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Evaluation of Data Analysis Platforms and Compatibility with MALDI-TOF Imaging Mass Spectrometry Data Sets.
Journal of the American Society for Mass Spectrometry ( IF 3.2 ) Pub Date : 2020-05-07 , DOI: 10.1021/jasms.0c00039
Gordon T Luu 1 , Alanna R Condren 1 , Lisa Juliane Kahl 2 , Lars E P Dietrich 2 , Laura M Sanchez 1
Affiliation  

Imaging mass spectrometry (IMS) has proven to be a useful tool when investigating the spatial distributions of metabolites and proteins in a biological system. One of the biggest advantages of IMS is the ability to maintain the 3D chemical composition of a sample and analyze it in a label-free manner. However, acquiring the spatial information leads to an increase in data size. Due to the increased availability of commercial mass spectrometers capable of IMS, there has been an exciting development of different statistical tools that can help decipher the spatial relevance of an analyte in a biological sample. To address this need, software packages like SCiLS and the open source R package Cardinal have been designed to perform unbiased spectral grouping based on the similarity of spectra in an IMS data set. In this note, we evaluate SCiLS and Cardinal compatibility with MALDI-TOF IMS data sets of the Gram-negative pathogen Pseudomonas aeruginosa PA14. Both software were able to perform unsupervised segmentation with similar performance. There were a few notable differences which are discussed related to the identification of statistically significant features which required optimization of preprocessing steps, region of interest, and manual analysis.

中文翻译:

评估数据分析平台以及与MALDI-TOF成像质谱数据集的兼容性。

当研究生物系统中代谢物和蛋白质的空间分布时,成像质谱(IMS)已被证明是有用的工具。IMS的最大优势之一是能够保持样品的3D化学成分并以无标签的方式对其进行分析。然而,获取空间信息导致数据大小的增加。由于支持IMS的商用质谱仪的可用性不断提高,因此各种统计工具得到了令人振奋的发展,这些统计工具可以帮助解密生物样品中分析物的空间相关性。为了满足这一需求,已经设计了像SCiLS和开源R包Cardinal这样的软件包,以基于IMS数据集中光谱的相似性来执行无偏光谱分组。在此说明中,我们评估了革兰氏阴性病菌铜绿假单胞菌PA14的MALDI-TOF IMS数据集的SCiLS和主要适应性。两种软件都能够以类似的性能执行无监督的分割。讨论了一些与统计上显着特征的识别有关的显着差异,这些差异需要优化预处理步骤,关注区域和手动分析。
更新日期:2020-04-24
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