混合物中，并且形成在每个孔的底部瓦特适当弯月ELL。如果弯液面不形成正常，细胞可生长在非球体形状或小团块。此外，必须注意不要将PBS与球状体的明胶。如果发生这种情况，使用200微升移液器明胶的顶部取出PBS。如果成本不是一个因素，超低结合圆底板是可商购的，并提供对这些步骤的简化。而其它组织包埋方法也可能是昂贵的和非质谱兼容，明胶包埋已被证明是既便宜和通用性。上述制备的策略已被优化为三维细胞培养物，以获得最高质量的数据。而明胶包埋已被证明是与质谱分析兼容，该方法确实缩小由于共结晶的可用矩阵。一旦冻结，所述三维细胞培养物可稳定几个月，只要它们不冻结 - 解冻。冻结当明胶变得不透明，并且3D细胞文化是一个类似的颜色，所以它是冻结记录三维细胞培养安置切片，以帮助前为宜。 当制备载玻片，基体可以用几种不同的方法被应用，但应注意的是，一些矩阵已经发现共crystalize与明胶，如阿魏酸，使该样品不能使用。较小的矩阵晶体产生更一致的质谱。而handspotting是最简单的矩阵应用的方法，该大的溶剂体积可以导致较大的晶体尺寸和显著分析物的迁移。 在质谱仪，先进的MALDI-MSI技术已经降低了所需的开始分析的专门知识。数据采集​​和分析是直接在大多数系统上，让即使是新手，以获得ITO涂层幻灯片高质量的信息。仔细选择仪器参数，优化对相邻的非图像值得三维细胞文化性ES，是为了获得高品质的数据的关键。例如，增加激光功率可能会增加峰值强度，但降低激光功率可提高分辨率并给予更对称的峰形。 3D细胞培养应迅速切片，以确保最佳的样品质量后使用。蛋白信号的退化可能在不到一周的时间没有适当的存储（干燥器/ -80℃冷冻器）中可以看出，特别是在高质量区域（高于20 kDa的）。由于不断增长的需求，许多不同的可视化的软件程序已经开发并可以自由地研究公开。大多数成像质谱仪已经安装了必要的可视化单一群众对每台仪器使用的专有格式的软件。这些软件程序可以用于获得单质的图像和导出数据。大多数软件还允许两个或多个群众利益的叠加。此外，许多不同的观众MSI的数据都可以免费下载，如MSiReader的ðBioMap。32,33获得，也可以处理收购后的轻松，带来了更多有用的信息，以最前沿的质谱数据。 从制药到脂质与蛋白质，上面概述的系统允许快速采集的数据，以评估感兴趣分子的整个三维细胞培养结构的分布。连续切片可以通过从三维细胞培养物的一个片段的每个2D图像构建被带到图像整个3D结构。在协议的技术和注意事项将使用以希望开始三维细胞培养为单层培养和动物模型之间的桥梁的研究人员。一旦掌握，这些技术可以应用到多种类型的三维细胞培养物，组织和细胞培养物，使研究人员能够像它们选择任何样品。

Mass spectrometry imaging (MSI) is a powerful technique to examine the distribution of molecular species across samples of interest. Researchers have imaged biological samples from whole animals down to single cells with this technique.1&#8211;4 Using MSI hundreds of analytes may be imaged at a single time, rather than single-substrate techniques requiring the development of additional fluorophores for traditional confocal microscopy, or staining for histology.5&#8211;7 Additionally, MSI can be used in either a targeted or a discovery-based fashion, making it an attractive approach to look at the overlap between the distribution of chemical species. Presented within are methods for the growth, preparation, and matrix assisted laser desorption ionization/desorption (MALDI) imaging of small samples (~1 mm in diameter) of three-dimensional multicellular cell cultures.8&#8211;11
3D cell cultures are of particular interest to the biological community as an intermediary between traditional monolayer culture and in vivo tumors. As the name implies, 3D cell cultures are heterogeneous cellular aggregates that contain many of the chemical gradients in the microenvironment observed in small avascular tumor nodules, making them a more realistic model system to the native tumor environment than monolayer culture.10 Many human cell lines can be grown as 3D cultures, including cell lines derived from colon, breast, ovary, prostate, kidney and lung tissues.10 There are inherent challenges in imaging three dimensional cell cultures as they are smaller than many samples commonly used for mass spectrometry imaging and therefore require careful sample preparation.7 However, the advantages of these tractable model systems include lower cost and faster growth and analysis time compared to animal models. As a result, studies involving three dimensional cell cultures can be higher throughput than traditional animal studies.12&#8211;14
All of these advantages have resulted in increasing popularity for three dimensional cell cultures in biological research; there is a corresponding need to develop new analytical strategies to explore both the composition and spatial distribution of molecules in these systems.12,15&#8211;21 The goal of this manuscript is to describe the adaptation of mass spectrometry imaging methods and sample preparation to three dimensional cell cultures.

<table border="0" cellpadding="0" cellspacing="0" width="600">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:204px;">Name of Material/Equipment</td>
			<td style="width:103px;">Company</td>
			<td style="width:119px;">Catalog Number</td>
			<td style="width:175px;">Comments</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">HCT116 Cell line</td>
			<td>ATCC</td>
			<td>ATCC CCL-247</td>
			<td>Potential hazard, handle with care</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">McCoy&#39;s 5A media</td>
			<td>Gibco</td>
			<td>16600-108</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Fetal Bovine serum</td>
			<td>HyClone</td>
			<td>SH30071.03</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">0.25% Trypsin-EDTA solution</td>
			<td>Gibco</td>
			<td>25200-056</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Agarose</td>
			<td>Sigma-Aldrich</td>
			<td>A9539</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Phosphate Buffered Saline</td>
			<td>Gibco</td>
			<td>10010049</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Gelatin, unflavored</td>
			<td>Knox</td>
			<td>--</td>
			<td>Available at most grocery stores in single-packets</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">ITO-coated glass slides</td>
			<td>Delta Technologies, Limited</td>
			<td>CG-90IN-S115</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">&#945;-Cyano-4-hydroxycinnamic acid (CHCA)&#160;</td>
			<td>Sigma-Aldrich</td>
			<td>C8982</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Sinapic Acid</td>
			<td>Sigma-Aldrich</td>
			<td>85429</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">0.3mm Gravity Feed Dual-Action Airbrush Paint Spray Gun Kit Set</td>
			<td>RoyalMax Airbrush</td>
			<td>--</td>
			<td>Many options available on sites such as Amazon.com</td>
		</tr>
	</tbody>
</table>

sample preparation strategies for mass spectrometry imaging of 3d cell culture models

Three dimensional cell cultures are attractive models for biological research. They combine the flexibility and cost-effectiveness of cell culture with some of the spatial and molecular complexity of tissue. For example, many cell lines form 3D structures given appropriate in vitro conditions. Colon cancer cell lines form 3D cell culture spheroids, in vitro mimics of avascular tumor nodules. While immunohistochemistry and other classical imaging methods are popular for monitoring the distribution of specific analytes, mass spectrometric imaging examines the distribution of classes of molecules in an unbiased fashion. While MALDI mass spectrometric imaging was originally developed to interrogate samples obtained from humans or animal models, this report describes the analysis of in vitro three dimensional cell cultures, including improvements in sample preparation strategies. Herein is described methods for growth, harvesting, sectioning, washing, and analysis of 3D cell cultures via matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) imaging. Using colon carcinoma 3D cell cultures as a model system, this protocol demonstrates the ability to monitor analytes in an unbiased fashion across the 3D cell culture system with MALDI-MSI.

微星成像有揭示在三维细胞培养物中的许多不同的分子的分布的可能性。使用上文概述的方法，由小分子（ 图1）到大的蛋白质（ 图2）物种可能跨越文化进行跟踪。这些结果显示与游离工具MSiReader 32结果可用于单离子与可视化软件在整个三维细胞培养物的兴趣或者在感兴趣或一个区域中的整个扫描区域进行分析的单个离子的可视化。另外，大多数软件会自动可视高于某个阈值由用户，这可能有助于发现努力设置离子。一旦单个离子的地图获得，大多数软件包括叠加图像，查看离子共存的能力。无论是在发现为基础的方法或者以靶向方式，质谱成像是一种强大的工具，来分析三维细胞培养物。 图3D细胞培养中生长和切片。左）一个完整的大肠癌HCT-116 3D细胞培养结构为前收获观看第14天光学图像1.代表性的结果 。右图 ​​）大肠3D细胞培养解冻大约赤道片的光学影像安装在涂有ITO的幻灯片图像。 <a href="https://www.jove.com/files/ftp_upload/52313/52313fig1large.jpg" target="_blank">请点击此处查看该图的放大版本。</a> <img alt="图2" src="/files/ftp_upload/52313/52313fig2highres.jpg" /> 图中的小分子的MALDI-MSI 2.代表性结果的三维细胞培养。顶）平均质谱中的低质量（小分子）的范围实现了与α-CHCA 的赤道部分 。底部）代表图像单质：327.8米/ Z主要定位于所述三维细胞培养物和内部429.7米/ Z主要定位于所述三维细胞培养物的边缘。虚线表示球体的近似边缘。 <a href="https://www.jove.com/files/ftp_upload/52313/52313fig2large.jpg" target="_blank">请点击此处查看该图的放大版本。</a> <img alt="图3" src="/files/ftp_upload/52313/52313fig3highres.jpg" /> 图蛋白成像的代表性的结果的三维细胞培养物。顶）平均质谱实现了与芥子酸在较高（蛋白）的质量范围的赤道部分的通过MALDI-MSI。底部）单质的代表性图像：10871米/ Z主要定位于球体的边缘，并12184米/ Z更朝向旋转椭圆体的内部进行本地化。虚线表示旋转椭圆体的近似边缘。 <a href="https://www.jove.com/files/ftp_upload/52313/52313fig3large.jpg" target="_blank">请点击此处查看该图的放大版本。</a>

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Sample Preparation Strategies for Mass Spectrometry Imaging of 3D Cell Culture Models

永生化癌细胞系可以种植三维细胞培养物，生物研究的一个有价值的模型。本协议描述的3D细胞培养，包括改进的样品制备平台质谱成像。该协议的目的是为了指导用户以制备三维细胞培养物用于质谱成像分析。

样品制备策略的3D细胞培养模型质谱成像

Three dimensional cell cultures are attractive models for biological research. They combine the flexibility and cost-effectiveness of cell culture with ...

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18.0K 次观看.  University of Notre Dame. 永生化癌细胞系可以种植三维细胞培养物，生物研究的一个有价值的模型。本协议描述的3D细胞培养，包括改进的样品制备平台质谱成像。该协议的目的是为了指导用户以制备三维细胞培养物用于质谱成像分析。 

视频: Sample Preparation Strategies for Mass Spectrometry Imaging of 3D Cell Culture Models

A Simple Hanging Drop Cell Culture Protocol for Generation of 3D Spheroids

Studies of cell-cell cohesion and cell-substratum adhesion have historically been performed on monolayer cultures adherent to rigid substrates. Cells within a tissue, however, are typically encased within a closely packed tissue mass in which cells establish intimate connections with many near-neighbors and with extracellular matrix components. Accordingly, the chemical milieu and physical forces experienced by cells within a 3D tissue are fundamentally different than those experienced by cells grown in monolayer culture. This has been shown to markedly impact cellular morphology and signaling. Several methods have been devised to generate 3D cell cultures including encapsulation of cells in collagen gels1or in biomaterial scaffolds2. Such methods, while useful, do not recapitulate the intimate direct cell-cell adhesion architecture found in normal tissues. Rather, they more closely approximate culture systems in which single cells are loosely dispersed within a 3D meshwork of ECM products. Here, we describe a simple method in which cells are placed in hanging drop culture and incubated under physiological conditions until they form true 3D spheroids in which cells are in direct contact with each other and with extracellular matrix components. The method requires no specialized equipment and can be adapted to include addition of any biological agent in very small quantities that may be of interest in elucidating effects on cell-cell or cell-ECM interaction. The method can also be used to co-culture two (or more) different cell populations so as to elucidate the role of cell-cell or cell-ECM interactions in specifying spatial relationships between cells. Cell-cell cohesion and cell-ECM adhesion are the cornerstones of studies of embryonic development, tumor-stromal cell interaction in malignant invasion, wound healing, and for applications to tissue engineering. This simple method will provide a means of generating tissue-like cellular aggregates for measurement of biomechanical properties or for molecular and biochemical analysis in a physiologically relevant model.

We describe a simple, rapid method of generating 3D tissue-like spheroids and their potential application to quantify differences in cell-cell interactions.

一个简单的悬滴细胞生成三维球体文化协议

Studies of cell-cell cohesion and cell-substratum adhesion have historically been performed on monolayer cultures adherent to rigid substrates. Cells ...

科研

生物工程

Preparation of 3D Fibrin Scaffolds for Stem Cell Culture Applications

Stem cells are found in naturally occurring 3D microenvironments in vivo, which are often referred to as the stem cell niche 1. Culturing stem cells inside of 3D biomaterial scaffolds provides a way to accurately mimic these microenvironments, providing an advantage over traditional 2D culture methods using polystyrene as well as a method for engineering replacement tissues 2. While 2D tissue culture polystrene has been used for the majority of cell culture experiments, 3D biomaterial scaffolds can more closely replicate the microenvironments found in vivo by enabling more accurate establishment of cell polarity in the environment and possessing biochemical and mechanical properties similar to soft tissue.3 A variety of naturally derived and synthetic biomaterial scaffolds have been investigated as 3D environments for supporting stem cell growth. While synthetic scaffolds can be synthesized to have a greater range of mechanical and chemical properties and often have greater reproducibility, natural biomaterials are often composed of proteins and polysaccharides found in the extracelluar matrix and as a result contain binding sites for cell adhesion and readily support cell culture. Fibrin scaffolds, produced by polymerizing the protein fibrinogen obtained from plasma, have been widely investigated for a variety of tissue engineering applications both in vitro and in vivo 4. Such scaffolds can be modified using a variety of methods to incorporate controlled release systems for delivering therapeutic factors 5. Previous work has shown that such scaffolds can be used to successfully culture embryonic stem cells and this scaffold-based culture system can be used to screen the effects of various growth factors on the differentiation of the stem cells seeded inside 6,7.
 This protocol details the process of polymerizing fibrin scaffolds from fibrinogen solutions using the enzymatic activity of thrombin. The process takes 2 days to complete, including an overnight dialysis step for the fibrinogen solution to remove citrates that inhibit polymerization. These detailed methods rely on fibrinogen concentrations determined to be optimal for embryonic and induced pluripotent stem cell culture. Other groups have further investigated fibrin scaffolds for a wide range of cell types and applications - demonstrating the versatility of this approach 8-12.

This work details the preparation of 3D fibrin scaffolds for culturing and differentiating plutipotent stem cells. Such scaffolds can be used to screen the effects of various biological compounds on stem cell behavior as well as modified to contain drug delivery systems.

制备纤维蛋白三维支架干细胞培养应用

Stem cells are found in naturally occurring 3D microenvironments in vivo, which are often referred to as the stem cell niche 1. Culturing stem cells ...

Imaging of Biological Tissues by Desorption Electrospray Ionization Mass Spectrometry

Mass spectrometry imaging (MSI) provides untargeted molecular information with the highest specificity and spatial resolution for investigating biological tissues at the hundreds to tens of microns scale. When performed under ambient conditions, sample pre-treatment becomes unnecessary, thus simplifying the protocol while maintaining the high quality of information obtained. Desorption electrospray ionization (DESI) is a spray-based ambient MSI technique that allows for the direct sampling of surfaces in the open air, even in vivo. When used with a software-controlled sample stage, the sample is rastered underneath the DESI ionization probe, and through the time domain, m/z information is correlated with the chemical species' spatial distribution. The fidelity of the DESI-MSI output depends on the source orientation and positioning with respect to the sample surface and mass spectrometer inlet. Herein, we review how to prepare tissue sections for DESI imaging and additional experimental conditions that directly affect image quality. Specifically, we describe the protocol for the imaging of rat brain tissue sections by DESI-MSI.

Desorption electrospray ionization mass spectrometry (DESI-MS) is an ambient method by which samples, including biological tissues, can be imaged with minimal sample preparation. By rastering the sample below the ionization probe, this spray-based technique provides sufficient spatial resolution to discern molecular features of interest within tissue sections.

解吸电喷雾电离质谱成像的生物组织

Mass spectrometry imaging (MSI) provides untargeted molecular information with the highest specificity and spatial resolution for investigating biological ...

Selective Cell Elimination from Mixed 3D Culture Using a Near Infrared Photoimmunotherapy Technique

Recent developments in tissue engineering offer innovative solutions for many diseases. For example, tissue engineering using induced pluripotent stem cell (iPS) emerged as a new method in regenerative medicine. Although this tissue regeneration is promising, contamination with unwanted cells during tissue cultures is a major concern. Moreover, there is a safety concern regarding tumorigenicity after transplantation. Therefore, there is an urgent need for eliminating specific cells without damaging other cells that need to be protected, especially in established tissue. Here, we present a method for specific cell elimination from a mixed 3D cell culture in vitro with near infrared photoimmunotherapy (NIR-PIT) without damaging non-targeted cells. This technique enables the elimination of specific cells from mixed cell cultures or tissues.

Eliminating specific cells without damaging other cells is extremely difficult, especially in established tissue, yet there is an urgent need for a cell elimination method in the tissue engineering field. Here, we present a method for specific cell elimination from a mixed 3D cell culture using near infrared photoimmunotherapy (NIR-PIT).

从混合三维培养使用近红外Photoimmunotherapy技术选择性细胞消除

Recent developments in tissue engineering offer innovative solutions for many diseases. For example, tissue engineering using induced pluripotent stem ...

Whole-body Mass Spectrometry Imaging by Infrared Matrix-assisted Laser Desorption Electrospray Ionization (IR-MALDESI)

Ambient ionization sources for mass spectrometry (MS) have been the subject of much interest in the past decade. Matrix-assisted laser desorption electrospray ionization (MALDESI) is an example of such methods, where features of matrix-assisted laser desorption/ionization (MALDI) (e.g., pulsed nature of desorption) and electrospray ionization (ESI) (e.g., soft-ionization) are combined. One of the major advantages of MALDESI is its inherent versatility. In MALDESI experiments, an ultraviolet (UV) or infrared (IR) laser can be used to resonantly excite an endogenous or exogenous matrix. The choice of matrix is not analyte dependent, and depends solely on the laser wavelength used for excitation. In IR-MALDESI experiments, a thin layer of ice is deposited on the sample surface as an energy-absorbing matrix. The IR-MALDESI source geometry has been optimized using statistical design of experiments (DOE) for analysis of liquid samples as well as biological tissue specimens. Furthermore, a robust IR-MALDESI imaging source has been developed, where a tunable mid-IR laser is synchronized with a computer controlled XY translational stage and a high resolving power mass spectrometer. A custom graphical user interface (GUI) allows user selection of the repetition rate of the laser, number of shots per voxel, step-size of the sample stage, and the delay between the desorption and scan events for the source. IR-MALDESI has been used in variety of applications such as forensic analysis of fibers and dyes and MSI of biological tissue sections. Distribution of different analytes ranging from endogenous metabolites to exogenous xenobiotics within tissue sections can be measured and quantified using this technique. The protocol presented in this manuscript describes major steps necessary for IR-MALDESI MSI of whole-body tissue sections.

Whole-body Mass Spectrometry Imaging by Infrared Matrix-assisted Laser Desorption Electrospray Ionization IR-MALDESI

A mass spectrometry imaging (MSI) source operated at atmospheric pressure was developed by coupling mid-infrared laser desorption and electrospray post-ionization. Exogenous ice matrix was used as the energy-absorbing matrix to facilitate resonant desorption of tissue-related material. This manuscript provides a step-by-step protocol for performing IR-MALDESI MSI of whole-body neonatal mouse.

全身质谱成像红外基质辅助激光解吸电喷雾电离（IR-MALDESI）

Ambient ionization sources for mass spectrometry (MS) have been the subject of much interest in the past decade. Matrix-assisted laser desorption ...

Preparation of 3D Collagen Gels and Microchannels for the Study of 3D Interactions In Vivo

Historically, most cellular processes have been studied in only 2 dimensions. While these studies have been informative about general cell signaling mechanisms, they neglect important cellular cues received from the structural and mechanical properties of the local microenvironment and extracellular matrix (ECM). To understand how cells interact within a physiological ECM, it is important to study them in the context of 3 dimensional assays. Cell migration, cell differentiation, and cell proliferation are only a few processes that have been shown to be impacted by local changes in the mechanical properties of a 3-dimensional ECM. Collagen I, a core fibrillar component of the ECM, is more than a simple structural element of a tissue. Under normal conditions, mechanical cues from the collagen network direct morphogenesis and maintain cellular structures. In diseased microenvironments, such as the tumor microenvironment, the collagen network is often dramatically remodeled, demonstrating altered composition, enhanced deposition and altered fiber organization. In breast cancer, the degree of fiber alignment is important, as an increase in aligned fibers perpendicular to the tumor boundary has been correlated to poorer patient prognosis1. Aligned collagen matrices result in increased dissemination of tumor cells via persistent migration2,3. The following is a simple protocol for embedding cells within a 3-dimensional, fibrillar collagen hydrogel. This protocol is readily adaptable to many platforms, and can reproducibly generate both aligned and random collagen matrices for investigation of cell migration, cell division, and other cellular processes in a tunable, 3-dimensional, physiological microenvironment.

Preparation of 3D Collagen Gels and Microchannels for the Study of 3D Interactions In Vivo

Collagen is a core component of the ECM, and provides essential cues for several cellular processes ranging from migration to differentiation and proliferation. Provided here is a protocol for embedding cells within 3D collagen hydrogels, and a more advanced technique for generating randomized or aligned collagen matrices using PDMS microchannels.

3D胶原凝胶和微通道3D相互作用的研究准备<em&gt;在体内</em

Historically, most cellular processes have been studied in only 2 dimensions.  While these studies have been informative about general cell signaling ...

Tunable Hydrogels from Pulmonary Extracellular Matrix for 3D Cell Culture

Here we present a method for establishing multiple component cell culture hydrogels for in vitro lung cell culture. Beginning with healthy en bloc lung tissue from porcine, rat, or mouse, the tissue is perfused and submerged in subsequent chemical detergents to remove the cellular debris. Histological comparison of the tissue before and after processing confirms removal of over 95% of double stranded DNA and alpha galactosidase staining suggests the majority of cellular debris is removed. After decellularization, the tissue is lyophilized and then cryomilled into a powder. The matrix powder is digested for 48 hr in an acidic pepsin digestion solution and then neutralized to form the pregel solution. Gelation of the pregel solution can be induced by incubation at 37 &#176;C and can be used immediately following neutralization or stored at 4 &#176;C for up to two weeks. Coatings can be formed using the pregel solution on a non-treated plate for cell attachment. Cells can be suspended in the pregel prior to self-assembly to achieve a 3D culture, plated on the surface of a formed gel from which the cells can migrate through the scaffold, or plated on the coatings. Alterations to the strategy presented can impact gelation temperature, strength, or protein fragment sizes. Beyond hydrogel formation, the hydrogel stiffness may be increased using genipin.

This is a method to create a 3-dimensional cell culture scaffold from pulmonary extracellular matrix. Intact lung is processed into hydrogels that can support the growth of cells in three-dimensions.

可调水凝胶由肺细胞外基质的三维细胞培养

Here we present a method for establishing multiple component cell culture hydrogels for in vitro lung cell culture. Beginning with healthy en bloc lung ...

Simultaneous Quantification of Selected Kynurenines Analyzed by Liquid Chromatography-Mass Spectrometry in Medium Collected from Cancer Cell Cultures

The kynurenine pathway and the tryptophan catabolites called kynurenines have received increased attention for their involvement in immune regulation and cancer biology. An in vitro cell culture assay is often used to learn about the contribution of different tryptophan catabolites in a disease mechanism and for testing therapeutic strategies. Cell culture medium that is rich in secreted metabolites and signaling molecules reflects the status of tryptophan metabolism and other cellular events. New protocols for the reliable quantification of multiple kynurenines in the complex cell culture medium are desired to allow for a reliable and quick analysis of multiple samples. This can be accomplished with liquid chromatography coupled with mass spectrometry. This powerful technique is employed in many clinical and research laboratories for the quantification of metabolites and can be used for measuring kynurenines.
Presented here is the use of liquid chromatography coupled with single quadrupole mass spectrometry (LC-SQ) for the simultaneous determination of four kynurenines, i.e., kynurenine, 3-hydroxykynurenine, 3-hydroxyanthranilic, and xanthurenic acid in the medium collected from in vitro cultured cancer cells. SQ detector is simple to use and less expensive compared to other mass spectrometers. In the SQ-MS analysis, multiple ions from the sample are generated and separated according to their specific mass-to-charge ratio (m/z), followed by the detection using a Single Ion Monitoring (SIM) mode.
This paper draws the attention on the advantages of the reported method and indicates some weak points. It is focused on critical elements of LC-SQ analysis including sample preparation along with chromatography and mass spectrometry analysis. The quality control, method calibration conditions and matrix effect issues are also discussed. We described a simple application of 3-nitrotyrosine as one analog standard for all target analytes. As confirmed by experiments with human ovary and breast cancer cells, the proposed LC-SQ method&#160;generates reliable results and can be further applied to other in vitro cellular models.

Described here is a protocol for the determination of four different tryptophan metabolites generated in the kynurenine pathway (kynurenine, 3-hydroxykynurenine, xanthurenic acid, 3-hydroxyanthranilic acid) in the medium collected from cancer cell cultures analyzed by liquid chromatography coupled with a single quadrupole mass spectrometry.

从癌细胞培养物中收集的介质光谱分析的选定金核素的同步量化

The kynurenine pathway and the tryptophan catabolites called kynurenines have received increased attention for their involvement in immune regulation and ...

In Vitro 3D Cell-Cultured Arterial Models for Studying Vascular Drug Targeting Under Flow

The use of three-dimensional (3D) models of human arteries, which are designed with the correct dimensions and anatomy, enables the proper modeling of various important processes in the cardiovascular system. Recently, although several biological studies have been performed using such 3D models of human arteries, they have not been applied to study vascular targeting. This paper presents a new method to fabricate real-sized, reconstructed human arterial models using a 3D printing technique, line them with human endothelial cells (ECs), and study particle targeting under physiological flow. These models have the advantage of replicating the physiological size and conditions of blood vessels in the human body using low-cost components. This technique may serve as a new platform for studying and understanding drug targeting in the cardiovascular system and may improve the design of new injectable nanomedicines. Moreover, the presented approach may provide significant tools for the study of targeted delivery of different agents for cardiovascular diseases under patient-specific flow and physiological conditions.

In Vitro 3D Cell-Cultured Arterial Models for Studying Vascular Drug Targeting Under Flow

Here, we present a new protocol to study and map the targeted deposition of drug carriers to endothelial cells in fabricated, real-sized, three-dimensional human artery models under physiological flow. The presented method may serve as a new platform for targeting drug carriers within the vascular system.

研究流动下血管药物靶向的体外3D细胞培养动脉模型

The use of three-dimensional (3D) models of human arteries, which are designed with the correct dimensions and anatomy, enables the proper modeling of ...

使用 3D 声学组装装置可扩展生成均匀的单元球体

Three-Dimensional Acoustic Assembly Device for Mass Manufacturing of Cell Spheroids

Cell spheroids are promising three-dimensional (3D) models that have gained wide applications in many biological fields. This protocol presents a method for manufacturing high-quality and high-throughput cell spheroids using a 3D acoustic assembly device through maneuverable procedures. The acoustic assembly device consists of three lead zirconate titanate (PZT) transducers, each arranged in the X/Y/Z plane of a square polymethyl methacrylate (PMMA) chamber. This configuration enables the generation of a 3D dot-array pattern of levitated acoustic nodes (LANs) when three signals are applied. As a result, cells in the gelatin methacryloyl (GelMA) solution can be driven to the LANs, forming uniform cell aggregates in three dimensions. The GelMA solution is then UV-photocured and crosslinked to serve as a scaffold that supports the growth of cell aggregates. Finally, masses of matured spheroids are obtained and retrieved by subsequently dissolving the GelMA scaffolds under mild conditions. The proposed new 3D acoustic cell assembly device will enable the scale-up fabrication of cell spheroids, and even organoids, offering great potential technology in the biological field.

作者聚焦：用于高质量 3D 细胞球状体培养的无支架声学组装方法的开发 

Cell spheroids have been considered one potential model in the field of biological applications. This article describes protocols for scalably generating cell spheroids using a 3D acoustic assembly device, which provides an efficient method for the robust and rapid fabrication of uniform cell spheroids.

用于细胞球体批量生产的三维声学装配装置

Cell spheroids are promising three-dimensional (3D) models that have gained wide applications in many biological fields. This protocol presents a method ...