MSIGen: An Open-Source Python Package for Processing and Visualizing Mass Spectrometry Imaging Data.

IF 3.1 2区 化学 Q2 BIOCHEMICAL RESEARCH METHODS
Emerson Hernly, Hang Hu, Julia Laskin
{"title":"MSIGen: An Open-Source Python Package for Processing and Visualizing Mass Spectrometry Imaging Data.","authors":"Emerson Hernly, Hang Hu, Julia Laskin","doi":"10.1021/jasms.4c00178","DOIUrl":null,"url":null,"abstract":"<p><p>Mass spectrometry imaging (MSI) provides information about the spatial localization of molecules in complex samples with high sensitivity and molecular selectivity. Although point-wise data acquisition, in which mass spectra are acquired at predefined points in a grid pattern, is common in MSI, several MSI techniques use line-wise data acquisition. In line-wise mode, the imaged surface is continuously sampled along consecutive parallel lines and MSI data are acquired as a collection of line scans across the sample. Furthermore, aside from the standard imaging mode in which full mass spectra are acquired, other acquisition modes have been developed to enhance molecular specificity, enable separation of isobaric and isomeric species, and improve sensitivity to facilitate the imaging of low abundance species. These methods, including MS/MS-MSI in both MS<sup>2</sup> and MS<sup>3</sup> modes, multiple-reaction monitoring (MRM)-MSI, and ion mobility spectrometry (IMS)-MSI have all demonstrated their capabilities, but their broader implementation is limited by the existing MSI analysis software. Here, we present MSIGen, an open-source Python package for the visualization of MSI experiments performed in line-wise acquisition mode containing MS<sup>1</sup>, MS<sup>2</sup>, MRM, and IMS data, which is available at https://github.com/LabLaskin/MSIGen. The package supports multiple vendor-specific and open-source data formats and contains tools for targeted extraction of ion images, normalization, and exportation as images, arrays, or publication-style images. MSIGen offers multiple interfaces, allowing for accessibility and easy integration with other workflows. Considering its support for a wide variety of MSI imaging modes and vendor formats, MSIGen is a valuable tool for the visualization and analysis of MSI data.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1000,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of the American Society for Mass Spectrometry","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1021/jasms.4c00178","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/9/2 0:00:00","PubModel":"Epub","JCR":"Q2","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0

Abstract

Mass spectrometry imaging (MSI) provides information about the spatial localization of molecules in complex samples with high sensitivity and molecular selectivity. Although point-wise data acquisition, in which mass spectra are acquired at predefined points in a grid pattern, is common in MSI, several MSI techniques use line-wise data acquisition. In line-wise mode, the imaged surface is continuously sampled along consecutive parallel lines and MSI data are acquired as a collection of line scans across the sample. Furthermore, aside from the standard imaging mode in which full mass spectra are acquired, other acquisition modes have been developed to enhance molecular specificity, enable separation of isobaric and isomeric species, and improve sensitivity to facilitate the imaging of low abundance species. These methods, including MS/MS-MSI in both MS2 and MS3 modes, multiple-reaction monitoring (MRM)-MSI, and ion mobility spectrometry (IMS)-MSI have all demonstrated their capabilities, but their broader implementation is limited by the existing MSI analysis software. Here, we present MSIGen, an open-source Python package for the visualization of MSI experiments performed in line-wise acquisition mode containing MS1, MS2, MRM, and IMS data, which is available at https://github.com/LabLaskin/MSIGen. The package supports multiple vendor-specific and open-source data formats and contains tools for targeted extraction of ion images, normalization, and exportation as images, arrays, or publication-style images. MSIGen offers multiple interfaces, allowing for accessibility and easy integration with other workflows. Considering its support for a wide variety of MSI imaging modes and vendor formats, MSIGen is a valuable tool for the visualization and analysis of MSI data.

Abstract Image

MSIGen:用于处理和可视化质谱成像数据的开源 Python 软件包。
质谱成像(MSI)以高灵敏度和分子选择性提供复杂样品中分子的空间定位信息。尽管点式数据采集(在网格模式中的预定点采集质谱)在 MSI 中很常见,但也有几种 MSI 技术使用线式数据采集。在线性模式下,成像表面沿着连续的平行线连续采样,MSI 数据是作为整个样品的线性扫描集合采集的。此外,除了采集全质谱的标准成像模式外,还开发了其他采集模式,以提高分子特异性,实现等压和同分异构物种的分离,并提高灵敏度以方便低丰度物种的成像。这些方法包括 MS2 和 MS3 模式下的 MS/MS-MSI、多重反应监测(MRM)-MSI 和离子迁移率光谱法(IMS)-MSI,它们都已证明了自己的能力,但其更广泛的应用受到现有 MSI 分析软件的限制。在此,我们介绍一款开源 Python 软件包 MSIGen,该软件包用于将 MS1、MS2、MRM 和 IMS 数据在线性采集模式下进行的 MSI 实验可视化,可在 https://github.com/LabLaskin/MSIGen 上获取。该软件包支持多种供应商特定的开源数据格式,并包含用于有针对性地提取离子图像、归一化以及导出为图像、阵列或出版式图像的工具。MSIGen 提供多种接口,便于访问并与其他工作流程轻松集成。MSIGen 支持多种 MSI 成像模式和供应商格式,是 MSI 数据可视化和分析的重要工具。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
CiteScore
5.50
自引率
9.40%
发文量
257
审稿时长
1 months
期刊介绍: The Journal of the American Society for Mass Spectrometry presents research papers covering all aspects of mass spectrometry, incorporating coverage of fields of scientific inquiry in which mass spectrometry can play a role. Comprehensive in scope, the journal publishes papers on both fundamentals and applications of mass spectrometry. Fundamental subjects include instrumentation principles, design, and demonstration, structures and chemical properties of gas-phase ions, studies of thermodynamic properties, ion spectroscopy, chemical kinetics, mechanisms of ionization, theories of ion fragmentation, cluster ions, and potential energy surfaces. In addition to full papers, the journal offers Communications, Application Notes, and Accounts and Perspectives
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信